transfusion_RL.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "toc_visible": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "6a5oOkHqw6rr"
      },
      "source": [
        "# Setup"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "IzfXoA08EPXc"
      },
      "source": [
        "# Import libraries\n",
        "import os\n",
        "import warnings\n",
        "warnings.filterwarnings(\"ignore\")\n",
        "\n",
        "# Set up environment variables\n",
        "#project_id='arctic-welder-307905' # change to your id\n",
        "project_id='tesimimic' # change to your id\n",
        "os.environ[\"GOOGLE_CLOUD_PROJECT\"]=project_id\n",
        "\n",
        "# Access data using Google BigQuery.\n",
        "from google.colab import auth\n",
        "from google.cloud import bigquery\n",
        "from IPython.display import display, HTML\n",
        "import matplotlib.pyplot as plt\n",
        "import scipy.stats as ss\n",
        "import numpy as np\n",
        "np.random.seed(42)\n",
        "\n",
        "import pandas as pd\n",
        "pd.set_option('mode.chained_assignment', None)\n",
        "\n",
        "# authenticate\n",
        "auth.authenticate_user()"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "UD72t-dQ1WJF"
      },
      "source": [
        "# Data Extraction"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Ip--ZR151WJG"
      },
      "source": [
        "client = bigquery.Client(project=project_id)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# MIMIC 4 Treatment cohort\n",
        "\n",
        "First icustay of the patients in which he received just 1 blood sac"
      ],
      "metadata": {
        "id": "z33b8kpp1WJH"
      }
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "LEo1OGTDz7pD"
      },
      "outputs": [],
      "source": [
        "#patients trated with a blood sac in mimic 4\n",
        "tx_mimic4 = client.query(\"\"\"\n",
        "WITH all_criteria AS (SELECT DISTINCT(stay_id)\n",
        "FROM `physionet-data.mimic_derived.sofa`\n",
        "WHERE stay_id IN(SELECT DISTINCT(stay_id)\n",
        "                    FROM `physionet-data.mimic_derived.icustay_detail`\n",
        "                    WHERE icustay_seq = 1\n",
        "                    AND first_icu_stay= TRUE\n",
        "                    AND (admission_age BETWEEN 18 AND 89)\n",
        "  AND stay_id NOT IN(SELECT DISTINCT(i.stay_id)\n",
        "        FROM `physionet-data.mimic_hosp.diagnoses_icd` d\n",
        "        INNER JOIN `physionet-data.mimic_icu.icustays` i\n",
        "            ON d.hadm_id=i.hadm_id\n",
        "        INNER JOIN `physionet-data.mimic_derived.icustay_detail` a\n",
        "            ON d.HADM_ID=a.hadm_id\n",
        "        WHERE icd_code IN (\n",
        "                --ref: https://www.bmj.com/content/bmj/suppl/2015/02/03/bmj.h246.DC1/junm020747.ww1_default.pdf\n",
        "                --intracranial bleeding\n",
        "                '430', --Subarachnoid\n",
        "                '431', --intracerebral\n",
        "                '4320', --other and unspecified intracranial bleeding\n",
        "                '4321', --subdural\n",
        "                '4329', --unspecified intracranial bleeding\n",
        "                --upper gastrointestinal\n",
        "                '5310', --acute gastric ulcer with bleeding without obstruction\n",
        "                '5312', --acute gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5314', --chronic or unspecified gastric ulcer with bleeding without obstruction\n",
        "                '5316', --chronic or unspecified gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5320', --acute duodenal ulcer with bleeding without obstruction\n",
        "                '5322', --acute duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5324', --chronic or unspecified duodenal ulcer with bleeding without obstruction\n",
        "                '5326', --chronic or unspecified duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5330', --acute peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5332', --acute peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5334', --chronic or unspecified peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5336', --chronic or unspecified peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5340', --acute gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5342', --acute gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5344', --chronic or unspecified gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5346', --chronic or unspecified gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5780', --hematemesis\n",
        "                '5781', --blood in stool\n",
        "                '5789', --bleeding of gastrointestinal tract unspecified\n",
        "                --Lower GI\n",
        "                '5693', --bleeding of rectum and anus\n",
        "                --Other Bleeding\n",
        "                '2878', --other unspecified hemorrhagic conditions\n",
        "                '2879', --unspecified hemorrhagic conditions\n",
        "                '5967', --bleeding into bladder wall\n",
        "                '7848', --bleeding from throat\n",
        "                '5997', --hematuria, unspecified\n",
        "                '6271', --postmenopausal bleeding\n",
        "                '4590', --bleeding unspecified\n",
        "                '7191', --hemarthrosis site unspecified\n",
        "                '7863', --hemoptysis, unspecified\n",
        "                '72992', --nontraumatic hematoma soft tissue\n",
        "                '9582' --secondary or recurrent following trauma\n",
        "            )\n",
        "        OR icd_code LIKE '900%' --vessel injuries\n",
        "        OR icd_code LIKE '901%' --vessel injuries\n",
        "        OR icd_code LIKE '902%' --vessel injuries\n",
        "        OR icd_code LIKE '903%' --vessel injuries\n",
        "        OR icd_code LIKE '904%' --vessel injuries\n",
        "\n",
        "        OR UPPER(LAST_CAREUNIT) LIKE '%TSICU%'\n",
        "        OR UPPER(FIRST_CAREUNIT) LIKE '%TSICU%' )) )\n",
        ", demographics AS (\n",
        "    SELECT\n",
        "        ie.subject_id,\n",
        "        ie.hadm_id,\n",
        "        ie.stay_id -- patient level factors\n",
        ",\n",
        "        pat.gender,\n",
        "        pat.dod -- hospital level factors\n",
        ",\n",
        "        adm.admittime,\n",
        "        adm.dischtime,\n",
        "        pat.anchor_age AS age,\n",
        "        adm.admission_type,\n",
        "        adm.hospital_expire_flag,\n",
        "        adm.deathtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY adm.subject_id\n",
        "            ORDER BY\n",
        "                adm.admittime\n",
        "        ) AS hospstay_seq,\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY adm.subject_id\n",
        "                ORDER BY\n",
        "                    adm.admittime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_hosp_stay -- icu level factors\n",
        ",\n",
        "        ie.intime,\n",
        "        ie.outtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY ie.hadm_id\n",
        "            ORDER BY\n",
        "                ie.intime\n",
        "        ) AS icustay_seq -- first ICU stay *for the current hospitalization*\n",
        ",\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY ie.hadm_id\n",
        "                ORDER BY\n",
        "                    ie.intime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_icu_stay\n",
        "    FROM\n",
        "        `physionet-data.mimic_icu.icustays` ie\n",
        "        INNER JOIN `physionet-data.mimic_core.admissions` adm ON ie.hadm_id = adm.hadm_id\n",
        "        INNER JOIN `physionet-data.mimic_core.patients` pat ON ie.subject_id = pat.subject_id\n",
        "    ORDER BY\n",
        "        ie.subject_id,\n",
        "        adm.admittime,\n",
        "        ie.intime\n",
        ")\n",
        ",\n",
        "first_adm_offset AS (\n",
        "    SELECT\n",
        "        stay_id AS id,\n",
        "        intime,\n",
        "        outtime\n",
        "    FROM\n",
        "        demographics\n",
        "    WHERE\n",
        "        first_icu_stay = TRUE),\n",
        "pivoted_sofa AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        `physionet-data.mimic_derived.sofa` ps\n",
        "        LEFT JOIN first_adm_offset f ON ps.stay_id = f.id\n",
        "        AND ps.endtime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "),\n",
        "pivoted_lab AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        (\n",
        "            WITH pivoted_lab AS (\n",
        "                -- create a table which has fuzzy boundaries on ICU admission (+- 12 hours from documented time)\n",
        "                -- this is used to assign icustay_id to lab data, which can be collected outside ICU\n",
        "                -- involves first creating a lag/lead version of intime/outtime\n",
        "                WITH i AS (\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        stay_id,\n",
        "                        intime,\n",
        "                        outtime,\n",
        "                        lag (outtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS outtime_lag,\n",
        "                        lead (intime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS intime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimic_icu.icustays`\n",
        "                ),\n",
        "                iid_assign AS (\n",
        "                    SELECT\n",
        "                        i.subject_id,\n",
        "                        i.stay_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN i.outtime_lag IS NOT NULL\n",
        "                            AND i.outtime_lag > DATETIME_SUB(i.intime, INTERVAL 24 HOUR) THEN DATETIME_SUB(\n",
        "                                i.intime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime, i.outtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(i.intime, INTERVAL 12 HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN i.intime_lead IS NOT NULL\n",
        "                            AND i.intime_lead < DATETIME_ADD(i.outtime, INTERVAL 24 HOUR) THEN DATETIME_ADD(\n",
        "                                i.outtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime_lead, i.outtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(i.outtime, INTERVAL 12 HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        i\n",
        "                ) -- also create fuzzy boundaries on hospitalization\n",
        ",\n",
        "                h AS (\n",
        "                    SELECT\n",
        "                        subject_id,hadm_id,admittime,dischtime,\n",
        "                        lag (dischtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS dischtime_lag,\n",
        "                        lead (admittime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS admittime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimic_core.admissions`\n",
        "                ),\n",
        "                adm AS (\n",
        "                    SELECT\n",
        "                        h.subject_id,\n",
        "                        h.hadm_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN h.dischtime_lag IS NOT NULL\n",
        "                            AND h.dischtime_lag > DATETIME_SUB(h.admittime, INTERVAL '24' HOUR) THEN DATETIME_SUB(\n",
        "                                h.admittime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime, h.dischtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(h.admittime, INTERVAL '12' HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN h.admittime_lead IS NOT NULL\n",
        "                            AND h.admittime_lead < DATETIME_ADD(h.dischtime, INTERVAL '24' HOUR) THEN DATETIME_ADD(\n",
        "                                h.dischtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime_lead, h.dischtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(h.dischtime, INTERVAL '12' HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        h\n",
        "                ),\n",
        "                le AS (\n",
        "                    -- begin query that extracts the data\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        charttime -- here we assign labels to ITEMIDs\n",
        "                        -- this also fuses together multiple ITEMIDs containing the same data\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN itemid = 50868 THEN 'ANION GAP'\n",
        "                            WHEN itemid = 50862 THEN 'ALBUMIN'\n",
        "                            WHEN itemid = 51144 THEN 'BANDS'\n",
        "                            WHEN itemid = 50882 THEN 'BICARBONATE'\n",
        "                            WHEN itemid = 50885 THEN 'BILIRUBIN'\n",
        "                            WHEN itemid = 50912 THEN 'CREATININE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50806 THEN 'CHLORIDE'\n",
        "                            WHEN itemid = 50902 THEN 'CHLORIDE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50809 THEN 'GLUCOSE'\n",
        "                            WHEN itemid = 50931 THEN 'GLUCOSE' -- exclude blood gas\n",
        "                            --WHEN itemid = 50810 THEN 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221 THEN 'HEMATOCRIT' -- exclude blood gas\n",
        "                            --WHEN itemid = 50811 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813 THEN 'LACTATE'\n",
        "                            WHEN itemid = 51265 THEN 'PLATELET' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50822 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 50971 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 51275 THEN 'PTT'\n",
        "                            WHEN itemid = 51237 THEN 'INR'\n",
        "                            WHEN itemid = 51274 THEN 'PT' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50824 THEN 'SODIUM'\n",
        "                            WHEN itemid = 50983 THEN 'SODIUM'\n",
        "                            WHEN itemid = 51006 THEN 'BUN'\n",
        "                            WHEN itemid = 51300 THEN 'WBC'\n",
        "                            WHEN itemid = 51301 THEN 'WBC'\n",
        "                            ELSE NULL\n",
        "                        END AS label,\n",
        "                        -- add in some sanity checks on the values\n",
        "                        -- the where clause below requires all valuenum to be > 0, so these are only upper limit checks\n",
        "                        CASE\n",
        "                            WHEN itemid = 50862\n",
        "                            AND valuenum > 10 THEN NULL -- g/dL 'ALBUMIN'\n",
        "                            WHEN itemid = 50868\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'ANION GAP'\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum < 0 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum > 100 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 50882\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'BICARBONATE'\n",
        "                            WHEN itemid = 50885\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'BILIRUBIN'\n",
        "                            WHEN itemid = 50806\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50902\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50912\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'CREATININE'\n",
        "                            WHEN itemid = 50809\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50931\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50810\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 50811\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813\n",
        "                            AND valuenum > 50 THEN NULL -- mmol/L 'LACTATE'\n",
        "                            WHEN itemid = 51265\n",
        "                            AND valuenum > 10000 THEN NULL -- K/uL 'PLATELET'\n",
        "                            WHEN itemid = 50822\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 50971\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 51275\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PTT'\n",
        "                            WHEN itemid = 51237\n",
        "                            AND valuenum > 50 THEN NULL -- 'INR'\n",
        "                            WHEN itemid = 51274\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PT'\n",
        "                            WHEN itemid = 50824\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 50983\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 51006\n",
        "                            AND valuenum > 300 THEN NULL -- 'BUN'\n",
        "                            WHEN itemid = 51300\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            WHEN itemid = 51301\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            ELSE valuenum\n",
        "                        END AS valuenum\n",
        "                    FROM\n",
        "                        `physionet-data.mimic_hosp.labevents`\n",
        "                    WHERE\n",
        "                        ITEMID IN (\n",
        "                            -- comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS\n",
        "                            50868, -- ANION GAP | CHEMISTRY | BLOOD | 769895\n",
        "                            50862, -- ALBUMIN | CHEMISTRY | BLOOD | 146697\n",
        "                            51144, -- BANDS - hematology\n",
        "                            50882, -- BICARBONATE | CHEMISTRY | BLOOD | 780733\n",
        "                            50885, -- BILIRUBIN, TOTAL | CHEMISTRY | BLOOD | 238277\n",
        "                            50912, -- CREATININE | CHEMISTRY | BLOOD | 797476\n",
        "                            50902, -- CHLORIDE | CHEMISTRY | BLOOD | 795568\n",
        "                            -- 50806, -- CHLORIDE, WHOLE BLOOD | BLOOD GAS | BLOOD | 48187\n",
        "                            50931, -- GLUCOSE | CHEMISTRY | BLOOD | 748981\n",
        "                            -- 50809, -- GLUCOSE | BLOOD GAS | BLOOD | 196734\n",
        "                            51221, -- HEMATOCRIT | HEMATOLOGY | BLOOD | 881846\n",
        "                            -- 50810, -- HEMATOCRIT, CALCULATED | BLOOD GAS | BLOOD | 89715\n",
        "                            51222, -- HEMOGLOBIN | HEMATOLOGY | BLOOD | 752523\n",
        "                            -- 50811, -- HEMOGLOBIN | BLOOD GAS | BLOOD | 89712\n",
        "                            50813, -- LACTATE | BLOOD GAS | BLOOD | 187124\n",
        "                            51265, -- PLATELET COUNT | HEMATOLOGY | BLOOD | 778444\n",
        "                            50971, -- POTASSIUM | CHEMISTRY | BLOOD | 845825\n",
        "                            -- 50822, -- POTASSIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 192946\n",
        "                            51275, -- PTT | HEMATOLOGY | BLOOD | 474937\n",
        "                            51237, -- INR(PT) | HEMATOLOGY | BLOOD | 471183\n",
        "                            51274, -- PT | HEMATOLOGY | BLOOD | 469090\n",
        "                            50983, -- SODIUM | CHEMISTRY | BLOOD | 808489\n",
        "                            -- 50824, -- SODIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 71503\n",
        "                            51006, -- UREA NITROGEN | CHEMISTRY | BLOOD | 791925\n",
        "                            51301, -- WHITE BLOOD CELLS | HEMATOLOGY | BLOOD | 753301\n",
        "                            51300  -- WBC COUNT | HEMATOLOGY | BLOOD | 2371\n",
        "                        )\n",
        "                        AND valuenum IS NOT NULL\n",
        "                        AND valuenum > 0 -- lab values cannot be 0 and cannot be negative\n",
        "                ),\n",
        "                le_avg AS (\n",
        "                    SELECT\n",
        "                        le.subject_id,\n",
        "                        le.charttime,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ANION GAP' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ANIONGAP,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ALBUMIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ALBUMIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BANDS' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BANDS,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BICARBONATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BICARBONATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BILIRUBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BILIRUBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CREATININE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CREATININE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CHLORIDE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CHLORIDE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'GLUCOSE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS GLUCOSE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMATOCRIT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMATOCRIT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMOGLOBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMOGLOBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'LACTATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS LACTATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PLATELET' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PLATELET,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'POTASSIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS POTASSIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PTT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PTT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'INR' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS INR,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'SODIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS SODIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BUN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BUN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'WBC' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS WBC\n",
        "                    FROM\n",
        "                        le\n",
        "                    GROUP BY\n",
        "                        le.subject_id,\n",
        "                        le.charttime\n",
        "                )\n",
        "                SELECT\n",
        "                    iid.stay_id,\n",
        "                    adm.hadm_id,\n",
        "                    le_avg.*\n",
        "                FROM\n",
        "                    le_avg\n",
        "                    LEFT JOIN adm ON le_avg.subject_id = adm.subject_id\n",
        "                    AND le_avg.charttime >= adm.data_start\n",
        "                    AND le_avg.charttime < adm.data_end\n",
        "                    LEFT JOIN iid_assign iid ON le_avg.subject_id = iid.subject_id\n",
        "                    AND le_avg.charttime >= iid.data_start\n",
        "                    AND le_avg.charttime < iid.data_end\n",
        "                ORDER BY\n",
        "                    le_avg.subject_id,\n",
        "                    le_avg.charttime\n",
        "            )\n",
        "            SELECT\n",
        "                *\n",
        "            FROM\n",
        "                pivoted_lab\n",
        "        ) AS pl\n",
        "        LEFT JOIN first_adm_offset f ON pl.stay_id = f.id\n",
        "        AND pl.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        ")\n",
        ",\n",
        "mechvent AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        charttime -- case statement determining whether it is an instance of mech vent\n",
        ",\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN itemid IS NULL\n",
        "                OR value IS NULL THEN 0 -- can't have null values\n",
        "                WHEN itemid = 720\n",
        "                AND value != 'Other/Remarks' THEN 1 -- VentTypeRecorded\n",
        "                WHEN itemid = 223848\n",
        "                AND value != 'Other' THEN 1\n",
        "                WHEN itemid = 223849 THEN 1 -- ventilator mode\n",
        "                WHEN itemid = 467\n",
        "                AND value = 'Ventilator' THEN 1 -- O2 delivery device == ventilator\n",
        "                WHEN itemid IN(\n",
        "                    445,\n",
        "                    448,\n",
        "                    449,\n",
        "                    450,\n",
        "                    1340,\n",
        "                    1486,\n",
        "                    1600,\n",
        "                    224687 -- minute volume\n",
        ",\n",
        "                    639,\n",
        "                    654,\n",
        "                    681,\n",
        "                    682,\n",
        "                    683,\n",
        "                    684,\n",
        "                    224685,\n",
        "                    224684,\n",
        "                    224686 -- tidal volume\n",
        ",\n",
        "                    218,\n",
        "                    436,\n",
        "                    535,\n",
        "                    444,\n",
        "                    459,\n",
        "                    224697,\n",
        "                    224695,\n",
        "                    224696,\n",
        "                    224746,\n",
        "                    224747 -- High/Low/Peak/Mean/Neg insp force (\"RespPressure\")\n",
        ",\n",
        "                    221,\n",
        "                    1,\n",
        "                    1211,\n",
        "                    1655,\n",
        "                    2000,\n",
        "                    226873,\n",
        "                    224738,\n",
        "                    224419,\n",
        "                    224750,\n",
        "                    227187 -- Insp pressure\n",
        ",\n",
        "                    543 -- PlateauPressure\n",
        ",\n",
        "                    5865,\n",
        "                    5866,\n",
        "                    224707,\n",
        "                    224709,\n",
        "                    224705,\n",
        "                    224706 -- APRV pressure\n",
        ",\n",
        "                    60,\n",
        "                    437,\n",
        "                    505,\n",
        "                    506,\n",
        "                    686,\n",
        "                    220339,\n",
        "                    224700 -- PEEP\n",
        ",\n",
        "                    3459 -- high pressure relief\n",
        ",\n",
        "                    501,\n",
        "                    502,\n",
        "                    503,\n",
        "                    224702 -- PCV\n",
        ",\n",
        "                    223,\n",
        "                    667,\n",
        "                    668,\n",
        "                    669,\n",
        "                    670,\n",
        "                    671,\n",
        "                    672 -- TCPCV\n",
        ",\n",
        "                    224701 -- PSVlevel\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS ventmarker\n",
        "    FROM\n",
        "        `physionet-data.mimic_icu.chartevents` ce\n",
        "        LEFT JOIN first_adm_offset f ON ce.stay_id = f.id\n",
        "        AND ce.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "    WHERE\n",
        "        ce.value IS NOT NULL -- exclude rows marked as error\n",
        "        --AND ce.error != 1 -- the below are settings used to indicate ventilation\n",
        "        AND itemid IN(\n",
        "            720,\n",
        "            223849 -- vent mode\n",
        ",\n",
        "            223848 -- vent type\n",
        ",\n",
        "            445,\n",
        "            448,\n",
        "            449,\n",
        "            450,\n",
        "            1340,\n",
        "            1486,\n",
        "            1600,\n",
        "            224687 -- minute volume\n",
        ",\n",
        "            639,\n",
        "            654,\n",
        "            681,\n",
        "            682,\n",
        "            683,\n",
        "            684,\n",
        "            224685,\n",
        "            224684,\n",
        "            224686 -- tidal volume\n",
        ",\n",
        "            218,\n",
        "            436,\n",
        "            535,\n",
        "            444,\n",
        "            224697,\n",
        "            224695,\n",
        "            224696,\n",
        "            224746,\n",
        "            224747 -- High/Low/Peak/Mean (\"RespPressure\")\n",
        ",\n",
        "            221,\n",
        "            1,\n",
        "            1211,\n",
        "            1655,\n",
        "            2000,\n",
        "            226873,\n",
        "            224738,\n",
        "            224419,\n",
        "            224750,\n",
        "            227187 -- Insp pressure\n",
        ",\n",
        "            543 -- PlateauPressure\n",
        ",\n",
        "            5865,\n",
        "            5866,\n",
        "            224707,\n",
        "            224709,\n",
        "            224705,\n",
        "            224706 -- APRV pressure\n",
        ",\n",
        "            60,\n",
        "            437,\n",
        "            505,\n",
        "            506,\n",
        "            686,\n",
        "            220339,\n",
        "            224700 -- PEEP\n",
        ",\n",
        "            3459 -- high pressure relief\n",
        ",\n",
        "            501,\n",
        "            502,\n",
        "            503,\n",
        "            224702 -- PCV\n",
        ",\n",
        "            223,\n",
        "            667,\n",
        "            668,\n",
        "            669,\n",
        "            670,\n",
        "            671,\n",
        "            672 -- TCPCV\n",
        ",\n",
        "            224701 -- PSVlevel\n",
        "            -- the below are settings used to indicate extubation\n",
        ",\n",
        "            640 -- extubated\n",
        "            -- the below indicate oxygen/NIV, i.e. the end of a mechanical vent event\n",
        ",\n",
        "            468 -- O2 Delivery Device#2\n",
        ",\n",
        "            469 -- O2 Delivery Mode\n",
        ",\n",
        "            470 -- O2 Flow (lpm)\n",
        ",\n",
        "            471 -- O2 Flow (lpm) #2\n",
        ",\n",
        "            227287 -- O2 Flow (additional cannula)\n",
        ",\n",
        "            226732 -- O2 Delivery Device(s)\n",
        ",\n",
        "            223834 -- O2 Flow\n",
        "            -- used in both oxygen + vent calculation\n",
        ",\n",
        "            467 -- O2 Delivery Device\n",
        "        )\n",
        "    GROUP BY\n",
        "        stay_id,\n",
        "        charttime\n",
        ")\n",
        ",\n",
        "sepsis AS (\n",
        "    -- ICD-9 codes for Angus criteria of sepsis\n",
        "    SELECT\n",
        "        hadm_id,\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd_code, 1, 3) IN (\n",
        "                    '001','002','003','004','005',\n",
        "                    '008','009','010','011','012',\n",
        "                    '013','014','015','016','017',\n",
        "                    '018','020','021','022','023',\n",
        "                    '024','025','026','027','030',\n",
        "                    '031','032','033','034','035',\n",
        "                    '036','037','038','039','040',\n",
        "                    '041','090','091','092','093',\n",
        "                    '094','095','096','097','098',\n",
        "                    '100','101','102','103','104',\n",
        "                    '110','111','112','114','115',\n",
        "                    '116','117','118','320','322',\n",
        "                    '324','325','420','421','451',\n",
        "                    '461','462','463','464','465',\n",
        "                    '481','482','485','486','494',\n",
        "                    '510','513','540','541','542',\n",
        "                    '566','567','590','597','601',\n",
        "                    '614','615','616','681','682',\n",
        "                    '683','686','730'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd_code, 1, 4) IN (\n",
        "                    '5695','5720','5721','5750',\n",
        "                    '5990','7110','7907','9966',\n",
        "                    '9985','9993'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd_code, 1, 5) IN (\n",
        "                    '49121','56201','56203',\n",
        "                    '56211','56213','56983'\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS sepsisflag\n",
        "    FROM\n",
        "        `physionet-data.mimic_hosp.diagnoses_icd`\n",
        "    GROUP BY\n",
        "        hadm_id\n",
        "),\n",
        "--,\n",
        "--vasopressor_duration AS (\n",
        "    --SELECT\n",
        "        --*\n",
        "    --FROM\n",
        "        --`physionet-data.mimiciii_derived.vasopressordurations`\n",
        "--),\n",
        "premorbid AS (\n",
        "    WITH icd AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            CAST(icd_code AS STRING) AS icd_code\n",
        "        FROM\n",
        "            `physionet-data.mimic_hosp.diagnoses_icd`\n",
        "    ),\n",
        "    eliflg AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            icd_code -- note that these codes will seem incomplete at first\n",
        "            -- for example, CHF is missing a lot of codes referenced in the literature (402.11, 402.91, etc)\n",
        "            -- these codes are captured by hypertension flags instead\n",
        "            -- later there are some complicated rules which confirm/reject those codes as CHF\n",
        ",\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd_code, 1, 3) IN(\n",
        "                    '410', --Acute myocardial infarction\n",
        "                    '411', --Other acute and subacute forms of ischemic heart disease\n",
        "                    '412', --Old myocardial infarction\n",
        "                    '413', --Angina pectoris\n",
        "                    '414'  --Other forms of chronic ischemic heart disease\n",
        "                ) THEN 1\n",
        "            END AS IHD,\n",
        "            CASE\n",
        "                WHEN icd_code = '39891' THEN 1\n",
        "                WHEN icd_code BETWEEN '4280 '\n",
        "                AND '4289 ' THEN 1\n",
        "            END AS CHF\n",
        "            /* Congestive heart failure */\n",
        "            -- cardiac arrhythmias is removed in up to date versions\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code BETWEEN '4400 '\n",
        "                AND '4409 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '44100'\n",
        "                AND '4419 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '4420 '\n",
        "                AND '4429 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '4431 '\n",
        "                AND '4439 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '44421'\n",
        "                AND '44422' THEN 1\n",
        "                WHEN icd_code = '4471 ' THEN 1\n",
        "                WHEN icd_code = '449  ' THEN 1\n",
        "                WHEN icd_code = '5571 ' THEN 1\n",
        "                WHEN icd_code = '5579 ' THEN 1\n",
        "                WHEN icd_code = 'V434 ' THEN 1\n",
        "            END AS PERIVASC\n",
        "            /* Peripheral vascular disorder */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40200' THEN 1\n",
        "                WHEN icd_code = '40210' THEN 1\n",
        "                WHEN icd_code = '40290' THEN 1\n",
        "                WHEN icd_code = '40509' THEN 1\n",
        "                WHEN icd_code = '40519' THEN 1\n",
        "                WHEN icd_code = '40599' THEN 1\n",
        "            END AS HTNWOCHF\n",
        "            /* Hypertensive heart disease without heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40201' THEN 1\n",
        "                WHEN icd_code = '40211' THEN 1\n",
        "                WHEN icd_code = '40291' THEN 1\n",
        "            END AS HTNWCHF\n",
        "            /* Hypertensive heart disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40301' THEN 1\n",
        "                WHEN icd_code = '40311' THEN 1\n",
        "                WHEN icd_code = '40391' THEN 1\n",
        "            END AS HRENWRF\n",
        "            /* Hypertensive renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40401' THEN 1\n",
        "                WHEN icd_code = '40411' THEN 1\n",
        "                WHEN icd_code = '40491' THEN 1\n",
        "            END AS HHRWCHF\n",
        "            /* Hypertensive heart and renal disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40402' THEN 1\n",
        "                WHEN icd_code = '40412' THEN 1\n",
        "                WHEN icd_code = '40492' THEN 1\n",
        "            END AS HHRWRF\n",
        "            /* Hypertensive heart and renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40403' THEN 1\n",
        "                WHEN icd_code = '40413' THEN 1\n",
        "                WHEN icd_code = '40493' THEN 1\n",
        "            END AS HHRWHRF\n",
        "            /* Hypertensive heart and renal disease with heart and renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '585  ' THEN 1 -- discontinued code\n",
        "                WHEN icd_code = '5853 ' THEN 1\n",
        "                WHEN icd_code = '5854 ' THEN 1\n",
        "                WHEN icd_code = '5855 ' THEN 1\n",
        "                WHEN icd_code = '5856 ' THEN 1\n",
        "                WHEN icd_code = '5859 ' THEN 1\n",
        "                WHEN icd_code = '586  ' THEN 1\n",
        "                WHEN icd_code = 'V420 ' THEN 1\n",
        "                WHEN icd_code = 'V451 ' THEN 1\n",
        "                WHEN icd_code BETWEEN 'V560 '\n",
        "                AND 'V5632' THEN 1\n",
        "                WHEN icd_code = 'V568 ' THEN 1\n",
        "                WHEN icd_code BETWEEN 'V4511'\n",
        "                AND 'V4512' THEN 1\n",
        "            END AS RENLFAIL\n",
        "            /* Renal failure */\n",
        "        FROM\n",
        "            icd\n",
        "    ),\n",
        "    eligrp AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            MAX(ihd) AS ihd,\n",
        "            MAX(chf) AS chf,\n",
        "            MAX(perivasc) AS perivasc,\n",
        "            MAX(htnwchf) AS htnwchf,\n",
        "            MAX(hrenwrf) AS hrenwrf,\n",
        "            MAX(hhrwchf) AS hhrwchf,\n",
        "            MAX(hhrwrf) AS hhrwrf,\n",
        "            MAX(hhrwhrf) AS hhrwhrf,\n",
        "            MAX(renlfail) AS renlfail\n",
        "        FROM\n",
        "            eliflg\n",
        "        GROUP BY\n",
        "            hadm_id\n",
        "    )\n",
        "    SELECT\n",
        "        adm.subject_id,\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN ihd = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS ISCHEMIC_HEART_DISEASE,\n",
        "        CASE\n",
        "            WHEN chf = 1 THEN 1\n",
        "            WHEN htnwchf = 1 THEN 1\n",
        "            WHEN hhrwchf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS CONGESTIVE_HEART_FAILURE,\n",
        "        CASE\n",
        "            WHEN perivasc = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS PERIPHERAL_VASCULAR,\n",
        "        CASE\n",
        "            WHEN renlfail = 1 THEN 1\n",
        "            WHEN hrenwrf = 1 THEN 1\n",
        "            WHEN hhrwrf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS RENAL_FAILURE\n",
        "    FROM\n",
        "        `physionet-data.mimic_core.admissions` adm\n",
        "        LEFT JOIN eligrp eli ON adm.hadm_id = eli.hadm_id\n",
        "    ORDER BY\n",
        "        adm.hadm_id\n",
        "),\n",
        "surgflag AS (\n",
        "    SELECT\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN LOWER(curr_service) LIKE '%surg%' THEN 1\n",
        "            ELSE 0\n",
        "        END AS surgical,\n",
        "        ROW_NUMBER() OVER(\n",
        "            PARTITION BY adm.HADM_ID\n",
        "            ORDER BY\n",
        "                TRANSFERTIME\n",
        "        ) AS serviceOrder\n",
        "    FROM\n",
        "        `physionet-data.mimic_core.admissions` adm\n",
        "        LEFT JOIN `physionet-data.mimic_hosp.services` se ON adm.hadm_id = se.hadm_id\n",
        ")\n",
        ",\n",
        "tx_raw AS (\n",
        "    -- BLOOD TRANSFUSED in mL\n",
        "    -- carevue not in MIMIC 4\n",
        "    -- include all MIMIC 4 add carvue from MIMIC 3\n",
        "    WITH inputevents AS (\n",
        "        SELECT\n",
        "            ipe.stay_id,\n",
        "            ipe.starttime AS charttime,\n",
        "            ROUND(ipe.amount) AS amount,\n",
        "        FROM\n",
        "            `physionet-data.mimic_icu.inputevents` ipe\n",
        "        WHERE\n",
        "            ipe.itemid IN(\n",
        "                225168, -- Packed Red Blood Cells\n",
        "                220996, -- Packed Red Cells\n",
        "                221013,  -- Whole blood\n",
        "                226368, -- OR Packed RBC Intake\n",
        "                227070 -- PACU Packed RBC Intake\n",
        "            )\n",
        "            AND amount > 100\n",
        "            --AND ipe.statusdescription != 'Rewritten'\n",
        "    )\n",
        "    SELECT\n",
        "        ipe.stay_id,\n",
        "        charttime,\n",
        "        SUM(amount) AS rbc_volume,\n",
        "    FROM\n",
        "        inputevents ipe\n",
        "    GROUP BY\n",
        "        ipe.stay_id,\n",
        "        ipe.charttime\n",
        "),\n",
        "tx AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        TIMESTAMP_SECONDS(60 * DIV(UNIX_SECONDS(TIMESTAMP(charttime)), 60)) AS episode,\n",
        "        --some samples have duplicate readings every 15 minutes - we take an hourly window and average the volume across this window\n",
        "        --doing so reduces errors significantly\n",
        "        MIN(charttime) AS charttime,\n",
        "        --get the first timestamp of each window\n",
        "        AVG(rbc_volume) AS rbc_volume\n",
        "    FROM tx_raw\n",
        "    GROUP BY stay_id, episode\n",
        "    ORDER BY stay_id, episode\n",
        "),\n",
        "tx_counts AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        COUNT(charttime) AS tx_episodes,\n",
        "        SUM(rbc_volume) AS rbc_volume,\n",
        "        CEIL(SUM(rbc_volume) / 350) AS rbc_units\n",
        "    FROM tx\n",
        "    WHERE\n",
        "        stay_id IS NOT NULL\n",
        "    GROUP BY\n",
        "        stay_id\n",
        "),\n",
        "pivoted_hemoglobin AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        charttime,\n",
        "        hemoglobin\n",
        "    FROM\n",
        "        pivoted_lab\n",
        "    WHERE\n",
        "        stay_id IS NOT NULL\n",
        "        AND charttime IS NOT NULL\n",
        "        AND hemoglobin IS NOT NULL\n",
        "    ORDER BY\n",
        "        stay_id\n",
        ")\n",
        ", tx_hgb_paired AS (\n",
        "        SELECT\n",
        "            w.stay_id,\n",
        "            w.last_hb_in_window,\n",
        "            MIN(p.hemoglobin) AS hemoglobin,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume,\n",
        "            DATETIME_DIFF(w.tx_offset, w.last_hb_in_window, SECOND) AS delta_tx_hgb_seconds,\n",
        "        FROM\n",
        "            (\n",
        "                SELECT\n",
        "                    p.stay_id,\n",
        "                    t.charttime AS tx_offset,\n",
        "                    t.rbc_volume,\n",
        "                    MAX(p.charttime) AS last_hb_in_window,\n",
        "                    p.hemoglobin\n",
        "                FROM tx t --`arctic-welder-307905.blood_transfusion.tx` t\n",
        "                    INNER JOIN pivoted_hemoglobin p ON p.stay_id = t.stay_id\n",
        "                    AND p.charttime BETWEEN DATETIME_SUB(t.charttime, INTERVAL 6 HOUR)\n",
        "                    AND t.charttime --we search the 6 hours prior to transfusion for minimum hemoglobin levels associated with that transfusion\n",
        "                GROUP BY\n",
        "                    p.stay_id,\n",
        "                    t.charttime,\n",
        "                    t.rbc_volume,\n",
        "                    p.hemoglobin\n",
        "                ORDER BY\n",
        "                    stay_id,\n",
        "                    last_hb_in_window\n",
        "            ) w\n",
        "            INNER JOIN pivoted_hemoglobin p ON p.stay_id = w.stay_id\n",
        "            AND p.charttime = w.last_hb_in_window\n",
        "        GROUP BY\n",
        "            w.stay_id,\n",
        "            w.last_hb_in_window,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume\n",
        "        ORDER BY\n",
        "            stay_id,\n",
        "             last_hb_in_window,\n",
        "             tx_offset\n",
        ")\n",
        ", tx_hgb_filtered AS (\n",
        "        SELECT\n",
        "            *,\n",
        "            ROW_NUMBER() OVER(x) AS event_number\n",
        "        FROM tx_hgb_paired\n",
        "        WINDOW x AS(\n",
        "                PARTITION BY stay_id\n",
        "                ORDER BY tx_offset\n",
        "            )\n",
        "        ORDER BY stay_id\n",
        "\n",
        ")\n",
        ", closest_tx_hb_pairing AS (SELECT stay_id,\n",
        "      ROW_NUMBER() OVER(PARTITION BY stay_id ORDER BY tx_offset) AS tx_episode,\n",
        "     last_hb_in_window, hemoglobin,\n",
        "      tx_offset, rbc_volume,\n",
        "      delta_tx_hgb_seconds/60 AS delta_offset_minutes\n",
        "    FROM tx_hgb_filtered\n",
        "    ORDER BY stay_id, event_number),\n",
        "\n",
        "closest_tx_hb_pairing_icu_time AS (SELECT a.*,b.INTIME,b.OUTTIME,ROUND((rbc_volume/ 350),0) AS rbc_units\n",
        "FROM closest_tx_hb_pairing  a\n",
        "INNER JOIN  `physionet-data.mimic_icu.icustays` b\n",
        "ON a.stay_id= b.stay_id\n",
        "AND a.tx_offset BETWEEN b.INTIME and b.OUTTIME\n",
        "ORDER BY a.stay_id)\n",
        "\n",
        "SELECT * FROM closest_tx_hb_pairing_icu_time\n",
        "\"\"\").to_dataframe()"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "df1= tx_mimic4.copy()\n",
        "df1.sort_values(by = ['stay_id', 'tx_offset','delta_offset_minutes'], ascending = [True, True,True], inplace=True)\n",
        "#Keep only the first ICU stay out of all the possible stays\n",
        "df1.drop_duplicates(subset=['stay_id'], keep= 'first', inplace=True)\n",
        "#Consider only patient that received just 1 blood unit\n",
        "treatment_mimic4_1rbc = df1.loc[df1['rbc_units'] == 1.0]\n",
        "#First ICUstay for the patients treated with just 1 blood unit, mimic 4\n",
        "treatment_mimic4_1rbc.head()"
      ],
      "metadata": {
        "id": "8oF0JtNh9shu",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 444
        },
        "outputId": "922829ab-7e69-472f-8fd3-c1341cadfaf4"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    stay_id  tx_episode   last_hb_in_window  hemoglobin           tx_offset  \\\n",
              "0  30001446           1 2186-04-12 02:00:00         7.9 2186-04-12 04:28:00   \n",
              "1  30001555           1 2177-09-27 11:50:00         7.6 2177-09-27 16:00:00   \n",
              "3  30001947           1 2162-12-26 18:25:00         6.9 2162-12-26 21:04:00   \n",
              "7  30003372           1 2170-06-11 04:17:00         7.8 2170-06-11 08:45:00   \n",
              "9  30003749           2 2120-11-05 16:30:00         6.3 2120-11-05 17:48:00   \n",
              "\n",
              "   rbc_volume  delta_offset_minutes              INTIME             OUTTIME  \\\n",
              "0       375.0                 148.0 2186-04-12 03:49:00 2186-04-13 19:45:47   \n",
              "1       350.0                 250.0 2177-09-27 11:23:13 2177-09-28 18:26:00   \n",
              "3       375.0                 159.0 2162-12-26 15:04:30 2162-12-27 22:31:00   \n",
              "7       350.0                 268.0 2170-06-10 03:15:10 2170-06-12 15:54:41   \n",
              "9       375.0                  78.0 2120-11-05 16:03:00 2120-11-07 08:19:44   \n",
              "\n",
              "   rbc_units  \n",
              "0        1.0  \n",
              "1        1.0  \n",
              "3        1.0  \n",
              "7        1.0  \n",
              "9        1.0  "
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-b29cc738-f928-4d42-8fe2-3c7716eb7355\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
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              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>stay_id</th>\n",
              "      <th>tx_episode</th>\n",
              "      <th>last_hb_in_window</th>\n",
              "      <th>hemoglobin</th>\n",
              "      <th>tx_offset</th>\n",
              "      <th>rbc_volume</th>\n",
              "      <th>delta_offset_minutes</th>\n",
              "      <th>INTIME</th>\n",
              "      <th>OUTTIME</th>\n",
              "      <th>rbc_units</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>30001446</td>\n",
              "      <td>1</td>\n",
              "      <td>2186-04-12 02:00:00</td>\n",
              "      <td>7.9</td>\n",
              "      <td>2186-04-12 04:28:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>148.0</td>\n",
              "      <td>2186-04-12 03:49:00</td>\n",
              "      <td>2186-04-13 19:45:47</td>\n",
              "      <td>1.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>30001555</td>\n",
              "      <td>1</td>\n",
              "      <td>2177-09-27 11:50:00</td>\n",
              "      <td>7.6</td>\n",
              "      <td>2177-09-27 16:00:00</td>\n",
              "      <td>350.0</td>\n",
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              "      <td>2177-09-27 11:23:13</td>\n",
              "      <td>2177-09-28 18:26:00</td>\n",
              "      <td>1.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>30001947</td>\n",
              "      <td>1</td>\n",
              "      <td>2162-12-26 18:25:00</td>\n",
              "      <td>6.9</td>\n",
              "      <td>2162-12-26 21:04:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>159.0</td>\n",
              "      <td>2162-12-26 15:04:30</td>\n",
              "      <td>2162-12-27 22:31:00</td>\n",
              "      <td>1.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>30003372</td>\n",
              "      <td>1</td>\n",
              "      <td>2170-06-11 04:17:00</td>\n",
              "      <td>7.8</td>\n",
              "      <td>2170-06-11 08:45:00</td>\n",
              "      <td>350.0</td>\n",
              "      <td>268.0</td>\n",
              "      <td>2170-06-10 03:15:10</td>\n",
              "      <td>2170-06-12 15:54:41</td>\n",
              "      <td>1.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>30003749</td>\n",
              "      <td>2</td>\n",
              "      <td>2120-11-05 16:30:00</td>\n",
              "      <td>6.3</td>\n",
              "      <td>2120-11-05 17:48:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>78.0</td>\n",
              "      <td>2120-11-05 16:03:00</td>\n",
              "      <td>2120-11-07 08:19:44</td>\n",
              "      <td>1.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
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            ]
          },
          "metadata": {},
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      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Carevue MIMIC 3 Treatment\n",
        "First icustay of the patients in which he received just 1 blood sac"
      ],
      "metadata": {
        "id": "ulHiGwj82g0I"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "#patients trated with a blood sac in mimic 3 carevue (metavision has overlaps with mimic 4)\n",
        "tx_mimic3_carevue = client.query(\"\"\"\n",
        "WITH\n",
        "all_criteria AS (SELECT DISTINCT(icustay_id)\n",
        "FROM `physionet-data.mimiciii_derived.pivoted_sofa`\n",
        "WHERE icustay_id IN(SELECT DISTINCT(icustay_id)\n",
        "                    FROM `physionet-data.mimiciii_derived.icustay_detail`\n",
        "                    WHERE icustay_seq = 1\n",
        "                    AND first_icu_stay= TRUE\n",
        "                    AND (admission_age BETWEEN 18 AND 89)\n",
        "                    )\n",
        "    AND icustay_id NOT IN(SELECT DISTINCT(i.ICUSTAY_ID)\n",
        "        FROM `physionet-data.mimiciii_clinical.diagnoses_icd` d\n",
        "        INNER JOIN `physionet-data.mimiciii_clinical.icustays` i\n",
        "            ON d.hadm_id=i.hadm_id\n",
        "        INNER JOIN `physionet-data.mimiciii_derived.icustay_detail` a\n",
        "            ON d.HADM_ID=a.hadm_id\n",
        "        WHERE icd9_code IN (\n",
        "                --ref: https://www.bmj.com/content/bmj/suppl/2015/02/03/bmj.h246.DC1/junm020747.ww1_default.pdf\n",
        "                --intracranial bleeding\n",
        "                '430', --Subarachnoid\n",
        "                '431', --intracerebral\n",
        "                '4320', --other and unspecified intracranial bleeding\n",
        "                '4321', --subdural\n",
        "                '4329', --unspecified intracranial bleeding\n",
        "                --upper gastrointestinal\n",
        "                '5310', --acute gastric ulcer with bleeding without obstruction\n",
        "                '5312', --acute gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5314', --chronic or unspecified gastric ulcer with bleeding without obstruction\n",
        "                '5316', --chronic or unspecified gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5320', --acute duodenal ulcer with bleeding without obstruction\n",
        "                '5322', --acute duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5324', --chronic or unspecified duodenal ulcer with bleeding without obstruction\n",
        "                '5326', --chronic or unspecified duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5330', --acute peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5332', --acute peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5334', --chronic or unspecified peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5336', --chronic or unspecified peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5340', --acute gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5342', --acute gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5344', --chronic or unspecified gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5346', --chronic or unspecified gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5780', --hematemesis\n",
        "                '5781', --blood in stool\n",
        "                '5789', --bleeding of gastrointestinal tract unspecified\n",
        "                --Lower GI\n",
        "                '5693', --bleeding of rectum and anus\n",
        "                --Other Bleeding\n",
        "                '2878', --other unspecified hemorrhagic conditions\n",
        "                '2879', --unspecified hemorrhagic conditions\n",
        "                '5967', --bleeding into bladder wall\n",
        "                '7848', --bleeding from throat\n",
        "                '5997', --hematuria, unspecified\n",
        "                '6271', --postmenopausal bleeding\n",
        "                '4590', --bleeding unspecified\n",
        "                '7191', --hemarthrosis site unspecified\n",
        "                '7863', --hemoptysis, unspecified\n",
        "                '72992', --nontraumatic hematoma soft tissue\n",
        "                '9582' --secondary or recurrent following trauma\n",
        "            )\n",
        "        OR icd9_code LIKE '900%' --vessel injuries\n",
        "        OR icd9_code LIKE '901%' --vessel injuries\n",
        "        OR icd9_code LIKE '902%' --vessel injuries\n",
        "        OR icd9_code LIKE '903%' --vessel injuries\n",
        "        OR icd9_code LIKE '904%' --vessel injuries\n",
        "\n",
        "        OR UPPER(LAST_CAREUNIT) LIKE '%TSICU%'\n",
        "        OR UPPER(FIRST_CAREUNIT) LIKE '%TSICU%' ))\n",
        " ,\n",
        " demographics AS (\n",
        "    SELECT\n",
        "        ie.subject_id,\n",
        "        ie.hadm_id,\n",
        "        ie.icustay_id -- patient level factors\n",
        ",\n",
        "        pat.gender,\n",
        "        pat.dod -- hospital level factors\n",
        ",\n",
        "        adm.admittime,\n",
        "        adm.dischtime,\n",
        "        DATETIME_DIFF(adm.admittime, pat.dob, YEAR) AS age,\n",
        "        adm.admission_type,\n",
        "        adm.hospital_expire_flag,\n",
        "        adm.deathtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY adm.subject_id\n",
        "            ORDER BY\n",
        "                adm.admittime\n",
        "        ) AS hospstay_seq,\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY adm.subject_id\n",
        "                ORDER BY\n",
        "                    adm.admittime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_hosp_stay -- icu level factors\n",
        ",\n",
        "        ie.intime,\n",
        "        ie.outtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY ie.hadm_id\n",
        "            ORDER BY\n",
        "                ie.intime\n",
        "        ) AS icustay_seq -- first ICU stay *for the current hospitalization*\n",
        ",\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY ie.hadm_id\n",
        "                ORDER BY\n",
        "                    ie.intime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_icu_stay\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.icustays` ie\n",
        "        INNER JOIN `physionet-data.mimiciii_clinical.admissions` adm ON ie.hadm_id = adm.hadm_id\n",
        "        INNER JOIN `physionet-data.mimiciii_clinical.patients` pat ON ie.subject_id = pat.subject_id\n",
        "    ORDER BY\n",
        "        ie.subject_id,\n",
        "        adm.admittime,\n",
        "        ie.intime\n",
        "),\n",
        "first_adm_offset AS (\n",
        "    SELECT\n",
        "        icustay_id AS id,\n",
        "        intime,\n",
        "        outtime\n",
        "    FROM\n",
        "        demographics\n",
        "    WHERE\n",
        "        first_icu_stay = TRUE\n",
        "),\n",
        "pivoted_sofa AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_derived.pivoted_sofa` ps\n",
        "        LEFT JOIN first_adm_offset f ON ps.icustay_id = f.id\n",
        "        AND ps.endtime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "),\n",
        "pivoted_lab AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        (\n",
        "            WITH pivoted_lab AS (\n",
        "                -- create a table which has fuzzy boundaries on ICU admission (+- 12 hours from documented time)\n",
        "                -- this is used to assign icustay_id to lab data, which can be collected outside ICU\n",
        "                -- involves first creating a lag/lead version of intime/outtime\n",
        "                WITH i AS (\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        icustay_id,\n",
        "                        intime,\n",
        "                        outtime,\n",
        "                        lag (outtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS outtime_lag,\n",
        "                        lead (intime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS intime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimiciii_clinical.icustays`\n",
        "                ),\n",
        "                iid_assign AS (\n",
        "                    SELECT\n",
        "                        i.subject_id,\n",
        "                        i.icustay_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN i.outtime_lag IS NOT NULL\n",
        "                            AND i.outtime_lag > DATETIME_SUB(i.intime, INTERVAL 24 HOUR) THEN DATETIME_SUB(\n",
        "                                i.intime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime, i.outtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(i.intime, INTERVAL 12 HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN i.intime_lead IS NOT NULL\n",
        "                            AND i.intime_lead < DATETIME_ADD(i.outtime, INTERVAL 24 HOUR) THEN DATETIME_ADD(\n",
        "                                i.outtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime_lead, i.outtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(i.outtime, INTERVAL 12 HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        i\n",
        "                ) -- also create fuzzy boundaries on hospitalization\n",
        ",\n",
        "                h AS (\n",
        "                    SELECT\n",
        "                        subject_id,hadm_id,admittime,dischtime,\n",
        "                        lag (dischtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS dischtime_lag,\n",
        "                        lead (admittime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS admittime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimiciii_clinical.admissions`\n",
        "                ),\n",
        "                adm AS (\n",
        "                    SELECT\n",
        "                        h.subject_id,\n",
        "                        h.hadm_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN h.dischtime_lag IS NOT NULL\n",
        "                            AND h.dischtime_lag > DATETIME_SUB(h.admittime, INTERVAL '24' HOUR) THEN DATETIME_SUB(\n",
        "                                h.admittime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime, h.dischtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(h.admittime, INTERVAL '12' HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN h.admittime_lead IS NOT NULL\n",
        "                            AND h.admittime_lead < DATETIME_ADD(h.dischtime, INTERVAL '24' HOUR) THEN DATETIME_ADD(\n",
        "                                h.dischtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime_lead, h.dischtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(h.dischtime, INTERVAL '12' HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        h\n",
        "                ),\n",
        "                le AS (\n",
        "                    -- begin query that extracts the data\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        charttime -- here we assign labels to ITEMIDs\n",
        "                        -- this also fuses together multiple ITEMIDs containing the same data\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN itemid = 50868 THEN 'ANION GAP'\n",
        "                            WHEN itemid = 50862 THEN 'ALBUMIN'\n",
        "                            WHEN itemid = 51144 THEN 'BANDS'\n",
        "                            WHEN itemid = 50882 THEN 'BICARBONATE'\n",
        "                            WHEN itemid = 50885 THEN 'BILIRUBIN'\n",
        "                            WHEN itemid = 50912 THEN 'CREATININE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50806 THEN 'CHLORIDE'\n",
        "                            WHEN itemid = 50902 THEN 'CHLORIDE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50809 THEN 'GLUCOSE'\n",
        "                            WHEN itemid = 50931 THEN 'GLUCOSE' -- exclude blood gas\n",
        "                            --WHEN itemid = 50810 THEN 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221 THEN 'HEMATOCRIT' -- exclude blood gas\n",
        "                            --WHEN itemid = 50811 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813 THEN 'LACTATE'\n",
        "                            WHEN itemid = 51265 THEN 'PLATELET' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50822 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 50971 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 51275 THEN 'PTT'\n",
        "                            WHEN itemid = 51237 THEN 'INR'\n",
        "                            WHEN itemid = 51274 THEN 'PT' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50824 THEN 'SODIUM'\n",
        "                            WHEN itemid = 50983 THEN 'SODIUM'\n",
        "                            WHEN itemid = 51006 THEN 'BUN'\n",
        "                            WHEN itemid = 51300 THEN 'WBC'\n",
        "                            WHEN itemid = 51301 THEN 'WBC'\n",
        "                            ELSE NULL\n",
        "                        END AS label,\n",
        "                        -- add in some sanity checks on the values\n",
        "                        -- the where clause below requires all valuenum to be > 0, so these are only upper limit checks\n",
        "                        CASE\n",
        "                            WHEN itemid = 50862\n",
        "                            AND valuenum > 10 THEN NULL -- g/dL 'ALBUMIN'\n",
        "                            WHEN itemid = 50868\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'ANION GAP'\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum < 0 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum > 100 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 50882\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'BICARBONATE'\n",
        "                            WHEN itemid = 50885\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'BILIRUBIN'\n",
        "                            WHEN itemid = 50806\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50902\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50912\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'CREATININE'\n",
        "                            WHEN itemid = 50809\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50931\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50810\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 50811\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813\n",
        "                            AND valuenum > 50 THEN NULL -- mmol/L 'LACTATE'\n",
        "                            WHEN itemid = 51265\n",
        "                            AND valuenum > 10000 THEN NULL -- K/uL 'PLATELET'\n",
        "                            WHEN itemid = 50822\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 50971\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 51275\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PTT'\n",
        "                            WHEN itemid = 51237\n",
        "                            AND valuenum > 50 THEN NULL -- 'INR'\n",
        "                            WHEN itemid = 51274\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PT'\n",
        "                            WHEN itemid = 50824\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 50983\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 51006\n",
        "                            AND valuenum > 300 THEN NULL -- 'BUN'\n",
        "                            WHEN itemid = 51300\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            WHEN itemid = 51301\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            ELSE valuenum\n",
        "                        END AS valuenum\n",
        "                    FROM\n",
        "                        `physionet-data.mimiciii_clinical.labevents`\n",
        "                    WHERE\n",
        "                        ITEMID IN (\n",
        "                            -- comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS\n",
        "                            50868, -- ANION GAP | CHEMISTRY | BLOOD | 769895\n",
        "                            50862, -- ALBUMIN | CHEMISTRY | BLOOD | 146697\n",
        "                            51144, -- BANDS - hematology\n",
        "                            50882, -- BICARBONATE | CHEMISTRY | BLOOD | 780733\n",
        "                            50885, -- BILIRUBIN, TOTAL | CHEMISTRY | BLOOD | 238277\n",
        "                            50912, -- CREATININE | CHEMISTRY | BLOOD | 797476\n",
        "                            50902, -- CHLORIDE | CHEMISTRY | BLOOD | 795568\n",
        "                            -- 50806, -- CHLORIDE, WHOLE BLOOD | BLOOD GAS | BLOOD | 48187\n",
        "                            50931, -- GLUCOSE | CHEMISTRY | BLOOD | 748981\n",
        "                            -- 50809, -- GLUCOSE | BLOOD GAS | BLOOD | 196734\n",
        "                            51221, -- HEMATOCRIT | HEMATOLOGY | BLOOD | 881846\n",
        "                            -- 50810, -- HEMATOCRIT, CALCULATED | BLOOD GAS | BLOOD | 89715\n",
        "                            51222, -- HEMOGLOBIN | HEMATOLOGY | BLOOD | 752523\n",
        "                            -- 50811, -- HEMOGLOBIN | BLOOD GAS | BLOOD | 89712\n",
        "                            50813, -- LACTATE | BLOOD GAS | BLOOD | 187124\n",
        "                            51265, -- PLATELET COUNT | HEMATOLOGY | BLOOD | 778444\n",
        "                            50971, -- POTASSIUM | CHEMISTRY | BLOOD | 845825\n",
        "                            -- 50822, -- POTASSIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 192946\n",
        "                            51275, -- PTT | HEMATOLOGY | BLOOD | 474937\n",
        "                            51237, -- INR(PT) | HEMATOLOGY | BLOOD | 471183\n",
        "                            51274, -- PT | HEMATOLOGY | BLOOD | 469090\n",
        "                            50983, -- SODIUM | CHEMISTRY | BLOOD | 808489\n",
        "                            -- 50824, -- SODIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 71503\n",
        "                            51006, -- UREA NITROGEN | CHEMISTRY | BLOOD | 791925\n",
        "                            51301, -- WHITE BLOOD CELLS | HEMATOLOGY | BLOOD | 753301\n",
        "                            51300  -- WBC COUNT | HEMATOLOGY | BLOOD | 2371\n",
        "                        )\n",
        "                        AND valuenum IS NOT NULL\n",
        "                        AND valuenum > 0 -- lab values cannot be 0 and cannot be negative\n",
        "                ),\n",
        "                le_avg AS (\n",
        "                    SELECT\n",
        "                        le.subject_id,\n",
        "                        le.charttime,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ANION GAP' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ANIONGAP,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ALBUMIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ALBUMIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BANDS' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BANDS,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BICARBONATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BICARBONATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BILIRUBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BILIRUBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CREATININE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CREATININE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CHLORIDE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CHLORIDE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'GLUCOSE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS GLUCOSE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMATOCRIT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMATOCRIT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMOGLOBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMOGLOBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'LACTATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS LACTATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PLATELET' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PLATELET,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'POTASSIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS POTASSIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PTT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PTT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'INR' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS INR,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'SODIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS SODIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BUN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BUN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'WBC' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS WBC\n",
        "                    FROM\n",
        "                        le\n",
        "                    GROUP BY\n",
        "                        le.subject_id,\n",
        "                        le.charttime\n",
        "                )\n",
        "                SELECT\n",
        "                    iid.icustay_id,\n",
        "                    adm.hadm_id,\n",
        "                    le_avg.*\n",
        "                FROM\n",
        "                    le_avg\n",
        "                    LEFT JOIN adm ON le_avg.subject_id = adm.subject_id\n",
        "                    AND le_avg.charttime >= adm.data_start\n",
        "                    AND le_avg.charttime < adm.data_end\n",
        "                    LEFT JOIN iid_assign iid ON le_avg.subject_id = iid.subject_id\n",
        "                    AND le_avg.charttime >= iid.data_start\n",
        "                    AND le_avg.charttime < iid.data_end\n",
        "                ORDER BY\n",
        "                    le_avg.subject_id,\n",
        "                    le_avg.charttime\n",
        "            )\n",
        "            SELECT\n",
        "                *\n",
        "            FROM\n",
        "                pivoted_lab\n",
        "        ) AS pl\n",
        "        LEFT JOIN first_adm_offset f ON pl.icustay_id = f.id\n",
        "        AND pl.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "),\n",
        "mechvent AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        charttime -- case statement determining whether it is an instance of mech vent\n",
        ",\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN itemid IS NULL\n",
        "                OR value IS NULL THEN 0 -- can't have null values\n",
        "                WHEN itemid = 720\n",
        "                AND value != 'Other/Remarks' THEN 1 -- VentTypeRecorded\n",
        "                WHEN itemid = 223848\n",
        "                AND value != 'Other' THEN 1\n",
        "                WHEN itemid = 223849 THEN 1 -- ventilator mode\n",
        "                WHEN itemid = 467\n",
        "                AND value = 'Ventilator' THEN 1 -- O2 delivery device == ventilator\n",
        "                WHEN itemid IN(\n",
        "                    445,\n",
        "                    448,\n",
        "                    449,\n",
        "                    450,\n",
        "                    1340,\n",
        "                    1486,\n",
        "                    1600,\n",
        "                    224687 -- minute volume\n",
        ",\n",
        "                    639,\n",
        "                    654,\n",
        "                    681,\n",
        "                    682,\n",
        "                    683,\n",
        "                    684,\n",
        "                    224685,\n",
        "                    224684,\n",
        "                    224686 -- tidal volume\n",
        ",\n",
        "                    218,\n",
        "                    436,\n",
        "                    535,\n",
        "                    444,\n",
        "                    459,\n",
        "                    224697,\n",
        "                    224695,\n",
        "                    224696,\n",
        "                    224746,\n",
        "                    224747 -- High/Low/Peak/Mean/Neg insp force (\"RespPressure\")\n",
        ",\n",
        "                    221,\n",
        "                    1,\n",
        "                    1211,\n",
        "                    1655,\n",
        "                    2000,\n",
        "                    226873,\n",
        "                    224738,\n",
        "                    224419,\n",
        "                    224750,\n",
        "                    227187 -- Insp pressure\n",
        ",\n",
        "                    543 -- PlateauPressure\n",
        ",\n",
        "                    5865,\n",
        "                    5866,\n",
        "                    224707,\n",
        "                    224709,\n",
        "                    224705,\n",
        "                    224706 -- APRV pressure\n",
        ",\n",
        "                    60,\n",
        "                    437,\n",
        "                    505,\n",
        "                    506,\n",
        "                    686,\n",
        "                    220339,\n",
        "                    224700 -- PEEP\n",
        ",\n",
        "                    3459 -- high pressure relief\n",
        ",\n",
        "                    501,\n",
        "                    502,\n",
        "                    503,\n",
        "                    224702 -- PCV\n",
        ",\n",
        "                    223,\n",
        "                    667,\n",
        "                    668,\n",
        "                    669,\n",
        "                    670,\n",
        "                    671,\n",
        "                    672 -- TCPCV\n",
        ",\n",
        "                    224701 -- PSVlevel\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS ventmarker\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.chartevents` ce\n",
        "        LEFT JOIN first_adm_offset f ON ce.icustay_id = f.id\n",
        "        AND ce.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "    WHERE\n",
        "        ce.value IS NOT NULL -- exclude rows marked as error\n",
        "        AND ce.error != 1 -- the below are settings used to indicate ventilation\n",
        "        AND itemid IN(\n",
        "            720,\n",
        "            223849 -- vent mode\n",
        ",\n",
        "            223848 -- vent type\n",
        ",\n",
        "            445,\n",
        "            448,\n",
        "            449,\n",
        "            450,\n",
        "            1340,\n",
        "            1486,\n",
        "            1600,\n",
        "            224687 -- minute volume\n",
        ",\n",
        "            639,\n",
        "            654,\n",
        "            681,\n",
        "            682,\n",
        "            683,\n",
        "            684,\n",
        "            224685,\n",
        "            224684,\n",
        "            224686 -- tidal volume\n",
        ",\n",
        "            218,\n",
        "            436,\n",
        "            535,\n",
        "            444,\n",
        "            224697,\n",
        "            224695,\n",
        "            224696,\n",
        "            224746,\n",
        "            224747 -- High/Low/Peak/Mean (\"RespPressure\")\n",
        ",\n",
        "            221,\n",
        "            1,\n",
        "            1211,\n",
        "            1655,\n",
        "            2000,\n",
        "            226873,\n",
        "            224738,\n",
        "            224419,\n",
        "            224750,\n",
        "            227187 -- Insp pressure\n",
        ",\n",
        "            543 -- PlateauPressure\n",
        ",\n",
        "            5865,\n",
        "            5866,\n",
        "            224707,\n",
        "            224709,\n",
        "            224705,\n",
        "            224706 -- APRV pressure\n",
        ",\n",
        "            60,\n",
        "            437,\n",
        "            505,\n",
        "            506,\n",
        "            686,\n",
        "            220339,\n",
        "            224700 -- PEEP\n",
        ",\n",
        "            3459 -- high pressure relief\n",
        ",\n",
        "            501,\n",
        "            502,\n",
        "            503,\n",
        "            224702 -- PCV\n",
        ",\n",
        "            223,\n",
        "            667,\n",
        "            668,\n",
        "            669,\n",
        "            670,\n",
        "            671,\n",
        "            672 -- TCPCV\n",
        ",\n",
        "            224701 -- PSVlevel\n",
        "            -- the below are settings used to indicate extubation\n",
        ",\n",
        "            640 -- extubated\n",
        "            -- the below indicate oxygen/NIV, i.e. the end of a mechanical vent event\n",
        ",\n",
        "            468 -- O2 Delivery Device#2\n",
        ",\n",
        "            469 -- O2 Delivery Mode\n",
        ",\n",
        "            470 -- O2 Flow (lpm)\n",
        ",\n",
        "            471 -- O2 Flow (lpm) #2\n",
        ",\n",
        "            227287 -- O2 Flow (additional cannula)\n",
        ",\n",
        "            226732 -- O2 Delivery Device(s)\n",
        ",\n",
        "            223834 -- O2 Flow\n",
        "            -- used in both oxygen + vent calculation\n",
        ",\n",
        "            467 -- O2 Delivery Device\n",
        "        )\n",
        "    GROUP BY\n",
        "        icustay_id,\n",
        "        charttime\n",
        "),\n",
        "sepsis AS (\n",
        "    -- ICD-9 codes for Angus criteria of sepsis\n",
        "    SELECT\n",
        "        hadm_id,\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd9_code, 1, 3) IN (\n",
        "                    '001','002','003','004','005',\n",
        "                    '008','009','010','011','012',\n",
        "                    '013','014','015','016','017',\n",
        "                    '018','020','021','022','023',\n",
        "                    '024','025','026','027','030',\n",
        "                    '031','032','033','034','035',\n",
        "                    '036','037','038','039','040',\n",
        "                    '041','090','091','092','093',\n",
        "                    '094','095','096','097','098',\n",
        "                    '100','101','102','103','104',\n",
        "                    '110','111','112','114','115',\n",
        "                    '116','117','118','320','322',\n",
        "                    '324','325','420','421','451',\n",
        "                    '461','462','463','464','465',\n",
        "                    '481','482','485','486','494',\n",
        "                    '510','513','540','541','542',\n",
        "                    '566','567','590','597','601',\n",
        "                    '614','615','616','681','682',\n",
        "                    '683','686','730'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd9_code, 1, 4) IN (\n",
        "                    '5695','5720','5721','5750',\n",
        "                    '5990','7110','7907','9966',\n",
        "                    '9985','9993'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd9_code, 1, 5) IN (\n",
        "                    '49121','56201','56203',\n",
        "                    '56211','56213','56983'\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS sepsisflag\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.diagnoses_icd`\n",
        "    GROUP BY\n",
        "        hadm_id\n",
        "),\n",
        "vasopressor_duration AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_derived.vasopressordurations`\n",
        "),\n",
        "premorbid AS (\n",
        "    WITH icd AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            CAST(icd9_code AS STRING) AS icd9_code\n",
        "        FROM\n",
        "            `physionet-data.mimiciii_clinical.diagnoses_icd`\n",
        "    ),\n",
        "    eliflg AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            icd9_code -- note that these codes will seem incomplete at first\n",
        "            -- for example, CHF is missing a lot of codes referenced in the literature (402.11, 402.91, etc)\n",
        "            -- these codes are captured by hypertension flags instead\n",
        "            -- later there are some complicated rules which confirm/reject those codes as CHF\n",
        ",\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd9_code, 1, 3) IN(\n",
        "                    '410', --Acute myocardial infarction\n",
        "                    '411', --Other acute and subacute forms of ischemic heart disease\n",
        "                    '412', --Old myocardial infarction\n",
        "                    '413', --Angina pectoris\n",
        "                    '414'  --Other forms of chronic ischemic heart disease\n",
        "                ) THEN 1\n",
        "            END AS IHD,\n",
        "            CASE\n",
        "                WHEN icd9_code = '39891' THEN 1\n",
        "                WHEN icd9_code BETWEEN '4280 '\n",
        "                AND '4289 ' THEN 1\n",
        "            END AS CHF\n",
        "            /* Congestive heart failure */\n",
        "            -- cardiac arrhythmias is removed in up to date versions\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code BETWEEN '4400 '\n",
        "                AND '4409 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '44100'\n",
        "                AND '4419 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '4420 '\n",
        "                AND '4429 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '4431 '\n",
        "                AND '4439 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '44421'\n",
        "                AND '44422' THEN 1\n",
        "                WHEN icd9_code = '4471 ' THEN 1\n",
        "                WHEN icd9_code = '449  ' THEN 1\n",
        "                WHEN icd9_code = '5571 ' THEN 1\n",
        "                WHEN icd9_code = '5579 ' THEN 1\n",
        "                WHEN icd9_code = 'V434 ' THEN 1\n",
        "            END AS PERIVASC\n",
        "            /* Peripheral vascular disorder */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40200' THEN 1\n",
        "                WHEN icd9_code = '40210' THEN 1\n",
        "                WHEN icd9_code = '40290' THEN 1\n",
        "                WHEN icd9_code = '40509' THEN 1\n",
        "                WHEN icd9_code = '40519' THEN 1\n",
        "                WHEN icd9_code = '40599' THEN 1\n",
        "            END AS HTNWOCHF\n",
        "            /* Hypertensive heart disease without heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40201' THEN 1\n",
        "                WHEN icd9_code = '40211' THEN 1\n",
        "                WHEN icd9_code = '40291' THEN 1\n",
        "            END AS HTNWCHF\n",
        "            /* Hypertensive heart disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40301' THEN 1\n",
        "                WHEN icd9_code = '40311' THEN 1\n",
        "                WHEN icd9_code = '40391' THEN 1\n",
        "            END AS HRENWRF\n",
        "            /* Hypertensive renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40401' THEN 1\n",
        "                WHEN icd9_code = '40411' THEN 1\n",
        "                WHEN icd9_code = '40491' THEN 1\n",
        "            END AS HHRWCHF\n",
        "            /* Hypertensive heart and renal disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40402' THEN 1\n",
        "                WHEN icd9_code = '40412' THEN 1\n",
        "                WHEN icd9_code = '40492' THEN 1\n",
        "            END AS HHRWRF\n",
        "            /* Hypertensive heart and renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40403' THEN 1\n",
        "                WHEN icd9_code = '40413' THEN 1\n",
        "                WHEN icd9_code = '40493' THEN 1\n",
        "            END AS HHRWHRF\n",
        "            /* Hypertensive heart and renal disease with heart and renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '585  ' THEN 1 -- discontinued code\n",
        "                WHEN icd9_code = '5853 ' THEN 1\n",
        "                WHEN icd9_code = '5854 ' THEN 1\n",
        "                WHEN icd9_code = '5855 ' THEN 1\n",
        "                WHEN icd9_code = '5856 ' THEN 1\n",
        "                WHEN icd9_code = '5859 ' THEN 1\n",
        "                WHEN icd9_code = '586  ' THEN 1\n",
        "                WHEN icd9_code = 'V420 ' THEN 1\n",
        "                WHEN icd9_code = 'V451 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN 'V560 '\n",
        "                AND 'V5632' THEN 1\n",
        "                WHEN icd9_code = 'V568 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN 'V4511'\n",
        "                AND 'V4512' THEN 1\n",
        "            END AS RENLFAIL\n",
        "            /* Renal failure */\n",
        "        FROM\n",
        "            icd\n",
        "    ),\n",
        "    eligrp AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            MAX(ihd) AS ihd,\n",
        "            MAX(chf) AS chf,\n",
        "            MAX(perivasc) AS perivasc,\n",
        "            MAX(htnwchf) AS htnwchf,\n",
        "            MAX(hrenwrf) AS hrenwrf,\n",
        "            MAX(hhrwchf) AS hhrwchf,\n",
        "            MAX(hhrwrf) AS hhrwrf,\n",
        "            MAX(hhrwhrf) AS hhrwhrf,\n",
        "            MAX(renlfail) AS renlfail\n",
        "        FROM\n",
        "            eliflg\n",
        "        GROUP BY\n",
        "            hadm_id\n",
        "    )\n",
        "    SELECT\n",
        "        adm.subject_id,\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN ihd = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS ISCHEMIC_HEART_DISEASE,\n",
        "        CASE\n",
        "            WHEN chf = 1 THEN 1\n",
        "            WHEN htnwchf = 1 THEN 1\n",
        "            WHEN hhrwchf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS CONGESTIVE_HEART_FAILURE,\n",
        "        CASE\n",
        "            WHEN perivasc = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS PERIPHERAL_VASCULAR,\n",
        "        CASE\n",
        "            WHEN renlfail = 1 THEN 1\n",
        "            WHEN hrenwrf = 1 THEN 1\n",
        "            WHEN hhrwrf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS RENAL_FAILURE\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.admissions` adm\n",
        "        LEFT JOIN eligrp eli ON adm.hadm_id = eli.hadm_id\n",
        "    ORDER BY\n",
        "        adm.hadm_id\n",
        "),\n",
        "surgflag AS (\n",
        "    SELECT\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN LOWER(curr_service) LIKE '%surg%' THEN 1\n",
        "            ELSE 0\n",
        "        END AS surgical,\n",
        "        ROW_NUMBER() OVER(\n",
        "            PARTITION BY adm.HADM_ID\n",
        "            ORDER BY\n",
        "                TRANSFERTIME\n",
        "        ) AS serviceOrder\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.admissions` adm\n",
        "        LEFT JOIN `physionet-data.mimiciii_clinical.services` se ON adm.hadm_id = se.hadm_id\n",
        "),\n",
        "tx_raw AS (\n",
        "    -- BLOOD TRANSFUSED in mL\n",
        "    WITH carevue AS (\n",
        "        SELECT\n",
        "            cv.icustay_id,\n",
        "            cv.charttime,\n",
        "            -- carevue always has units in millilitres (or null)\n",
        "            ROUND(cv.amount) AS amount\n",
        "        FROM\n",
        "            `physionet-data.mimiciii_clinical.inputevents_cv` cv\n",
        "        WHERE\n",
        "            cv.itemid IN(\n",
        "                30001,  -- Packed RBC's\n",
        "                30002,  -- Whole Blood\n",
        "                30004,  -- Washed PRBC's\n",
        "                30104,  -- OR Packed RBC's\n",
        "                30179,  -- PRBC's\n",
        "                42588,  -- VICU PRBC\n",
        "                42239,  -- CC7 PRBC\n",
        "                42186,\t-- Pre admit PRBC\n",
        "                42239,\t-- CC7 PRBC\n",
        "                42324,\t-- er prbc\n",
        "                42588,\t-- VICU PRBC\n",
        "                42740,\t-- prbc in er\n",
        "                43010,\t-- packed cells pacu\n",
        "                45020,\t-- RBC waste\n",
        "                46124,\t-- er in prbc\n",
        "                46407,\t-- ED PRBC\n",
        "                46612\t  -- E.R. prbc\n",
        "            )\n",
        "            AND amount > 100 --do not count any transfusions events <100mls\n",
        "    )\n",
        "    SELECT\n",
        "        cv.icustay_id,\n",
        "        charttime,\n",
        "        sum(amount) AS rbc_volume,\n",
        "    FROM\n",
        "        carevue cv\n",
        "        LEFT JOIN first_adm_offset f ON cv.icustay_id = f.id\n",
        "        AND cv.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "    GROUP BY\n",
        "        cv.icustay_id,\n",
        "        cv.charttime\n",
        "),\n",
        "tx AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        TIMESTAMP_SECONDS(60 * DIV(UNIX_SECONDS(TIMESTAMP(charttime)), 60)) AS episode,\n",
        "        --some samples have duplicate readings every 15 minutes - we take an hourly window and average the volume across this window\n",
        "        --doing so reduces errors significantly\n",
        "        MIN(charttime) AS charttime,\n",
        "        --get the first timestamp of each window\n",
        "        AVG(rbc_volume) AS rbc_volume\n",
        "    FROM tx_raw\n",
        "    GROUP BY icustay_id, episode\n",
        "    ORDER BY icustay_id, episode\n",
        "),\n",
        "tx_counts AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        COUNT(charttime) AS tx_episodes,\n",
        "        SUM(rbc_volume) AS rbc_volume,\n",
        "        CEIL(SUM(rbc_volume) / 350) AS rbc_units\n",
        "    FROM tx\n",
        "    WHERE\n",
        "        icustay_id IS NOT NULL\n",
        "    GROUP BY\n",
        "        icustay_id\n",
        "),\n",
        "pivoted_hemoglobin AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        charttime,\n",
        "        hemoglobin\n",
        "    FROM\n",
        "        pivoted_lab\n",
        "    WHERE\n",
        "        icustay_id IS NOT NULL\n",
        "        AND charttime IS NOT NULL\n",
        "        AND hemoglobin IS NOT NULL\n",
        "    ORDER BY\n",
        "        icustay_id\n",
        ")\n",
        ", tx_hgb_paired AS (\n",
        "        SELECT\n",
        "            w.icustay_id,\n",
        "            w.last_hb_in_window,\n",
        "            MIN(p.hemoglobin) AS hemoglobin,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume,\n",
        "            DATETIME_DIFF(w.tx_offset, w.last_hb_in_window, SECOND) AS delta_tx_hgb_seconds,\n",
        "        FROM\n",
        "            (\n",
        "                SELECT\n",
        "                    p.icustay_id,\n",
        "                    t.charttime AS tx_offset,\n",
        "                    t.rbc_volume,\n",
        "                    MAX(p.charttime) AS last_hb_in_window,\n",
        "                    p.hemoglobin\n",
        "                FROM tx t --`arctic-welder-307905.blood_transfusion.tx` t\n",
        "                    INNER JOIN pivoted_hemoglobin p ON p.icustay_id = t.icustay_id\n",
        "                    AND p.charttime BETWEEN DATETIME_SUB(t.charttime, INTERVAL 6 HOUR)\n",
        "                    AND t.charttime --we search the 6 hours prior to transfusion for minimum hemoglobin levels associated with that transfusion\n",
        "                GROUP BY\n",
        "                    p.icustay_id,\n",
        "                    t.charttime,\n",
        "                    t.rbc_volume,\n",
        "                    p.hemoglobin\n",
        "                ORDER BY\n",
        "                    icustay_id,\n",
        "                    last_hb_in_window\n",
        "            ) w\n",
        "            INNER JOIN pivoted_hemoglobin p ON p.icustay_id = w.icustay_id\n",
        "            AND p.charttime = w.last_hb_in_window\n",
        "        GROUP BY\n",
        "            w.icustay_id,\n",
        "            w.last_hb_in_window,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume\n",
        "        ORDER BY\n",
        "            icustay_id,\n",
        "             last_hb_in_window,\n",
        "             tx_offset\n",
        ")\n",
        ", tx_hgb_filtered AS (\n",
        "        SELECT\n",
        "            *,\n",
        "            ROW_NUMBER() OVER(x) AS event_number\n",
        "        FROM tx_hgb_paired\n",
        "        WINDOW x AS(\n",
        "                PARTITION BY icustay_id\n",
        "                ORDER BY tx_offset\n",
        "            )\n",
        "        ORDER BY icustay_id\n",
        "\n",
        ")\n",
        "--hr_tx_from_icu_intime AS\n",
        "--(\n",
        "  --select ih.icustay_id, ie.hadm_id\n",
        "  --, hr,ie.INTIME\n",
        "  -- start/endtime can be used to filter to values within this hour\n",
        "  --, DATETIME_SUB(ih.endtime, INTERVAL '1' HOUR) AS starttime\n",
        "  --, ih.endtime\n",
        "  --from `physionet-data.mimiciii_derived.icustay_hours` ih\n",
        "  --INNER JOIN `physionet-data.mimiciii_clinical.icustays` ie\n",
        "    --ON ih.icustay_id = ie.icustay_id\n",
        "--),\n",
        "--hours_from_icu_in_time AS(\n",
        "--select * from hr_tx_from_icu_intime\n",
        "--order by icustay_id, hr)\n",
        "\n",
        ", closest_tx_hb_pairing AS (SELECT icustay_id,\n",
        "      ROW_NUMBER() OVER(PARTITION BY icustay_id ORDER BY tx_offset) AS tx_episode,\n",
        "     last_hb_in_window, hemoglobin,\n",
        "      tx_offset, rbc_volume,\n",
        "      delta_tx_hgb_seconds/60 AS delta_offset_minutes\n",
        "    FROM tx_hgb_filtered\n",
        "    ORDER BY icustay_id, event_number),\n",
        "\n",
        "closest_tx_hb_pairing_icu_time AS (SELECT a.*,b.INTIME,b.OUTTIME,ROUND((rbc_volume/ 350),0) AS rbc_units\n",
        "FROM closest_tx_hb_pairing  a\n",
        "INNER JOIN  `physionet-data.mimiciii_clinical.icustays` b\n",
        "ON a.icustay_id= b.icustay_id\n",
        "AND a.tx_offset BETWEEN b.INTIME and b.OUTTIME\n",
        "ORDER BY a.icustay_id)\n",
        "\n",
        "SELECT * FROM closest_tx_hb_pairing_icu_time\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "F7wydbEk2YDL"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Repeat the same steps for mimic 3\n",
        "df= tx_mimic3_carevue.copy()\n",
        "df.sort_values(by = ['icustay_id', 'tx_offset','delta_offset_minutes'], ascending = [True, True,True], inplace=True)\n",
        "df.drop_duplicates(subset=['icustay_id'], keep= 'first', inplace=True)\n",
        "mimic3_carevue_1rbc = df.loc[df['rbc_units'] == 1.0]\n",
        "# rename icustay to stay_id\n",
        "mimic3_carevue_1rbc=mimic3_carevue_1rbc.rename(columns={\"icustay_id\": \"stay_id\"})\n",
        "mimic3_carevue_1rbc.head()"
      ],
      "metadata": {
        "id": "9Qpyr_4x4Ixx",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 444
        },
        "outputId": "9c5f6753-f007-48ed-bc33-1c4f6eb7e95a"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    stay_id  tx_episode   last_hb_in_window  hemoglobin           tx_offset  \\\n",
              "0    200009           1 2189-11-30 18:29:00        10.5 2189-11-30 23:00:00   \n",
              "4    200041           1 2129-04-01 19:15:00        10.1 2129-04-02 00:00:00   \n",
              "6    200059           2 2198-02-11 01:34:00         9.9 2198-02-11 01:45:00   \n",
              "13   200065           1 2120-03-23 12:25:00         7.5 2120-03-23 12:30:00   \n",
              "30   200077           1 2163-04-17 21:30:00         8.5 2163-04-18 02:15:00   \n",
              "\n",
              "    rbc_volume  delta_offset_minutes              INTIME             OUTTIME  \\\n",
              "0        375.0                 271.0 2189-11-30 10:34:32 2189-12-02 14:17:37   \n",
              "4        375.0                 285.0 2129-04-01 18:43:39 2129-04-03 22:56:02   \n",
              "6        375.0                  11.0 2198-02-10 06:05:00 2198-02-23 14:41:10   \n",
              "13       375.0                   5.0 2120-03-22 22:30:45 2120-04-05 15:33:42   \n",
              "30       375.0                 285.0 2163-04-08 17:36:00 2163-04-24 14:40:00   \n",
              "\n",
              "    rbc_units  \n",
              "0         1.0  \n",
              "4         1.0  \n",
              "6         1.0  \n",
              "13        1.0  \n",
              "30        1.0  "
            ],
            "text/html": [
              "\n",
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              "      <td>2163-04-24 14:40:00</td>\n",
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            ]
          },
          "metadata": {},
          "execution_count": 6
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Sepsis MIMIC 4"
      ],
      "metadata": {
        "id": "7yKLotRb6HbY"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "sepsis_mimic4 = client.query(\"\"\"\n",
        "SELECT *\n",
        "FROM `physionet-data.mimic_derived.sepsis3`\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "nnsccyGgk6Sz"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Keep only septic patients\n",
        "tx_mimic4_septic_1rbc=pd.merge(treatment_mimic4_1rbc,sepsis_mimic4,how='inner',on='stay_id')\n",
        "#Sepsis-3 cohort for treatment group mimic4\n",
        "tx_mimic4_septic_1rbc[treatment_mimic4_1rbc.columns]"
      ],
      "metadata": {
        "id": "qSc9mK7Gm0QH",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 835
        },
        "outputId": "7f476389-c10c-4656-8ef4-4374f79218bb"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "       stay_id  tx_episode   last_hb_in_window  hemoglobin  \\\n",
              "0     30001446           1 2186-04-12 02:00:00         7.9   \n",
              "1     30001555           1 2177-09-27 11:50:00         7.6   \n",
              "2     30003749           2 2120-11-05 16:30:00         6.3   \n",
              "3     30004018           1 2158-12-31 05:14:00         6.6   \n",
              "4     30004811           1 2139-10-06 18:03:00         8.8   \n",
              "...        ...         ...                 ...         ...   \n",
              "8081  39990055           1 2158-05-03 01:54:00         6.9   \n",
              "8082  39992167           1 2114-06-10 21:12:00         6.8   \n",
              "8083  39995213           1 2127-12-14 03:48:00         6.9   \n",
              "8084  39996044           1 2164-12-11 07:58:00         5.7   \n",
              "8085  39999172           1 2185-02-18 03:00:00         7.0   \n",
              "\n",
              "               tx_offset  rbc_volume  delta_offset_minutes  \\\n",
              "0    2186-04-12 04:28:00       375.0                 148.0   \n",
              "1    2177-09-27 16:00:00       350.0                 250.0   \n",
              "2    2120-11-05 17:48:00       375.0                  78.0   \n",
              "3    2158-12-31 10:02:00       375.0                 288.0   \n",
              "4    2139-10-06 19:03:00       375.0                  60.0   \n",
              "...                  ...         ...                   ...   \n",
              "8081 2158-05-03 03:39:00       276.0                 105.0   \n",
              "8082 2114-06-10 21:54:00       350.0                  42.0   \n",
              "8083 2127-12-14 04:56:00       350.0                  68.0   \n",
              "8084 2164-12-11 12:07:00       304.0                 249.0   \n",
              "8085 2185-02-18 05:57:00       375.0                 177.0   \n",
              "\n",
              "                  INTIME             OUTTIME  rbc_units  \n",
              "0    2186-04-12 03:49:00 2186-04-13 19:45:47        1.0  \n",
              "1    2177-09-27 11:23:13 2177-09-28 18:26:00        1.0  \n",
              "2    2120-11-05 16:03:00 2120-11-07 08:19:44        1.0  \n",
              "3    2158-12-27 21:32:00 2159-01-12 23:47:50        1.0  \n",
              "4    2139-10-06 10:40:29 2139-10-08 15:56:05        1.0  \n",
              "...                  ...                 ...        ...  \n",
              "8081 2158-05-01 23:32:15 2158-05-04 18:52:13        1.0  \n",
              "8082 2114-06-10 19:00:00 2114-06-20 20:09:43        1.0  \n",
              "8083 2127-12-11 18:03:43 2127-12-17 21:07:04        1.0  \n",
              "8084 2164-12-10 17:50:47 2164-12-17 18:23:16        1.0  \n",
              "8085 2185-02-17 15:01:00 2185-02-19 17:26:07        1.0  \n",
              "\n",
              "[8086 rows x 10 columns]"
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              "      <td>8.8</td>\n",
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              "      <td>375.0</td>\n",
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              "      <td>2139-10-06 10:40:29</td>\n",
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              "      <td>39990055</td>\n",
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              "      <td>2158-05-03 01:54:00</td>\n",
              "      <td>6.9</td>\n",
              "      <td>2158-05-03 03:39:00</td>\n",
              "      <td>276.0</td>\n",
              "      <td>105.0</td>\n",
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              "      <th>8082</th>\n",
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              "      <td>2114-06-10 21:12:00</td>\n",
              "      <td>6.8</td>\n",
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              "      <td>350.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>2114-06-10 19:00:00</td>\n",
              "      <td>2114-06-20 20:09:43</td>\n",
              "      <td>1.0</td>\n",
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              "    <tr>\n",
              "      <th>8083</th>\n",
              "      <td>39995213</td>\n",
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              "      <td>2127-12-14 03:48:00</td>\n",
              "      <td>6.9</td>\n",
              "      <td>2127-12-14 04:56:00</td>\n",
              "      <td>350.0</td>\n",
              "      <td>68.0</td>\n",
              "      <td>2127-12-11 18:03:43</td>\n",
              "      <td>2127-12-17 21:07:04</td>\n",
              "      <td>1.0</td>\n",
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              "    <tr>\n",
              "      <th>8084</th>\n",
              "      <td>39996044</td>\n",
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              "      <td>2164-12-11 07:58:00</td>\n",
              "      <td>5.7</td>\n",
              "      <td>2164-12-11 12:07:00</td>\n",
              "      <td>304.0</td>\n",
              "      <td>249.0</td>\n",
              "      <td>2164-12-10 17:50:47</td>\n",
              "      <td>2164-12-17 18:23:16</td>\n",
              "      <td>1.0</td>\n",
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              "      <th>8085</th>\n",
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              "      <td>375.0</td>\n",
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              "      <td>2185-02-19 17:26:07</td>\n",
              "      <td>1.0</td>\n",
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              "  </tbody>\n",
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              "<p>8086 rows × 10 columns</p>\n",
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              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
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              "\n",
              "    .colab-df-convert:hover {\n",
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              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-beadc453-861d-4120-bd73-8c70438946ed button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-beadc453-861d-4120-bd73-8c70438946ed');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
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              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 8
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Sepsis MIMIC 3"
      ],
      "metadata": {
        "id": "BfVXhb4_6L1W"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "sepsis_mimiciii= client.query(\"\"\"\n",
        "--- Exclusion refers to exclusion criteria set by the original code. Refer to github for further information\n",
        "-- patients <16 years old\n",
        "-- take into account only first icu addmission\n",
        "\n",
        "WITH sepsis3_cohort AS (with serv as\n",
        "(\n",
        "select hadm_id, curr_service\n",
        "    , ROW_NUMBER() over (partition by hadm_id order by transfertime) as rn\n",
        "    from `physionet-data.mimiciii_clinical.services`\n",
        ")\n",
        ", t1 as\n",
        "(\n",
        "select ie.icustay_id, ie.hadm_id\n",
        "    , ie.intime, ie.outtime\n",
        "    ---, round((cast(adm.admittime as date) - cast(pat.dob as date)) / 365.242, 4) as age\n",
        "    , ROUND(TIMESTAMP_DIFF(adm.admittime,pat.dob, DAY)/ 365.242,4) AS age\n",
        "    , pat.gender\n",
        "    , adm.ethnicity\n",
        "    , ie.dbsource\n",
        "    -- used to get first ICUSTAY_ID\n",
        "    , ROW_NUMBER() over (partition by ie.subject_id order by intime) as rn\n",
        "\n",
        "    -- exclusions\n",
        "    , s.curr_service as first_service\n",
        "    , adm.HAS_CHARTEVENTS_DATA\n",
        "\n",
        "    -- suspicion of infection using POE\n",
        "    , case when spoe.suspected_infection_time is not null then 1 else 0 end\n",
        "        as suspected_of_infection_poe\n",
        "    , spoe.suspected_infection_time as suspected_infection_time_poe\n",
        "    ,TIMESTAMP_DIFF(ie.intime,spoe.suspected_infection_time,SECOND)/ 60.0 / 60.0 / 24.0 as suspected_infection_time_poe_days\n",
        "    , spoe.specimen as specimen_poe\n",
        "    , spoe.positiveculture as positiveculture_poe\n",
        "    , spoe.antibiotic_time as antibiotic_time_poe\n",
        "\n",
        "from `physionet-data.mimiciii_clinical.icustays` ie\n",
        "inner join `physionet-data.mimiciii_clinical.admissions` adm\n",
        "    on ie.hadm_id = adm.hadm_id\n",
        "inner join `physionet-data.mimiciii_clinical.patients` pat\n",
        "    on ie.subject_id = pat.subject_id\n",
        "left join serv s\n",
        "    on ie.hadm_id = s.hadm_id\n",
        "    and s.rn = 1\n",
        "left join `physionet-data.mimiciii_derived.suspinfect_poe` spoe\n",
        "  on ie.icustay_id = spoe.icustay_id\n",
        ")\n",
        "select\n",
        "    t1.hadm_id, t1.icustay_id\n",
        "  , t1.intime, t1.outtime\n",
        "\n",
        "  -- set de-identified ages to median of 91.4\n",
        "  , case when age > 89 then 91.4 else age end as age\n",
        "  , gender\n",
        "  , ethnicity\n",
        "  , first_service\n",
        "  , dbsource\n",
        "\n",
        "  -- suspicion using POE\n",
        "  , suspected_of_infection_poe\n",
        "  , suspected_infection_time_poe\n",
        "  , suspected_infection_time_poe_days\n",
        "  , specimen_poe\n",
        "  , positiveculture_poe\n",
        "  , antibiotic_time_poe\n",
        "\n",
        "  -- exclusions\n",
        "  , case when t1.rn = 1 then 0 else 1 end as exclusion_secondarystay\n",
        "  , case when t1.age <= 16 then 1 else 0 end as exclusion_nonadult\n",
        "  , case when t1.first_service in ('CSURG','VSURG','TSURG') then 1 else 0 end as exclusion_csurg\n",
        "  , case when t1.dbsource != 'metavision' then 1 else 0 end as exclusion_carevue\n",
        "  , case when t1.suspected_infection_time_poe is not null\n",
        "          and t1.suspected_infection_time_poe < (t1.intime-interval '1' day) then 1\n",
        "      else 0 end as exclusion_early_suspicion\n",
        "  , case when t1.suspected_infection_time_poe is not null\n",
        "          and t1.suspected_infection_time_poe > (t1.intime+interval '1' day) then 1\n",
        "      else 0 end as exclusion_late_suspicion\n",
        "  , case when t1.HAS_CHARTEVENTS_DATA = 0 then 1\n",
        "         when t1.intime is null then 1\n",
        "         when t1.outtime is null then 1\n",
        "      else 0 end as exclusion_bad_data\n",
        "  -- , case when t1.suspected_of_infection = 0 then 1 else 0 end as exclusion_suspicion\n",
        "\n",
        "  -- the above flags are used to summarize patients excluded\n",
        "  -- below flag is used to actually exclude patients in future queries\n",
        "  , case when\n",
        "             t1.rn != 1\n",
        "          or t1.age <= 16\n",
        "          or t1.first_service in ('CSURG','VSURG','TSURG')\n",
        "          or t1.HAS_CHARTEVENTS_DATA = 0\n",
        "          or t1.intime is null\n",
        "          or t1.outtime is null\n",
        "          or t1.dbsource != 'metavision'\n",
        "          or (\n",
        "                  t1.suspected_infection_time_poe is not null\n",
        "              and t1.suspected_infection_time_poe < (t1.intime-interval '1' day)\n",
        "            )\n",
        "          or (\n",
        "                  t1.suspected_infection_time_poe is not null\n",
        "              and t1.suspected_infection_time_poe > (t1.intime+interval '1' day)\n",
        "            )\n",
        "          -- or t1.suspected_of_infection = 0\n",
        "            then 1\n",
        "        else 0 end as excluded\n",
        "from t1\n",
        "order by t1.icustay_id)\n",
        "\n",
        "select co.icustay_id, co.hadm_id\n",
        "-- exclusion criteria\n",
        "    , co.excluded\n",
        "    , co.intime, co.outtime\n",
        "    , ie.dbsource\n",
        "-- suspicion POE\n",
        "    , co.suspected_infection_time_poe\n",
        "    , co.suspected_infection_time_poe_days\n",
        "    , co.specimen_poe\n",
        "    , co.positiveculture_poe\n",
        "    , co.antibiotic_time_poe\n",
        "-- blood culture on admission\n",
        "    , bc.charttime as blood_culture_time\n",
        "    , bc.positiveculture as blood_culture_positive\n",
        "    , co.age\n",
        "    , co.gender\n",
        "    , case when co.gender = 'M' then 1 else 0 end as is_male\n",
        "    , co.ethnicity\n",
        "-- ethnicity flags\n",
        "    , case when co.ethnicity in\n",
        "    (\n",
        "'WHITE' --  40996\n",
        "       , 'WHITE - RUSSIAN' --    164\n",
        "       , 'WHITE - OTHER EUROPEAN' --     81\n",
        "       , 'WHITE - BRAZILIAN' --     59\n",
        "       , 'WHITE - EASTERN EUROPEAN' --     25\n",
        "    ) then 1 else 0 end as race_white\n",
        "    , case when co.ethnicity in\n",
        "    (\n",
        "'BLACK/AFRICAN AMERICAN' --   5440\n",
        "        , 'BLACK/CAPE VERDEAN' --    200\n",
        "        , 'BLACK/HAITIAN' --    101\n",
        "        , 'BLACK/AFRICAN' --     44\n",
        "        , 'CARIBBEAN ISLAND' --      9\n",
        "    ) then 1 else 0 end as race_black\n",
        "    , case when co.ethnicity in\n",
        "    (\n",
        "'HISPANIC OR LATINO' --   1696\n",
        "    , 'HISPANIC/LATINO - PUERTO RICAN' --    232\n",
        "    , 'HISPANIC/LATINO - DOMINICAN' --     78\n",
        "    , 'HISPANIC/LATINO - GUATEMALAN' --     40\n",
        "    , 'HISPANIC/LATINO - CUBAN' --     24\n",
        "    , 'HISPANIC/LATINO - SALVADORAN' --     19\n",
        "    , 'HISPANIC/LATINO - CENTRAL AMERICAN (OTHER)' --     13\n",
        "    , 'HISPANIC/LATINO - MEXICAN' --     13\n",
        "    , 'HISPANIC/LATINO - COLOMBIAN' --      9\n",
        "    , 'HISPANIC/LATINO - HONDURAN' --      4\n",
        "  ) then 1 else 0 end as race_hispanic\n",
        "  , case when co.ethnicity not in\n",
        "  (\n",
        "'WHITE' --  40996\n",
        "    , 'WHITE - RUSSIAN' --    164\n",
        "    , 'WHITE - OTHER EUROPEAN' --     81\n",
        "    , 'WHITE - BRAZILIAN' --     59\n",
        "    , 'WHITE - EASTERN EUROPEAN' --     25\n",
        "    , 'BLACK/AFRICAN AMERICAN' --   5440\n",
        "    , 'BLACK/CAPE VERDEAN' --    200\n",
        "    , 'BLACK/HAITIAN' --    101\n",
        "    , 'BLACK/AFRICAN' --     44\n",
        "    , 'CARIBBEAN ISLAND' --      9\n",
        "    , 'HISPANIC OR LATINO' --   1696\n",
        "    , 'HISPANIC/LATINO - PUERTO RICAN' --    232\n",
        "    , 'HISPANIC/LATINO - DOMINICAN' --     78\n",
        "    , 'HISPANIC/LATINO - GUATEMALAN' --     40\n",
        "    , 'HISPANIC/LATINO - CUBAN' --     24\n",
        "    , 'HISPANIC/LATINO - SALVADORAN' --     19\n",
        "    , 'HISPANIC/LATINO - CENTRAL AMERICAN (OTHER)' --     13\n",
        "    , 'HISPANIC/LATINO - MEXICAN' --     13\n",
        "    , 'HISPANIC/LATINO - COLOMBIAN' --      9\n",
        "    , 'HISPANIC/LATINO - HONDURAN' --      4\n",
        "  ) then 1 else 0 end as race_other\n",
        "-- other races\n",
        "-- , 'ASIAN' --   1509\n",
        "-- , 'ASIAN - CHINESE' --    277\n",
        "-- , 'ASIAN - ASIAN INDIAN' --     85\n",
        "-- , 'ASIAN - VIETNAMESE' --     53\n",
        "-- , 'ASIAN - FILIPINO' --     25\n",
        "-- , 'ASIAN - CAMBODIAN' --     17\n",
        "-- , 'ASIAN - OTHER' --     17\n",
        "-- , 'ASIAN - KOREAN' --     13\n",
        "-- , 'ASIAN - JAPANESE' --      7\n",
        "-- , 'ASIAN - THAI' --      4\n",
        "--\n",
        "-- , 'UNKNOWN/NOT SPECIFIED' --   4523\n",
        "-- , 'OTHER' --   1512\n",
        "-- , 'UNABLE TO OBTAIN' --    814\n",
        "-- , 'PATIENT DECLINED TO ANSWER' --    559\n",
        "-- , 'MULTI RACE ETHNICITY' --    130\n",
        "-- , 'PORTUGUESE' --     61\n",
        "-- , 'AMERICAN INDIAN/ALASKA NATIVE' --     51\n",
        "-- , 'MIDDLE EASTERN' --     43\n",
        "-- , 'NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER' --     18\n",
        "-- , 'SOUTH AMERICAN' --      8\n",
        "-- , 'AMERICAN INDIAN/ALASKA NATIVE FEDERALLY RECOGNIZED TRIBE' --      3\n",
        "    , eli.metastatic_cancer\n",
        "    , case when eli.diabetes_uncomplicated = 1\n",
        "or eli.diabetes_complicated = 1\n",
        "                then 1\n",
        "        else 0 end as diabetes\n",
        "    , ht.Height\n",
        "    , wt.Weight\n",
        "    , wt.Weight / (ht.Height/100*ht.Height/100) as bmi\n",
        "-- service type on hospital admission\n",
        "    , co.first_service\n",
        "-- outcomes\n",
        "    , adm.HOSPITAL_EXPIRE_FLAG\n",
        "    , case when pat.dod <=DATETIME_ADD(co.intime, INTERVAL 30 DAY) then 1 else 0 end\n",
        "as THIRTYDAY_EXPIRE_FLAG\n",
        "    , ie.los as icu_los\n",
        "    , TIMESTAMP_DIFF(adm.dischtime, adm.admittime, SECOND)/60.0/60.0/24.0 as hosp_los\n",
        "-- sepsis flags\n",
        "    , a.angus as sepsis_angus\n",
        "    , m.sepsis as sepsis_martin\n",
        "    , es.sepsis as sepsis_explicit\n",
        "    , es.septic_shock as septic_shock_explicit\n",
        "    , es.severe_sepsis as severe_sepsis_explicit\n",
        "    , nqf.sepsis as sepsis_nqf\n",
        "    , cdc.sepsis as sepsis_cdc\n",
        "    , cdc.sepsis_simple as sepsis_cdc_simple\n",
        "-- in-hospital mortality score (van Walraven et al.)\n",
        "    ,   CONGESTIVE_HEART_FAILURE    *(4)    + CARDIAC_ARRHYTHMIAS   *(4) +\n",
        "        VALVULAR_DISEASE            *(-3)   + PULMONARY_CIRCULATION *(0) +\n",
        "        PERIPHERAL_VASCULAR         *(0)    + HYPERTENSION*(-1) + PARALYSIS*(0) +\n",
        "        OTHER_NEUROLOGICAL          *(7)    + CHRONIC_PULMONARY*(0) +\n",
        "        DIABETES_UNCOMPLICATED      *(-1)   + DIABETES_COMPLICATED*(-4) +\n",
        "        HYPOTHYROIDISM              *(0)    + RENAL_FAILURE*(3) + LIVER_DISEASE*(4) +\n",
        "        PEPTIC_ULCER                *(-9)   + AIDS*(0) + LYMPHOMA*(7) +\n",
        "        METASTATIC_CANCER           *(9)    + SOLID_TUMOR*(0) + RHEUMATOID_ARTHRITIS*(0) +\n",
        "        COAGULOPATHY                *(3)    + OBESITY*(-5) +\n",
        "        WEIGHT_LOSS                 *(4)    + FLUID_ELECTROLYTE         *(6) +\n",
        "        BLOOD_LOSS_ANEMIA           *(0)    + DEFICIENCY_ANEMIAS      *(-4) +\n",
        "        ALCOHOL_ABUSE               *(0)    + DRUG_ABUSE*(-6) +\n",
        "        PSYCHOSES                   *(-5)   + DEPRESSION*(-8)\n",
        "as elixhauser_hospital\n",
        "    , case when vent.starttime is not null then 1 else 0 end as vent\n",
        "    , so.sofa as sofa\n",
        "    , lo.lods as lods\n",
        "    , si.sirs as sirs\n",
        "    , qs.qsofa as qsofa\n",
        "-- subcomponents for qSOFA\n",
        "    , qs.SysBP_score as qsofa_sysbp_score\n",
        "    , qs.GCS_score as qsofa_gcs_score\n",
        "    , qs.RespRate_score as qsofa_resprate_score\n",
        "from sepsis3_cohort co\n",
        "inner join `physionet-data.mimiciii_clinical.icustays` ie\n",
        " on co.icustay_id = ie.icustay_id\n",
        "inner join `physionet-data.mimiciii_clinical.admissions` adm\n",
        " on ie.hadm_id = adm.hadm_id\n",
        "inner join `physionet-data.mimiciii_clinical.patients`  pat\n",
        " on ie.subject_id = pat.subject_id\n",
        "left join  `physionet-data.mimiciii_derived.elixhauser_ahrq_v37` eli\n",
        " on ie.hadm_id = eli.hadm_id\n",
        "left join `physionet-data.mimiciii_derived.heightfirstday` ht\n",
        " on ie.icustay_id = ht.icustay_id\n",
        "left join `physionet-data.mimiciii_derived.weight_first_day` wt\n",
        " on ie.icustay_id = wt.icustay_id\n",
        "left join `physionet-data.mimiciii_derived.angus_sepsis` a\n",
        " on ie.hadm_id = a.hadm_id\n",
        "left join `physionet-data.mimiciii_derived.martin_sepsis` m\n",
        " on ie.hadm_id = m.hadm_id\n",
        "left join `physionet-data.mimiciii_derived.explicit_sepsis` es\n",
        " on ie.hadm_id = es.hadm_id\n",
        "left join `physionet-data.mimiciii_derived.sepsis_nqf_0500` nqf\n",
        " on ie.icustay_id = nqf.icustay_id\n",
        "left join `physionet-data.mimiciii_derived.sepsis_cdc_surveillance`cdc\n",
        " on ie.icustay_id = cdc.icustay_id\n",
        "left join `physionet-data.mimiciii_derived.blood_culture_icu_admit` bc\n",
        " on ie.icustay_id = bc.icustay_id\n",
        "\n",
        "left join ( select icustay_id, min(starttime) as starttime\n",
        "   from `physionet-data.mimiciii_derived.ventdurations`\n",
        "   group by icustay_id) vent\n",
        "on co.icustay_id = vent.icustay_id\n",
        "and vent.starttime >= DATETIME_ADD(co.intime, INTERVAL 4 HOUR)\n",
        "and vent.starttime <= DATETIME_SUB(co.intime, INTERVAL 1 DAY)\n",
        "left join `physionet-data.mimiciii_derived.sofa` so\n",
        " on co.icustay_id = so.icustay_id\n",
        "left join `physionet-data.mimiciii_derived.sirs` si\n",
        " on co.icustay_id = si.icustay_id\n",
        "left join  `physionet-data.mimiciii_derived.lods`  lo\n",
        " on co.icustay_id = lo.icustay_id\n",
        "left join `physionet-data.mimiciii_derived.qsofa` qs\n",
        " on co.icustay_id = qs.icustay_id\n",
        " order by co.icustay_id\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "0ABGgzzM6K3C"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Insert a new column about suspicion of infection\n",
        "sepsis_mimiciii['suspicion_poe'] = (~sepsis_mimiciii['suspected_infection_time_poe_days'].isnull())\n",
        "#If poe is true and sofa score is equal or bigger than 2 then we have sepsis\n",
        "sepsis_mimiciii['sepsis-3'] = ((sepsis_mimiciii['suspicion_poe']==1) & (sepsis_mimiciii['sofa']>=2)).astype(int)\n",
        "sepsis_mimiciii= sepsis_mimiciii[sepsis_mimiciii['sepsis-3']==1]\n",
        "sepsis_mimiciii.rename(columns = {'icustay_id':'stay_id'}, inplace = True)\n",
        "tx_mimic3_carevue_septic_1rbc=pd.merge(mimic3_carevue_1rbc,sepsis_mimiciii,how='inner',on='stay_id')\n",
        "#Sepsis-3 cohort for treatment group mimic3\n",
        "tx_mimic3_carevue_septic_1rbc.head()"
      ],
      "metadata": {
        "id": "BQEdyxSqn1QN",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 490
        },
        "outputId": "238b8708-1eac-429b-ff23-80d960be7df2"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "   stay_id  tx_episode   last_hb_in_window  hemoglobin           tx_offset  \\\n",
              "0   200112           1 2140-07-23 08:52:00         7.9 2140-07-23 09:00:00   \n",
              "1   200492           1 2102-06-12 01:55:00         7.3 2102-06-12 06:00:00   \n",
              "2   200535           1 2184-11-10 05:40:00         7.4 2184-11-10 11:15:00   \n",
              "3   200660           1 2193-07-09 04:00:00         9.5 2193-07-09 04:30:00   \n",
              "4   200793           1 2139-02-11 13:33:00         8.8 2139-02-11 16:00:00   \n",
              "\n",
              "   rbc_volume  delta_offset_minutes              INTIME             OUTTIME  \\\n",
              "0       375.0                   8.0 2140-07-23 05:40:40 2140-07-24 13:48:03   \n",
              "1       400.0                 245.0 2102-06-12 03:51:36 2102-06-14 14:40:25   \n",
              "2       375.0                 335.0 2184-11-10 07:40:35 2184-11-11 18:39:45   \n",
              "3       375.0                  30.0 2193-07-02 02:19:53 2193-07-10 00:43:35   \n",
              "4       300.0                 147.0 2139-02-10 20:03:07 2139-02-13 21:39:22   \n",
              "\n",
              "   rbc_units  ...  vent  sofa lods sirs qsofa qsofa_sysbp_score  \\\n",
              "0        1.0  ...     0     3    4    3     1               0.0   \n",
              "1        1.0  ...     0     4    7    4     3               1.0   \n",
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              "3        1.0  ...     0     6    6    4     2               1.0   \n",
              "4        1.0  ...     0    10    8    4     2               1.0   \n",
              "\n",
              "   qsofa_gcs_score qsofa_resprate_score  suspicion_poe sepsis-3  \n",
              "0              0.0                  1.0           True        1  \n",
              "1              1.0                  1.0           True        1  \n",
              "2              1.0                  0.0           True        1  \n",
              "3              0.0                  1.0           True        1  \n",
              "4              0.0                  1.0           True        1  \n",
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            ]
          },
          "metadata": {},
          "execution_count": 10
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Joining MIMIC 4 (METAVISION) with Mimic 3 (carevue) - FULL COHORT TREATMENT"
      ],
      "metadata": {
        "id": "RMeSX3nQ4-98"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "treatment_group = pd.concat([mimic3_carevue_1rbc,treatment_mimic4_1rbc])\n",
        "#All patient that received 1 blood sac (1st icustay)\n",
        "treatment_group.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 444
        },
        "id": "B8JDRfVP4687",
        "outputId": "767df6c5-f8db-4651-b2ee-16713a8c348d"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    stay_id  tx_episode   last_hb_in_window  hemoglobin           tx_offset  \\\n",
              "0    200009           1 2189-11-30 18:29:00        10.5 2189-11-30 23:00:00   \n",
              "4    200041           1 2129-04-01 19:15:00        10.1 2129-04-02 00:00:00   \n",
              "6    200059           2 2198-02-11 01:34:00         9.9 2198-02-11 01:45:00   \n",
              "13   200065           1 2120-03-23 12:25:00         7.5 2120-03-23 12:30:00   \n",
              "30   200077           1 2163-04-17 21:30:00         8.5 2163-04-18 02:15:00   \n",
              "\n",
              "    rbc_volume  delta_offset_minutes              INTIME             OUTTIME  \\\n",
              "0        375.0                 271.0 2189-11-30 10:34:32 2189-12-02 14:17:37   \n",
              "4        375.0                 285.0 2129-04-01 18:43:39 2129-04-03 22:56:02   \n",
              "6        375.0                  11.0 2198-02-10 06:05:00 2198-02-23 14:41:10   \n",
              "13       375.0                   5.0 2120-03-22 22:30:45 2120-04-05 15:33:42   \n",
              "30       375.0                 285.0 2163-04-08 17:36:00 2163-04-24 14:40:00   \n",
              "\n",
              "    rbc_units  \n",
              "0         1.0  \n",
              "4         1.0  \n",
              "6         1.0  \n",
              "13        1.0  \n",
              "30        1.0  "
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              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-601db865-2f69-48b3-b6c7-acb7ee266a70 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-601db865-2f69-48b3-b6c7-acb7ee266a70');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 11
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# SEPTIC - Joining MIMIC 4 (METAVISION) with Mimic 3 (carevue) for septic patients - FULL SEPTIC COHORT TREATMENT"
      ],
      "metadata": {
        "id": "BVn2AWzMov0I"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "treatment_group_septic = pd.concat([tx_mimic4_septic_1rbc,tx_mimic3_carevue_septic_1rbc])\n",
        "#All septic patients that received 1 blood sac (1st icustay)\n",
        "treatment_group_septic.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 490
        },
        "id": "9OXZKucEo7RR",
        "outputId": "23613de3-47b2-4106-d594-64ab03165d25"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    stay_id  tx_episode   last_hb_in_window  hemoglobin           tx_offset  \\\n",
              "0  30001446           1 2186-04-12 02:00:00         7.9 2186-04-12 04:28:00   \n",
              "1  30001555           1 2177-09-27 11:50:00         7.6 2177-09-27 16:00:00   \n",
              "2  30003749           2 2120-11-05 16:30:00         6.3 2120-11-05 17:48:00   \n",
              "3  30004018           1 2158-12-31 05:14:00         6.6 2158-12-31 10:02:00   \n",
              "4  30004811           1 2139-10-06 18:03:00         8.8 2139-10-06 19:03:00   \n",
              "\n",
              "   rbc_volume  delta_offset_minutes              INTIME             OUTTIME  \\\n",
              "0       375.0                 148.0 2186-04-12 03:49:00 2186-04-13 19:45:47   \n",
              "1       350.0                 250.0 2177-09-27 11:23:13 2177-09-28 18:26:00   \n",
              "2       375.0                  78.0 2120-11-05 16:03:00 2120-11-07 08:19:44   \n",
              "3       375.0                 288.0 2158-12-27 21:32:00 2159-01-12 23:47:50   \n",
              "4       375.0                  60.0 2139-10-06 10:40:29 2139-10-08 15:56:05   \n",
              "\n",
              "   rbc_units  ...  vent sofa lods sirs qsofa  qsofa_sysbp_score  \\\n",
              "0        1.0  ...   NaN  NaN  NaN  NaN   NaN                NaN   \n",
              "1        1.0  ...   NaN  NaN  NaN  NaN   NaN                NaN   \n",
              "2        1.0  ...   NaN  NaN  NaN  NaN   NaN                NaN   \n",
              "3        1.0  ...   NaN  NaN  NaN  NaN   NaN                NaN   \n",
              "4        1.0  ...   NaN  NaN  NaN  NaN   NaN                NaN   \n",
              "\n",
              "   qsofa_gcs_score  qsofa_resprate_score  suspicion_poe  sepsis-3  \n",
              "0              NaN                   NaN            NaN       NaN  \n",
              "1              NaN                   NaN            NaN       NaN  \n",
              "2              NaN                   NaN            NaN       NaN  \n",
              "3              NaN                   NaN            NaN       NaN  \n",
              "4              NaN                   NaN            NaN       NaN  \n",
              "\n",
              "[5 rows x 72 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-7c95aeb4-dede-44c7-a0b9-bc63b6acca7f\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
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              "    .dataframe tbody tr th {\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>stay_id</th>\n",
              "      <th>tx_episode</th>\n",
              "      <th>last_hb_in_window</th>\n",
              "      <th>hemoglobin</th>\n",
              "      <th>tx_offset</th>\n",
              "      <th>rbc_volume</th>\n",
              "      <th>delta_offset_minutes</th>\n",
              "      <th>INTIME</th>\n",
              "      <th>OUTTIME</th>\n",
              "      <th>rbc_units</th>\n",
              "      <th>...</th>\n",
              "      <th>vent</th>\n",
              "      <th>sofa</th>\n",
              "      <th>lods</th>\n",
              "      <th>sirs</th>\n",
              "      <th>qsofa</th>\n",
              "      <th>qsofa_sysbp_score</th>\n",
              "      <th>qsofa_gcs_score</th>\n",
              "      <th>qsofa_resprate_score</th>\n",
              "      <th>suspicion_poe</th>\n",
              "      <th>sepsis-3</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>30001446</td>\n",
              "      <td>1</td>\n",
              "      <td>2186-04-12 02:00:00</td>\n",
              "      <td>7.9</td>\n",
              "      <td>2186-04-12 04:28:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>148.0</td>\n",
              "      <td>2186-04-12 03:49:00</td>\n",
              "      <td>2186-04-13 19:45:47</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>30001555</td>\n",
              "      <td>1</td>\n",
              "      <td>2177-09-27 11:50:00</td>\n",
              "      <td>7.6</td>\n",
              "      <td>2177-09-27 16:00:00</td>\n",
              "      <td>350.0</td>\n",
              "      <td>250.0</td>\n",
              "      <td>2177-09-27 11:23:13</td>\n",
              "      <td>2177-09-28 18:26:00</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>30003749</td>\n",
              "      <td>2</td>\n",
              "      <td>2120-11-05 16:30:00</td>\n",
              "      <td>6.3</td>\n",
              "      <td>2120-11-05 17:48:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>78.0</td>\n",
              "      <td>2120-11-05 16:03:00</td>\n",
              "      <td>2120-11-07 08:19:44</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>30004018</td>\n",
              "      <td>1</td>\n",
              "      <td>2158-12-31 05:14:00</td>\n",
              "      <td>6.6</td>\n",
              "      <td>2158-12-31 10:02:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>288.0</td>\n",
              "      <td>2158-12-27 21:32:00</td>\n",
              "      <td>2159-01-12 23:47:50</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>30004811</td>\n",
              "      <td>1</td>\n",
              "      <td>2139-10-06 18:03:00</td>\n",
              "      <td>8.8</td>\n",
              "      <td>2139-10-06 19:03:00</td>\n",
              "      <td>375.0</td>\n",
              "      <td>60.0</td>\n",
              "      <td>2139-10-06 10:40:29</td>\n",
              "      <td>2139-10-08 15:56:05</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5 rows × 72 columns</p>\n",
              "</div>\n",
              "      <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-7c95aeb4-dede-44c7-a0b9-bc63b6acca7f')\"\n",
              "              title=\"Convert this dataframe to an interactive table.\"\n",
              "              style=\"display:none;\">\n",
              "        \n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
              "    <path d=\"M0 0h24v24H0V0z\" fill=\"none\"/>\n",
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              "  </svg>\n",
              "      </button>\n",
              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-7c95aeb4-dede-44c7-a0b9-bc63b6acca7f button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-7c95aeb4-dede-44c7-a0b9-bc63b6acca7f');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 12
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# MIMIC 4 Control"
      ],
      "metadata": {
        "id": "aJpNUGMz5w7Q"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "control_mimic4 = client.query(\"\"\"\n",
        "WITH all_criteria AS (SELECT DISTINCT(stay_id)\n",
        "FROM `physionet-data.mimic_derived.sofa`\n",
        "WHERE stay_id IN(SELECT DISTINCT(stay_id)\n",
        "                    FROM `physionet-data.mimic_derived.icustay_detail`\n",
        "                    WHERE icustay_seq = 1\n",
        "                    AND first_icu_stay= TRUE\n",
        "                    AND (admission_age BETWEEN 18 AND 89)\n",
        "  AND stay_id NOT IN(SELECT DISTINCT(i.stay_id)\n",
        "        FROM `physionet-data.mimic_hosp.diagnoses_icd` d\n",
        "        INNER JOIN `physionet-data.mimic_icu.icustays` i\n",
        "            ON d.hadm_id=i.hadm_id\n",
        "        INNER JOIN `physionet-data.mimic_derived.icustay_detail` a\n",
        "            ON d.HADM_ID=a.hadm_id\n",
        "        WHERE icd_code IN (\n",
        "                --ref: https://www.bmj.com/content/bmj/suppl/2015/02/03/bmj.h246.DC1/junm020747.ww1_default.pdf\n",
        "                --intracranial bleeding\n",
        "                '430', --Subarachnoid\n",
        "                '431', --intracerebral\n",
        "                '4320', --other and unspecified intracranial bleeding\n",
        "                '4321', --subdural\n",
        "                '4329', --unspecified intracranial bleeding\n",
        "                --upper gastrointestinal\n",
        "                '5310', --acute gastric ulcer with bleeding without obstruction\n",
        "                '5312', --acute gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5314', --chronic or unspecified gastric ulcer with bleeding without obstruction\n",
        "                '5316', --chronic or unspecified gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5320', --acute duodenal ulcer with bleeding without obstruction\n",
        "                '5322', --acute duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5324', --chronic or unspecified duodenal ulcer with bleeding without obstruction\n",
        "                '5326', --chronic or unspecified duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5330', --acute peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5332', --acute peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5334', --chronic or unspecified peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5336', --chronic or unspecified peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5340', --acute gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5342', --acute gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5344', --chronic or unspecified gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5346', --chronic or unspecified gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5780', --hematemesis\n",
        "                '5781', --blood in stool\n",
        "                '5789', --bleeding of gastrointestinal tract unspecified\n",
        "                --Lower GI\n",
        "                '5693', --bleeding of rectum and anus\n",
        "                --Other Bleeding\n",
        "                '2878', --other unspecified hemorrhagic conditions\n",
        "                '2879', --unspecified hemorrhagic conditions\n",
        "                '5967', --bleeding into bladder wall\n",
        "                '7848', --bleeding from throat\n",
        "                '5997', --hematuria, unspecified\n",
        "                '6271', --postmenopausal bleeding\n",
        "                '4590', --bleeding unspecified\n",
        "                '7191', --hemarthrosis site unspecified\n",
        "                '7863', --hemoptysis, unspecified\n",
        "                '72992', --nontraumatic hematoma soft tissue\n",
        "                '9582' --secondary or recurrent following trauma\n",
        "            )\n",
        "        OR icd_code LIKE '900%' --vessel injuries\n",
        "        OR icd_code LIKE '901%' --vessel injuries\n",
        "        OR icd_code LIKE '902%' --vessel injuries\n",
        "        OR icd_code LIKE '903%' --vessel injuries\n",
        "        OR icd_code LIKE '904%' --vessel injuries\n",
        "\n",
        "        OR UPPER(LAST_CAREUNIT) LIKE '%TSICU%'\n",
        "        OR UPPER(FIRST_CAREUNIT) LIKE '%TSICU%' )) )\n",
        ", demographics AS (\n",
        "    SELECT\n",
        "        ie.subject_id,\n",
        "        ie.hadm_id,\n",
        "        ie.stay_id -- patient level factors\n",
        ",\n",
        "        pat.gender,\n",
        "        pat.dod -- hospital level factors\n",
        ",\n",
        "        adm.admittime,\n",
        "        adm.dischtime,\n",
        "        pat.anchor_age AS age,\n",
        "        adm.admission_type,\n",
        "        adm.hospital_expire_flag,\n",
        "        adm.deathtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY adm.subject_id\n",
        "            ORDER BY\n",
        "                adm.admittime\n",
        "        ) AS hospstay_seq,\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY adm.subject_id\n",
        "                ORDER BY\n",
        "                    adm.admittime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_hosp_stay -- icu level factors\n",
        ",\n",
        "        ie.intime,\n",
        "        ie.outtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY ie.hadm_id\n",
        "            ORDER BY\n",
        "                ie.intime\n",
        "        ) AS icustay_seq -- first ICU stay *for the current hospitalization*\n",
        ",\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY ie.hadm_id\n",
        "                ORDER BY\n",
        "                    ie.intime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_icu_stay\n",
        "    FROM\n",
        "        `physionet-data.mimic_icu.icustays` ie\n",
        "        INNER JOIN `physionet-data.mimic_core.admissions` adm ON ie.hadm_id = adm.hadm_id\n",
        "        INNER JOIN `physionet-data.mimic_core.patients` pat ON ie.subject_id = pat.subject_id\n",
        "    ORDER BY\n",
        "        ie.subject_id,\n",
        "        adm.admittime,\n",
        "        ie.intime\n",
        ")\n",
        ",\n",
        "first_adm_offset AS (\n",
        "    SELECT\n",
        "        stay_id AS id,\n",
        "        intime,\n",
        "        outtime\n",
        "    FROM\n",
        "        demographics\n",
        "    WHERE\n",
        "        first_icu_stay = TRUE),\n",
        "pivoted_sofa AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        `physionet-data.mimic_derived.sofa` ps\n",
        "        LEFT JOIN first_adm_offset f ON ps.stay_id = f.id\n",
        "        AND ps.endtime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "),\n",
        "pivoted_lab AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        (\n",
        "            WITH pivoted_lab AS (\n",
        "                -- create a table which has fuzzy boundaries on ICU admission (+- 12 hours from documented time)\n",
        "                -- this is used to assign icustay_id to lab data, which can be collected outside ICU\n",
        "                -- involves first creating a lag/lead version of intime/outtime\n",
        "                WITH i AS (\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        stay_id,\n",
        "                        intime,\n",
        "                        outtime,\n",
        "                        lag (outtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS outtime_lag,\n",
        "                        lead (intime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS intime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimic_icu.icustays`\n",
        "                ),\n",
        "                iid_assign AS (\n",
        "                    SELECT\n",
        "                        i.subject_id,\n",
        "                        i.stay_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN i.outtime_lag IS NOT NULL\n",
        "                            AND i.outtime_lag > DATETIME_SUB(i.intime, INTERVAL 24 HOUR) THEN DATETIME_SUB(\n",
        "                                i.intime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime, i.outtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(i.intime, INTERVAL 12 HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN i.intime_lead IS NOT NULL\n",
        "                            AND i.intime_lead < DATETIME_ADD(i.outtime, INTERVAL 24 HOUR) THEN DATETIME_ADD(\n",
        "                                i.outtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime_lead, i.outtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(i.outtime, INTERVAL 12 HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        i\n",
        "                ) -- also create fuzzy boundaries on hospitalization\n",
        ",\n",
        "                h AS (\n",
        "                    SELECT\n",
        "                        subject_id,hadm_id,admittime,dischtime,\n",
        "                        lag (dischtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS dischtime_lag,\n",
        "                        lead (admittime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS admittime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimic_core.admissions`\n",
        "                ),\n",
        "                adm AS (\n",
        "                    SELECT\n",
        "                        h.subject_id,\n",
        "                        h.hadm_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN h.dischtime_lag IS NOT NULL\n",
        "                            AND h.dischtime_lag > DATETIME_SUB(h.admittime, INTERVAL '24' HOUR) THEN DATETIME_SUB(\n",
        "                                h.admittime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime, h.dischtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(h.admittime, INTERVAL '12' HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN h.admittime_lead IS NOT NULL\n",
        "                            AND h.admittime_lead < DATETIME_ADD(h.dischtime, INTERVAL '24' HOUR) THEN DATETIME_ADD(\n",
        "                                h.dischtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime_lead, h.dischtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(h.dischtime, INTERVAL '12' HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        h\n",
        "                ),\n",
        "                le AS (\n",
        "                    -- begin query that extracts the data\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        charttime -- here we assign labels to ITEMIDs\n",
        "                        -- this also fuses together multiple ITEMIDs containing the same data\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN itemid = 50868 THEN 'ANION GAP'\n",
        "                            WHEN itemid = 50862 THEN 'ALBUMIN'\n",
        "                            WHEN itemid = 51144 THEN 'BANDS'\n",
        "                            WHEN itemid = 50882 THEN 'BICARBONATE'\n",
        "                            WHEN itemid = 50885 THEN 'BILIRUBIN'\n",
        "                            WHEN itemid = 50912 THEN 'CREATININE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50806 THEN 'CHLORIDE'\n",
        "                            WHEN itemid = 50902 THEN 'CHLORIDE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50809 THEN 'GLUCOSE'\n",
        "                            WHEN itemid = 50931 THEN 'GLUCOSE' -- exclude blood gas\n",
        "                            --WHEN itemid = 50810 THEN 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221 THEN 'HEMATOCRIT' -- exclude blood gas\n",
        "                            --WHEN itemid = 50811 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813 THEN 'LACTATE'\n",
        "                            WHEN itemid = 51265 THEN 'PLATELET' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50822 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 50971 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 51275 THEN 'PTT'\n",
        "                            WHEN itemid = 51237 THEN 'INR'\n",
        "                            WHEN itemid = 51274 THEN 'PT' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50824 THEN 'SODIUM'\n",
        "                            WHEN itemid = 50983 THEN 'SODIUM'\n",
        "                            WHEN itemid = 51006 THEN 'BUN'\n",
        "                            WHEN itemid = 51300 THEN 'WBC'\n",
        "                            WHEN itemid = 51301 THEN 'WBC'\n",
        "                            ELSE NULL\n",
        "                        END AS label,\n",
        "                        -- add in some sanity checks on the values\n",
        "                        -- the where clause below requires all valuenum to be > 0, so these are only upper limit checks\n",
        "                        CASE\n",
        "                            WHEN itemid = 50862\n",
        "                            AND valuenum > 10 THEN NULL -- g/dL 'ALBUMIN'\n",
        "                            WHEN itemid = 50868\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'ANION GAP'\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum < 0 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum > 100 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 50882\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'BICARBONATE'\n",
        "                            WHEN itemid = 50885\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'BILIRUBIN'\n",
        "                            WHEN itemid = 50806\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50902\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50912\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'CREATININE'\n",
        "                            WHEN itemid = 50809\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50931\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50810\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 50811\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813\n",
        "                            AND valuenum > 50 THEN NULL -- mmol/L 'LACTATE'\n",
        "                            WHEN itemid = 51265\n",
        "                            AND valuenum > 10000 THEN NULL -- K/uL 'PLATELET'\n",
        "                            WHEN itemid = 50822\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 50971\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 51275\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PTT'\n",
        "                            WHEN itemid = 51237\n",
        "                            AND valuenum > 50 THEN NULL -- 'INR'\n",
        "                            WHEN itemid = 51274\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PT'\n",
        "                            WHEN itemid = 50824\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 50983\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 51006\n",
        "                            AND valuenum > 300 THEN NULL -- 'BUN'\n",
        "                            WHEN itemid = 51300\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            WHEN itemid = 51301\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            ELSE valuenum\n",
        "                        END AS valuenum\n",
        "                    FROM\n",
        "                        `physionet-data.mimic_hosp.labevents`\n",
        "                    WHERE\n",
        "                        ITEMID IN (\n",
        "                            -- comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS\n",
        "                            50868, -- ANION GAP | CHEMISTRY | BLOOD | 769895\n",
        "                            50862, -- ALBUMIN | CHEMISTRY | BLOOD | 146697\n",
        "                            51144, -- BANDS - hematology\n",
        "                            50882, -- BICARBONATE | CHEMISTRY | BLOOD | 780733\n",
        "                            50885, -- BILIRUBIN, TOTAL | CHEMISTRY | BLOOD | 238277\n",
        "                            50912, -- CREATININE | CHEMISTRY | BLOOD | 797476\n",
        "                            50902, -- CHLORIDE | CHEMISTRY | BLOOD | 795568\n",
        "                            -- 50806, -- CHLORIDE, WHOLE BLOOD | BLOOD GAS | BLOOD | 48187\n",
        "                            50931, -- GLUCOSE | CHEMISTRY | BLOOD | 748981\n",
        "                            -- 50809, -- GLUCOSE | BLOOD GAS | BLOOD | 196734\n",
        "                            51221, -- HEMATOCRIT | HEMATOLOGY | BLOOD | 881846\n",
        "                            -- 50810, -- HEMATOCRIT, CALCULATED | BLOOD GAS | BLOOD | 89715\n",
        "                            51222, -- HEMOGLOBIN | HEMATOLOGY | BLOOD | 752523\n",
        "                            -- 50811, -- HEMOGLOBIN | BLOOD GAS | BLOOD | 89712\n",
        "                            50813, -- LACTATE | BLOOD GAS | BLOOD | 187124\n",
        "                            51265, -- PLATELET COUNT | HEMATOLOGY | BLOOD | 778444\n",
        "                            50971, -- POTASSIUM | CHEMISTRY | BLOOD | 845825\n",
        "                            -- 50822, -- POTASSIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 192946\n",
        "                            51275, -- PTT | HEMATOLOGY | BLOOD | 474937\n",
        "                            51237, -- INR(PT) | HEMATOLOGY | BLOOD | 471183\n",
        "                            51274, -- PT | HEMATOLOGY | BLOOD | 469090\n",
        "                            50983, -- SODIUM | CHEMISTRY | BLOOD | 808489\n",
        "                            -- 50824, -- SODIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 71503\n",
        "                            51006, -- UREA NITROGEN | CHEMISTRY | BLOOD | 791925\n",
        "                            51301, -- WHITE BLOOD CELLS | HEMATOLOGY | BLOOD | 753301\n",
        "                            51300  -- WBC COUNT | HEMATOLOGY | BLOOD | 2371\n",
        "                        )\n",
        "                        AND valuenum IS NOT NULL\n",
        "                        AND valuenum > 0 -- lab values cannot be 0 and cannot be negative\n",
        "                ),\n",
        "                le_avg AS (\n",
        "                    SELECT\n",
        "                        le.subject_id,\n",
        "                        le.charttime,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ANION GAP' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ANIONGAP,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ALBUMIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ALBUMIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BANDS' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BANDS,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BICARBONATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BICARBONATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BILIRUBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BILIRUBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CREATININE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CREATININE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CHLORIDE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CHLORIDE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'GLUCOSE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS GLUCOSE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMATOCRIT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMATOCRIT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMOGLOBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMOGLOBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'LACTATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS LACTATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PLATELET' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PLATELET,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'POTASSIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS POTASSIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PTT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PTT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'INR' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS INR,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'SODIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS SODIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BUN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BUN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'WBC' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS WBC\n",
        "                    FROM\n",
        "                        le\n",
        "                    GROUP BY\n",
        "                        le.subject_id,\n",
        "                        le.charttime\n",
        "                )\n",
        "                SELECT\n",
        "                    iid.stay_id,\n",
        "                    adm.hadm_id,\n",
        "                    le_avg.*\n",
        "                FROM\n",
        "                    le_avg\n",
        "                    LEFT JOIN adm ON le_avg.subject_id = adm.subject_id\n",
        "                    AND le_avg.charttime >= adm.data_start\n",
        "                    AND le_avg.charttime < adm.data_end\n",
        "                    LEFT JOIN iid_assign iid ON le_avg.subject_id = iid.subject_id\n",
        "                    AND le_avg.charttime >= iid.data_start\n",
        "                    AND le_avg.charttime < iid.data_end\n",
        "                ORDER BY\n",
        "                    le_avg.subject_id,\n",
        "                    le_avg.charttime\n",
        "            )\n",
        "            SELECT\n",
        "                *\n",
        "            FROM\n",
        "                pivoted_lab\n",
        "        ) AS pl\n",
        "        LEFT JOIN first_adm_offset f ON pl.stay_id = f.id\n",
        "        AND pl.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        ")\n",
        ",\n",
        "mechvent AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        charttime -- case statement determining whether it is an instance of mech vent\n",
        ",\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN itemid IS NULL\n",
        "                OR value IS NULL THEN 0 -- can't have null values\n",
        "                WHEN itemid = 720\n",
        "                AND value != 'Other/Remarks' THEN 1 -- VentTypeRecorded\n",
        "                WHEN itemid = 223848\n",
        "                AND value != 'Other' THEN 1\n",
        "                WHEN itemid = 223849 THEN 1 -- ventilator mode\n",
        "                WHEN itemid = 467\n",
        "                AND value = 'Ventilator' THEN 1 -- O2 delivery device == ventilator\n",
        "                WHEN itemid IN(\n",
        "                    445,\n",
        "                    448,\n",
        "                    449,\n",
        "                    450,\n",
        "                    1340,\n",
        "                    1486,\n",
        "                    1600,\n",
        "                    224687 -- minute volume\n",
        ",\n",
        "                    639,\n",
        "                    654,\n",
        "                    681,\n",
        "                    682,\n",
        "                    683,\n",
        "                    684,\n",
        "                    224685,\n",
        "                    224684,\n",
        "                    224686 -- tidal volume\n",
        ",\n",
        "                    218,\n",
        "                    436,\n",
        "                    535,\n",
        "                    444,\n",
        "                    459,\n",
        "                    224697,\n",
        "                    224695,\n",
        "                    224696,\n",
        "                    224746,\n",
        "                    224747 -- High/Low/Peak/Mean/Neg insp force (\"RespPressure\")\n",
        ",\n",
        "                    221,\n",
        "                    1,\n",
        "                    1211,\n",
        "                    1655,\n",
        "                    2000,\n",
        "                    226873,\n",
        "                    224738,\n",
        "                    224419,\n",
        "                    224750,\n",
        "                    227187 -- Insp pressure\n",
        ",\n",
        "                    543 -- PlateauPressure\n",
        ",\n",
        "                    5865,\n",
        "                    5866,\n",
        "                    224707,\n",
        "                    224709,\n",
        "                    224705,\n",
        "                    224706 -- APRV pressure\n",
        ",\n",
        "                    60,\n",
        "                    437,\n",
        "                    505,\n",
        "                    506,\n",
        "                    686,\n",
        "                    220339,\n",
        "                    224700 -- PEEP\n",
        ",\n",
        "                    3459 -- high pressure relief\n",
        ",\n",
        "                    501,\n",
        "                    502,\n",
        "                    503,\n",
        "                    224702 -- PCV\n",
        ",\n",
        "                    223,\n",
        "                    667,\n",
        "                    668,\n",
        "                    669,\n",
        "                    670,\n",
        "                    671,\n",
        "                    672 -- TCPCV\n",
        ",\n",
        "                    224701 -- PSVlevel\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS ventmarker\n",
        "    FROM\n",
        "        `physionet-data.mimic_icu.chartevents` ce\n",
        "        LEFT JOIN first_adm_offset f ON ce.stay_id = f.id\n",
        "        AND ce.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "    WHERE\n",
        "        ce.value IS NOT NULL -- exclude rows marked as error\n",
        "        --AND ce.error != 1 -- the below are settings used to indicate ventilation\n",
        "        AND itemid IN(\n",
        "            720,\n",
        "            223849 -- vent mode\n",
        ",\n",
        "            223848 -- vent type\n",
        ",\n",
        "            445,\n",
        "            448,\n",
        "            449,\n",
        "            450,\n",
        "            1340,\n",
        "            1486,\n",
        "            1600,\n",
        "            224687 -- minute volume\n",
        ",\n",
        "            639,\n",
        "            654,\n",
        "            681,\n",
        "            682,\n",
        "            683,\n",
        "            684,\n",
        "            224685,\n",
        "            224684,\n",
        "            224686 -- tidal volume\n",
        ",\n",
        "            218,\n",
        "            436,\n",
        "            535,\n",
        "            444,\n",
        "            224697,\n",
        "            224695,\n",
        "            224696,\n",
        "            224746,\n",
        "            224747 -- High/Low/Peak/Mean (\"RespPressure\")\n",
        ",\n",
        "            221,\n",
        "            1,\n",
        "            1211,\n",
        "            1655,\n",
        "            2000,\n",
        "            226873,\n",
        "            224738,\n",
        "            224419,\n",
        "            224750,\n",
        "            227187 -- Insp pressure\n",
        ",\n",
        "            543 -- PlateauPressure\n",
        ",\n",
        "            5865,\n",
        "            5866,\n",
        "            224707,\n",
        "            224709,\n",
        "            224705,\n",
        "            224706 -- APRV pressure\n",
        ",\n",
        "            60,\n",
        "            437,\n",
        "            505,\n",
        "            506,\n",
        "            686,\n",
        "            220339,\n",
        "            224700 -- PEEP\n",
        ",\n",
        "            3459 -- high pressure relief\n",
        ",\n",
        "            501,\n",
        "            502,\n",
        "            503,\n",
        "            224702 -- PCV\n",
        ",\n",
        "            223,\n",
        "            667,\n",
        "            668,\n",
        "            669,\n",
        "            670,\n",
        "            671,\n",
        "            672 -- TCPCV\n",
        ",\n",
        "            224701 -- PSVlevel\n",
        "            -- the below are settings used to indicate extubation\n",
        ",\n",
        "            640 -- extubated\n",
        "            -- the below indicate oxygen/NIV, i.e. the end of a mechanical vent event\n",
        ",\n",
        "            468 -- O2 Delivery Device#2\n",
        ",\n",
        "            469 -- O2 Delivery Mode\n",
        ",\n",
        "            470 -- O2 Flow (lpm)\n",
        ",\n",
        "            471 -- O2 Flow (lpm) #2\n",
        ",\n",
        "            227287 -- O2 Flow (additional cannula)\n",
        ",\n",
        "            226732 -- O2 Delivery Device(s)\n",
        ",\n",
        "            223834 -- O2 Flow\n",
        "            -- used in both oxygen + vent calculation\n",
        ",\n",
        "            467 -- O2 Delivery Device\n",
        "        )\n",
        "    GROUP BY\n",
        "        stay_id,\n",
        "        charttime\n",
        ")\n",
        ",\n",
        "sepsis AS (\n",
        "    -- ICD-9 codes for Angus criteria of sepsis\n",
        "    SELECT\n",
        "        hadm_id,\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd_code, 1, 3) IN (\n",
        "                    '001','002','003','004','005',\n",
        "                    '008','009','010','011','012',\n",
        "                    '013','014','015','016','017',\n",
        "                    '018','020','021','022','023',\n",
        "                    '024','025','026','027','030',\n",
        "                    '031','032','033','034','035',\n",
        "                    '036','037','038','039','040',\n",
        "                    '041','090','091','092','093',\n",
        "                    '094','095','096','097','098',\n",
        "                    '100','101','102','103','104',\n",
        "                    '110','111','112','114','115',\n",
        "                    '116','117','118','320','322',\n",
        "                    '324','325','420','421','451',\n",
        "                    '461','462','463','464','465',\n",
        "                    '481','482','485','486','494',\n",
        "                    '510','513','540','541','542',\n",
        "                    '566','567','590','597','601',\n",
        "                    '614','615','616','681','682',\n",
        "                    '683','686','730'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd_code, 1, 4) IN (\n",
        "                    '5695','5720','5721','5750',\n",
        "                    '5990','7110','7907','9966',\n",
        "                    '9985','9993'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd_code, 1, 5) IN (\n",
        "                    '49121','56201','56203',\n",
        "                    '56211','56213','56983'\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS sepsisflag\n",
        "    FROM\n",
        "        `physionet-data.mimic_hosp.diagnoses_icd`\n",
        "    GROUP BY\n",
        "        hadm_id\n",
        "),\n",
        "--,\n",
        "--vasopressor_duration AS (\n",
        "    --SELECT\n",
        "        --*\n",
        "    --FROM\n",
        "        --`physionet-data.mimiciii_derived.vasopressordurations`\n",
        "--),\n",
        "premorbid AS (\n",
        "    WITH icd AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            CAST(icd_code AS STRING) AS icd_code\n",
        "        FROM\n",
        "            `physionet-data.mimic_hosp.diagnoses_icd`\n",
        "    ),\n",
        "    eliflg AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            icd_code -- note that these codes will seem incomplete at first\n",
        "            -- for example, CHF is missing a lot of codes referenced in the literature (402.11, 402.91, etc)\n",
        "            -- these codes are captured by hypertension flags instead\n",
        "            -- later there are some complicated rules which confirm/reject those codes as CHF\n",
        ",\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd_code, 1, 3) IN(\n",
        "                    '410', --Acute myocardial infarction\n",
        "                    '411', --Other acute and subacute forms of ischemic heart disease\n",
        "                    '412', --Old myocardial infarction\n",
        "                    '413', --Angina pectoris\n",
        "                    '414'  --Other forms of chronic ischemic heart disease\n",
        "                ) THEN 1\n",
        "            END AS IHD,\n",
        "            CASE\n",
        "                WHEN icd_code = '39891' THEN 1\n",
        "                WHEN icd_code BETWEEN '4280 '\n",
        "                AND '4289 ' THEN 1\n",
        "            END AS CHF\n",
        "            /* Congestive heart failure */\n",
        "            -- cardiac arrhythmias is removed in up to date versions\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code BETWEEN '4400 '\n",
        "                AND '4409 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '44100'\n",
        "                AND '4419 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '4420 '\n",
        "                AND '4429 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '4431 '\n",
        "                AND '4439 ' THEN 1\n",
        "                WHEN icd_code BETWEEN '44421'\n",
        "                AND '44422' THEN 1\n",
        "                WHEN icd_code = '4471 ' THEN 1\n",
        "                WHEN icd_code = '449  ' THEN 1\n",
        "                WHEN icd_code = '5571 ' THEN 1\n",
        "                WHEN icd_code = '5579 ' THEN 1\n",
        "                WHEN icd_code = 'V434 ' THEN 1\n",
        "            END AS PERIVASC\n",
        "            /* Peripheral vascular disorder */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40200' THEN 1\n",
        "                WHEN icd_code = '40210' THEN 1\n",
        "                WHEN icd_code = '40290' THEN 1\n",
        "                WHEN icd_code = '40509' THEN 1\n",
        "                WHEN icd_code = '40519' THEN 1\n",
        "                WHEN icd_code = '40599' THEN 1\n",
        "            END AS HTNWOCHF\n",
        "            /* Hypertensive heart disease without heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40201' THEN 1\n",
        "                WHEN icd_code = '40211' THEN 1\n",
        "                WHEN icd_code = '40291' THEN 1\n",
        "            END AS HTNWCHF\n",
        "            /* Hypertensive heart disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40301' THEN 1\n",
        "                WHEN icd_code = '40311' THEN 1\n",
        "                WHEN icd_code = '40391' THEN 1\n",
        "            END AS HRENWRF\n",
        "            /* Hypertensive renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40401' THEN 1\n",
        "                WHEN icd_code = '40411' THEN 1\n",
        "                WHEN icd_code = '40491' THEN 1\n",
        "            END AS HHRWCHF\n",
        "            /* Hypertensive heart and renal disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40402' THEN 1\n",
        "                WHEN icd_code = '40412' THEN 1\n",
        "                WHEN icd_code = '40492' THEN 1\n",
        "            END AS HHRWRF\n",
        "            /* Hypertensive heart and renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '40403' THEN 1\n",
        "                WHEN icd_code = '40413' THEN 1\n",
        "                WHEN icd_code = '40493' THEN 1\n",
        "            END AS HHRWHRF\n",
        "            /* Hypertensive heart and renal disease with heart and renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd_code = '585  ' THEN 1 -- discontinued code\n",
        "                WHEN icd_code = '5853 ' THEN 1\n",
        "                WHEN icd_code = '5854 ' THEN 1\n",
        "                WHEN icd_code = '5855 ' THEN 1\n",
        "                WHEN icd_code = '5856 ' THEN 1\n",
        "                WHEN icd_code = '5859 ' THEN 1\n",
        "                WHEN icd_code = '586  ' THEN 1\n",
        "                WHEN icd_code = 'V420 ' THEN 1\n",
        "                WHEN icd_code = 'V451 ' THEN 1\n",
        "                WHEN icd_code BETWEEN 'V560 '\n",
        "                AND 'V5632' THEN 1\n",
        "                WHEN icd_code = 'V568 ' THEN 1\n",
        "                WHEN icd_code BETWEEN 'V4511'\n",
        "                AND 'V4512' THEN 1\n",
        "            END AS RENLFAIL\n",
        "            /* Renal failure */\n",
        "        FROM\n",
        "            icd\n",
        "    ),\n",
        "    eligrp AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            MAX(ihd) AS ihd,\n",
        "            MAX(chf) AS chf,\n",
        "            MAX(perivasc) AS perivasc,\n",
        "            MAX(htnwchf) AS htnwchf,\n",
        "            MAX(hrenwrf) AS hrenwrf,\n",
        "            MAX(hhrwchf) AS hhrwchf,\n",
        "            MAX(hhrwrf) AS hhrwrf,\n",
        "            MAX(hhrwhrf) AS hhrwhrf,\n",
        "            MAX(renlfail) AS renlfail\n",
        "        FROM\n",
        "            eliflg\n",
        "        GROUP BY\n",
        "            hadm_id\n",
        "    )\n",
        "    SELECT\n",
        "        adm.subject_id,\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN ihd = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS ISCHEMIC_HEART_DISEASE,\n",
        "        CASE\n",
        "            WHEN chf = 1 THEN 1\n",
        "            WHEN htnwchf = 1 THEN 1\n",
        "            WHEN hhrwchf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS CONGESTIVE_HEART_FAILURE,\n",
        "        CASE\n",
        "            WHEN perivasc = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS PERIPHERAL_VASCULAR,\n",
        "        CASE\n",
        "            WHEN renlfail = 1 THEN 1\n",
        "            WHEN hrenwrf = 1 THEN 1\n",
        "            WHEN hhrwrf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS RENAL_FAILURE\n",
        "    FROM\n",
        "        `physionet-data.mimic_core.admissions` adm\n",
        "        LEFT JOIN eligrp eli ON adm.hadm_id = eli.hadm_id\n",
        "    ORDER BY\n",
        "        adm.hadm_id\n",
        "),\n",
        "surgflag AS (\n",
        "    SELECT\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN LOWER(curr_service) LIKE '%surg%' THEN 1\n",
        "            ELSE 0\n",
        "        END AS surgical,\n",
        "        ROW_NUMBER() OVER(\n",
        "            PARTITION BY adm.HADM_ID\n",
        "            ORDER BY\n",
        "                TRANSFERTIME\n",
        "        ) AS serviceOrder\n",
        "    FROM\n",
        "        `physionet-data.mimic_core.admissions` adm\n",
        "        LEFT JOIN `physionet-data.mimic_hosp.services` se ON adm.hadm_id = se.hadm_id\n",
        ")\n",
        ",\n",
        "tx_raw AS (\n",
        "    -- BLOOD TRANSFUSED in mL\n",
        "    -- carevue not in MIMIC 4\n",
        "    -- include all MIMIC 4 add carvue from MIMIC 3\n",
        "    WITH inputevents AS (\n",
        "        SELECT\n",
        "            ipe.stay_id,\n",
        "            ipe.starttime AS charttime,\n",
        "            ROUND(ipe.amount) AS amount,\n",
        "        FROM\n",
        "            `physionet-data.mimic_icu.inputevents` ipe\n",
        "        WHERE\n",
        "            ipe.itemid IN(\n",
        "                225168, -- Packed Red Blood Cells\n",
        "                220996, -- Packed Red Cells\n",
        "                221013,  -- Whole blood\n",
        "                226368, -- OR Packed RBC Intake\n",
        "                227070 -- PACU Packed RBC Intake\n",
        "            )\n",
        "            AND amount > 100\n",
        "            --AND ipe.statusdescription != 'Rewritten'\n",
        "    )\n",
        "    SELECT\n",
        "        ipe.stay_id,\n",
        "        charttime,\n",
        "        SUM(amount) AS rbc_volume,\n",
        "    FROM\n",
        "        inputevents ipe\n",
        "    GROUP BY\n",
        "        ipe.stay_id,\n",
        "        ipe.charttime\n",
        "),\n",
        "tx AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        TIMESTAMP_SECONDS(60 * DIV(UNIX_SECONDS(TIMESTAMP(charttime)), 60)) AS episode,\n",
        "        --some samples have duplicate readings every 15 minutes - we take an hourly window and average the volume across this window\n",
        "        --doing so reduces errors significantly\n",
        "        MIN(charttime) AS charttime,\n",
        "        --get the first timestamp of each window\n",
        "        AVG(rbc_volume) AS rbc_volume\n",
        "    FROM tx_raw\n",
        "    GROUP BY stay_id, episode\n",
        "    ORDER BY stay_id, episode\n",
        "),\n",
        "tx_counts AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        COUNT(charttime) AS tx_episodes,\n",
        "        SUM(rbc_volume) AS rbc_volume,\n",
        "        CEIL(SUM(rbc_volume) / 350) AS rbc_units\n",
        "    FROM tx\n",
        "    WHERE\n",
        "        stay_id IS NOT NULL\n",
        "    GROUP BY\n",
        "        stay_id\n",
        "),\n",
        "pivoted_hemoglobin AS (\n",
        "    SELECT\n",
        "        stay_id,\n",
        "        charttime,\n",
        "        hemoglobin\n",
        "    FROM\n",
        "        pivoted_lab\n",
        "    WHERE\n",
        "        stay_id IS NOT NULL\n",
        "        AND charttime IS NOT NULL\n",
        "        AND hemoglobin IS NOT NULL\n",
        "    ORDER BY\n",
        "        stay_id\n",
        ")\n",
        ", tx_hgb_paired AS (\n",
        "        SELECT\n",
        "            w.stay_id,\n",
        "            w.last_hb_in_window,\n",
        "            MIN(p.hemoglobin) AS hemoglobin,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume,\n",
        "            DATETIME_DIFF(w.tx_offset, w.last_hb_in_window, SECOND) AS delta_tx_hgb_seconds,\n",
        "        FROM\n",
        "            (\n",
        "                SELECT\n",
        "                    p.stay_id,\n",
        "                    t.charttime AS tx_offset,\n",
        "                    t.rbc_volume,\n",
        "                    MAX(p.charttime) AS last_hb_in_window,\n",
        "                    p.hemoglobin\n",
        "                FROM tx t --`arctic-welder-307905.blood_transfusion.tx` t\n",
        "                    INNER JOIN pivoted_hemoglobin p ON p.stay_id = t.stay_id\n",
        "                    AND p.charttime BETWEEN DATETIME_SUB(t.charttime, INTERVAL 6 HOUR)\n",
        "                    AND t.charttime --we search the 6 hours prior to transfusion for minimum hemoglobin levels associated with that transfusion\n",
        "                GROUP BY\n",
        "                    p.stay_id,\n",
        "                    t.charttime,\n",
        "                    t.rbc_volume,\n",
        "                    p.hemoglobin\n",
        "                ORDER BY\n",
        "                    stay_id,\n",
        "                    last_hb_in_window\n",
        "            ) w\n",
        "            INNER JOIN pivoted_hemoglobin p ON p.stay_id = w.stay_id\n",
        "            AND p.charttime = w.last_hb_in_window\n",
        "        GROUP BY\n",
        "            w.stay_id,\n",
        "            w.last_hb_in_window,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume\n",
        "        ORDER BY\n",
        "            stay_id,\n",
        "             last_hb_in_window,\n",
        "             tx_offset\n",
        ")\n",
        ", tx_hgb_filtered AS (\n",
        "        SELECT\n",
        "            *,\n",
        "            ROW_NUMBER() OVER(x) AS event_number\n",
        "        FROM tx_hgb_paired\n",
        "        WINDOW x AS(\n",
        "                PARTITION BY stay_id\n",
        "                ORDER BY tx_offset\n",
        "            )\n",
        "        ORDER BY stay_id\n",
        "\n",
        ")\n",
        ",\n",
        "tx_mimic_control AS (SELECT stay_id, hadm_id, subject_id, charttime, HEMOGLOBIN\n",
        "FROM pivoted_lab\n",
        "WHERE stay_id NOT IN ((SELECT DISTINCT(stay_id) FROM tx_hgb_filtered))),\n",
        "\n",
        "tx_mimic_control_hb_not_null AS (SELECT * FROM tx_mimic_control\n",
        "WHERE HEMOGLOBIN IS NOT NULL\n",
        "ORDER BY stay_id, HEMOGLOBIN),\n",
        "\n",
        "tx_mimic_control_hb_min_all_columns AS (SELECT *,\n",
        "ROW_NUMBER() OVER(PARTITION BY stay_id ORDER BY HEMOGLOBIN, charttime ASC) AS RowRank\n",
        "FROM tx_mimic_control_hb_not_null),\n",
        "\n",
        " tx_mimic_control_hb_min AS (SELECT stay_id, MIN(HEMOGLOBIN) as min_hemoglobin\n",
        "  FROM tx_mimic_control_hb_not_null\n",
        "  GROUP BY stay_id)\n",
        "\n",
        "SELECT stay_id, subject_id,charttime, HEMOGLOBIN FROM tx_mimic_control_hb_min_all_columns\n",
        "Where RowRank=1\n",
        "ORDER BY stay_id\n",
        "\n",
        "\"\"\").to_dataframe()\n",
        ""
      ],
      "metadata": {
        "id": "jp3pn2TPxEqU"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Hemoglobins level for control group - mimic4\n",
        "control_mimic4.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 206
        },
        "id": "ugIMqRPbxHTb",
        "outputId": "7460d601-82c8-4187-912b-c854e40f5df4"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    stay_id  subject_id           charttime  HEMOGLOBIN\n",
              "0  30000153    12466550 2174-10-01 05:35:00         8.1\n",
              "1  30000213    13180007 2162-06-22 04:00:00         7.4\n",
              "2  30000484    18421337 2136-01-15 04:28:00         8.1\n",
              "3  30000646    12207593 2194-04-29 02:33:00        12.9\n",
              "4  30001148    12980335 2156-08-30 13:50:00         8.5"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-91e5efcd-970d-4a8b-ba6b-3c8be3276d97\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>stay_id</th>\n",
              "      <th>subject_id</th>\n",
              "      <th>charttime</th>\n",
              "      <th>HEMOGLOBIN</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>30000153</td>\n",
              "      <td>12466550</td>\n",
              "      <td>2174-10-01 05:35:00</td>\n",
              "      <td>8.1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>30000213</td>\n",
              "      <td>13180007</td>\n",
              "      <td>2162-06-22 04:00:00</td>\n",
              "      <td>7.4</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>30000484</td>\n",
              "      <td>18421337</td>\n",
              "      <td>2136-01-15 04:28:00</td>\n",
              "      <td>8.1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>30000646</td>\n",
              "      <td>12207593</td>\n",
              "      <td>2194-04-29 02:33:00</td>\n",
              "      <td>12.9</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>30001148</td>\n",
              "      <td>12980335</td>\n",
              "      <td>2156-08-30 13:50:00</td>\n",
              "      <td>8.5</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "      <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-91e5efcd-970d-4a8b-ba6b-3c8be3276d97')\"\n",
              "              title=\"Convert this dataframe to an interactive table.\"\n",
              "              style=\"display:none;\">\n",
              "        \n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
              "    <path d=\"M0 0h24v24H0V0z\" fill=\"none\"/>\n",
              "    <path d=\"M18.56 5.44l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94zm-11 1L8.5 8.5l.94-2.06 2.06-.94-2.06-.94L8.5 2.5l-.94 2.06-2.06.94zm10 10l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94z\"/><path d=\"M17.41 7.96l-1.37-1.37c-.4-.4-.92-.59-1.43-.59-.52 0-1.04.2-1.43.59L10.3 9.45l-7.72 7.72c-.78.78-.78 2.05 0 2.83L4 21.41c.39.39.9.59 1.41.59.51 0 1.02-.2 1.41-.59l7.78-7.78 2.81-2.81c.8-.78.8-2.07 0-2.86zM5.41 20L4 18.59l7.72-7.72 1.47 1.35L5.41 20z\"/>\n",
              "  </svg>\n",
              "      </button>\n",
              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-91e5efcd-970d-4a8b-ba6b-3c8be3276d97 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-91e5efcd-970d-4a8b-ba6b-3c8be3276d97');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 14
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# MIMIC 3 control"
      ],
      "metadata": {
        "id": "Obixhff_53_l"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "control_mimic3 = client.query(\"\"\"\n",
        "WITH\n",
        "all_criteria AS (SELECT DISTINCT(icustay_id)\n",
        "FROM `physionet-data.mimiciii_derived.pivoted_sofa`\n",
        "WHERE icustay_id IN(SELECT DISTINCT(icustay_id)\n",
        "                    FROM `physionet-data.mimiciii_derived.icustay_detail`\n",
        "                    WHERE icustay_seq = 1\n",
        "                    AND first_icu_stay= TRUE\n",
        "                    AND (admission_age BETWEEN 18 AND 89)\n",
        "                    )\n",
        "    AND icustay_id NOT IN(SELECT DISTINCT(i.ICUSTAY_ID)\n",
        "        FROM `physionet-data.mimiciii_clinical.diagnoses_icd` d\n",
        "        INNER JOIN `physionet-data.mimiciii_clinical.icustays` i\n",
        "            ON d.hadm_id=i.hadm_id\n",
        "        INNER JOIN `physionet-data.mimiciii_derived.icustay_detail` a\n",
        "            ON d.HADM_ID=a.hadm_id\n",
        "        WHERE icd9_code IN (\n",
        "                --ref: https://www.bmj.com/content/bmj/suppl/2015/02/03/bmj.h246.DC1/junm020747.ww1_default.pdf\n",
        "                --intracranial bleeding\n",
        "                '430', --Subarachnoid\n",
        "                '431', --intracerebral\n",
        "                '4320', --other and unspecified intracranial bleeding\n",
        "                '4321', --subdural\n",
        "                '4329', --unspecified intracranial bleeding\n",
        "                --upper gastrointestinal\n",
        "                '5310', --acute gastric ulcer with bleeding without obstruction\n",
        "                '5312', --acute gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5314', --chronic or unspecified gastric ulcer with bleeding without obstruction\n",
        "                '5316', --chronic or unspecified gastric ulcer with bleeding and perforation without obstruction\n",
        "                '5320', --acute duodenal ulcer with bleeding without obstruction\n",
        "                '5322', --acute duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5324', --chronic or unspecified duodenal ulcer with bleeding without obstruction\n",
        "                '5326', --chronic or unspecified duodenal ulcer with bleeding and perforation without obstruction\n",
        "                '5330', --acute peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5332', --acute peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5334', --chronic or unspecified peptic ulcer of unspecified site with bleeding without obstruction\n",
        "                '5336', --chronic or unspecified peptic ulcer of unspecified site with bleeding and perforation without obstruction\n",
        "                '5340', --acute gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5342', --acute gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5344', --chronic or unspecified gastrojejunal ulcer with bleeding without obstruction\n",
        "                '5346', --chronic or unspecified gastrojejunal ulcer with bleeding and perforation without obstruction\n",
        "                '5780', --hematemesis\n",
        "                '5781', --blood in stool\n",
        "                '5789', --bleeding of gastrointestinal tract unspecified\n",
        "                --Lower GI\n",
        "                '5693', --bleeding of rectum and anus\n",
        "                --Other Bleeding\n",
        "                '2878', --other unspecified hemorrhagic conditions\n",
        "                '2879', --unspecified hemorrhagic conditions\n",
        "                '5967', --bleeding into bladder wall\n",
        "                '7848', --bleeding from throat\n",
        "                '5997', --hematuria, unspecified\n",
        "                '6271', --postmenopausal bleeding\n",
        "                '4590', --bleeding unspecified\n",
        "                '7191', --hemarthrosis site unspecified\n",
        "                '7863', --hemoptysis, unspecified\n",
        "                '72992', --nontraumatic hematoma soft tissue\n",
        "                '9582' --secondary or recurrent following trauma\n",
        "            )\n",
        "        OR icd9_code LIKE '900%' --vessel injuries\n",
        "        OR icd9_code LIKE '901%' --vessel injuries\n",
        "        OR icd9_code LIKE '902%' --vessel injuries\n",
        "        OR icd9_code LIKE '903%' --vessel injuries\n",
        "        OR icd9_code LIKE '904%' --vessel injuries\n",
        "\n",
        "        OR UPPER(LAST_CAREUNIT) LIKE '%TSICU%'\n",
        "        OR UPPER(FIRST_CAREUNIT) LIKE '%TSICU%' ))\n",
        " ,\n",
        " demographics AS (\n",
        "    SELECT\n",
        "        ie.subject_id,\n",
        "        ie.hadm_id,\n",
        "        ie.icustay_id -- patient level factors\n",
        ",\n",
        "        pat.gender,\n",
        "        pat.dod -- hospital level factors\n",
        ",\n",
        "        adm.admittime,\n",
        "        adm.dischtime,\n",
        "        DATETIME_DIFF(adm.admittime, pat.dob, YEAR) AS age,\n",
        "        adm.admission_type,\n",
        "        adm.hospital_expire_flag,\n",
        "        adm.deathtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY adm.subject_id\n",
        "            ORDER BY\n",
        "                adm.admittime\n",
        "        ) AS hospstay_seq,\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY adm.subject_id\n",
        "                ORDER BY\n",
        "                    adm.admittime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_hosp_stay -- icu level factors\n",
        ",\n",
        "        ie.intime,\n",
        "        ie.outtime,\n",
        "        DENSE_RANK() OVER (\n",
        "            PARTITION BY ie.hadm_id\n",
        "            ORDER BY\n",
        "                ie.intime\n",
        "        ) AS icustay_seq -- first ICU stay *for the current hospitalization*\n",
        ",\n",
        "        CASE\n",
        "            WHEN DENSE_RANK() OVER (\n",
        "                PARTITION BY ie.hadm_id\n",
        "                ORDER BY\n",
        "                    ie.intime\n",
        "            ) = 1 THEN TRUE\n",
        "            ELSE False\n",
        "        END AS first_icu_stay\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.icustays` ie\n",
        "        INNER JOIN `physionet-data.mimiciii_clinical.admissions` adm ON ie.hadm_id = adm.hadm_id\n",
        "        INNER JOIN `physionet-data.mimiciii_clinical.patients` pat ON ie.subject_id = pat.subject_id\n",
        "    ORDER BY\n",
        "        ie.subject_id,\n",
        "        adm.admittime,\n",
        "        ie.intime\n",
        "),\n",
        "first_adm_offset AS (\n",
        "    SELECT\n",
        "        icustay_id AS id,\n",
        "        intime,\n",
        "        outtime\n",
        "    FROM\n",
        "        demographics\n",
        "    WHERE\n",
        "        first_icu_stay = TRUE\n",
        "),\n",
        "pivoted_sofa AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_derived.pivoted_sofa` ps\n",
        "        LEFT JOIN first_adm_offset f ON ps.icustay_id = f.id\n",
        "        AND ps.endtime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "),\n",
        "pivoted_lab AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        (\n",
        "            WITH pivoted_lab AS (\n",
        "                -- create a table which has fuzzy boundaries on ICU admission (+- 12 hours from documented time)\n",
        "                -- this is used to assign icustay_id to lab data, which can be collected outside ICU\n",
        "                -- involves first creating a lag/lead version of intime/outtime\n",
        "                WITH i AS (\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        icustay_id,\n",
        "                        intime,\n",
        "                        outtime,\n",
        "                        lag (outtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS outtime_lag,\n",
        "                        lead (intime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                intime\n",
        "                        ) AS intime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimiciii_clinical.icustays`\n",
        "                ),\n",
        "                iid_assign AS (\n",
        "                    SELECT\n",
        "                        i.subject_id,\n",
        "                        i.icustay_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN i.outtime_lag IS NOT NULL\n",
        "                            AND i.outtime_lag > DATETIME_SUB(i.intime, INTERVAL 24 HOUR) THEN DATETIME_SUB(\n",
        "                                i.intime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime, i.outtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(i.intime, INTERVAL 12 HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN i.intime_lead IS NOT NULL\n",
        "                            AND i.intime_lead < DATETIME_ADD(i.outtime, INTERVAL 24 HOUR) THEN DATETIME_ADD(\n",
        "                                i.outtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(i.intime_lead, i.outtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(i.outtime, INTERVAL 12 HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        i\n",
        "                ) -- also create fuzzy boundaries on hospitalization\n",
        ",\n",
        "                h AS (\n",
        "                    SELECT\n",
        "                        subject_id,hadm_id,admittime,dischtime,\n",
        "                        lag (dischtime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS dischtime_lag,\n",
        "                        lead (admittime) over (\n",
        "                            PARTITION by subject_id\n",
        "                            ORDER BY\n",
        "                                admittime\n",
        "                        ) AS admittime_lead\n",
        "                    FROM\n",
        "                        `physionet-data.mimiciii_clinical.admissions`\n",
        "                ),\n",
        "                adm AS (\n",
        "                    SELECT\n",
        "                        h.subject_id,\n",
        "                        h.hadm_id -- this rule is:\n",
        "                        --  if there are two hospitalizations within 24 hours, set the start/stop\n",
        "                        --  time as half way between the two admissions\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN h.dischtime_lag IS NOT NULL\n",
        "                            AND h.dischtime_lag > DATETIME_SUB(h.admittime, INTERVAL '24' HOUR) THEN DATETIME_SUB(\n",
        "                                h.admittime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime, h.dischtime_lag, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_SUB(h.admittime, INTERVAL '12' HOUR)\n",
        "                        END AS data_start,\n",
        "                        CASE\n",
        "                            WHEN h.admittime_lead IS NOT NULL\n",
        "                            AND h.admittime_lead < DATETIME_ADD(h.dischtime, INTERVAL '24' HOUR) THEN DATETIME_ADD(\n",
        "                                h.dischtime,\n",
        "                                INTERVAL CAST(\n",
        "                                    DATETIME_DIFF(h.admittime_lead, h.dischtime, HOUR) / 2 AS INT64\n",
        "                                ) HOUR\n",
        "                            )\n",
        "                            ELSE DATETIME_ADD(h.dischtime, INTERVAL '12' HOUR)\n",
        "                        END AS data_end\n",
        "                    FROM\n",
        "                        h\n",
        "                ),\n",
        "                le AS (\n",
        "                    -- begin query that extracts the data\n",
        "                    SELECT\n",
        "                        subject_id,\n",
        "                        charttime -- here we assign labels to ITEMIDs\n",
        "                        -- this also fuses together multiple ITEMIDs containing the same data\n",
        ",\n",
        "                        CASE\n",
        "                            WHEN itemid = 50868 THEN 'ANION GAP'\n",
        "                            WHEN itemid = 50862 THEN 'ALBUMIN'\n",
        "                            WHEN itemid = 51144 THEN 'BANDS'\n",
        "                            WHEN itemid = 50882 THEN 'BICARBONATE'\n",
        "                            WHEN itemid = 50885 THEN 'BILIRUBIN'\n",
        "                            WHEN itemid = 50912 THEN 'CREATININE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50806 THEN 'CHLORIDE'\n",
        "                            WHEN itemid = 50902 THEN 'CHLORIDE' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50809 THEN 'GLUCOSE'\n",
        "                            WHEN itemid = 50931 THEN 'GLUCOSE' -- exclude blood gas\n",
        "                            --WHEN itemid = 50810 THEN 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221 THEN 'HEMATOCRIT' -- exclude blood gas\n",
        "                            --WHEN itemid = 50811 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222 THEN 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813 THEN 'LACTATE'\n",
        "                            WHEN itemid = 51265 THEN 'PLATELET' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50822 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 50971 THEN 'POTASSIUM'\n",
        "                            WHEN itemid = 51275 THEN 'PTT'\n",
        "                            WHEN itemid = 51237 THEN 'INR'\n",
        "                            WHEN itemid = 51274 THEN 'PT' -- exclude blood gas\n",
        "                            -- WHEN itemid = 50824 THEN 'SODIUM'\n",
        "                            WHEN itemid = 50983 THEN 'SODIUM'\n",
        "                            WHEN itemid = 51006 THEN 'BUN'\n",
        "                            WHEN itemid = 51300 THEN 'WBC'\n",
        "                            WHEN itemid = 51301 THEN 'WBC'\n",
        "                            ELSE NULL\n",
        "                        END AS label,\n",
        "                        -- add in some sanity checks on the values\n",
        "                        -- the where clause below requires all valuenum to be > 0, so these are only upper limit checks\n",
        "                        CASE\n",
        "                            WHEN itemid = 50862\n",
        "                            AND valuenum > 10 THEN NULL -- g/dL 'ALBUMIN'\n",
        "                            WHEN itemid = 50868\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'ANION GAP'\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum < 0 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 51144\n",
        "                            AND valuenum > 100 THEN NULL -- immature band forms, %\n",
        "                            WHEN itemid = 50882\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'BICARBONATE'\n",
        "                            WHEN itemid = 50885\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'BILIRUBIN'\n",
        "                            WHEN itemid = 50806\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50902\n",
        "                            AND valuenum > 10000 THEN NULL -- mEq/L 'CHLORIDE'\n",
        "                            WHEN itemid = 50912\n",
        "                            AND valuenum > 150 THEN NULL -- mg/dL 'CREATININE'\n",
        "                            WHEN itemid = 50809\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50931\n",
        "                            AND valuenum > 10000 THEN NULL -- mg/dL 'GLUCOSE'\n",
        "                            WHEN itemid = 50810\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 51221\n",
        "                            AND valuenum > 100 THEN NULL -- % 'HEMATOCRIT'\n",
        "                            WHEN itemid = 50811\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 51222\n",
        "                            AND valuenum > 50 THEN NULL -- g/dL 'HEMOGLOBIN'\n",
        "                            WHEN itemid = 50813\n",
        "                            AND valuenum > 50 THEN NULL -- mmol/L 'LACTATE'\n",
        "                            WHEN itemid = 51265\n",
        "                            AND valuenum > 10000 THEN NULL -- K/uL 'PLATELET'\n",
        "                            WHEN itemid = 50822\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 50971\n",
        "                            AND valuenum > 30 THEN NULL -- mEq/L 'POTASSIUM'\n",
        "                            WHEN itemid = 51275\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PTT'\n",
        "                            WHEN itemid = 51237\n",
        "                            AND valuenum > 50 THEN NULL -- 'INR'\n",
        "                            WHEN itemid = 51274\n",
        "                            AND valuenum > 150 THEN NULL -- sec 'PT'\n",
        "                            WHEN itemid = 50824\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 50983\n",
        "                            AND valuenum > 200 THEN NULL -- mEq/L == mmol/L 'SODIUM'\n",
        "                            WHEN itemid = 51006\n",
        "                            AND valuenum > 300 THEN NULL -- 'BUN'\n",
        "                            WHEN itemid = 51300\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            WHEN itemid = 51301\n",
        "                            AND valuenum > 1000 THEN NULL -- 'WBC'\n",
        "                            ELSE valuenum\n",
        "                        END AS valuenum\n",
        "                    FROM\n",
        "                        `physionet-data.mimiciii_clinical.labevents`\n",
        "                    WHERE\n",
        "                        ITEMID IN (\n",
        "                            -- comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS\n",
        "                            50868, -- ANION GAP | CHEMISTRY | BLOOD | 769895\n",
        "                            50862, -- ALBUMIN | CHEMISTRY | BLOOD | 146697\n",
        "                            51144, -- BANDS - hematology\n",
        "                            50882, -- BICARBONATE | CHEMISTRY | BLOOD | 780733\n",
        "                            50885, -- BILIRUBIN, TOTAL | CHEMISTRY | BLOOD | 238277\n",
        "                            50912, -- CREATININE | CHEMISTRY | BLOOD | 797476\n",
        "                            50902, -- CHLORIDE | CHEMISTRY | BLOOD | 795568\n",
        "                            -- 50806, -- CHLORIDE, WHOLE BLOOD | BLOOD GAS | BLOOD | 48187\n",
        "                            50931, -- GLUCOSE | CHEMISTRY | BLOOD | 748981\n",
        "                            -- 50809, -- GLUCOSE | BLOOD GAS | BLOOD | 196734\n",
        "                            51221, -- HEMATOCRIT | HEMATOLOGY | BLOOD | 881846\n",
        "                            -- 50810, -- HEMATOCRIT, CALCULATED | BLOOD GAS | BLOOD | 89715\n",
        "                            51222, -- HEMOGLOBIN | HEMATOLOGY | BLOOD | 752523\n",
        "                            -- 50811, -- HEMOGLOBIN | BLOOD GAS | BLOOD | 89712\n",
        "                            50813, -- LACTATE | BLOOD GAS | BLOOD | 187124\n",
        "                            51265, -- PLATELET COUNT | HEMATOLOGY | BLOOD | 778444\n",
        "                            50971, -- POTASSIUM | CHEMISTRY | BLOOD | 845825\n",
        "                            -- 50822, -- POTASSIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 192946\n",
        "                            51275, -- PTT | HEMATOLOGY | BLOOD | 474937\n",
        "                            51237, -- INR(PT) | HEMATOLOGY | BLOOD | 471183\n",
        "                            51274, -- PT | HEMATOLOGY | BLOOD | 469090\n",
        "                            50983, -- SODIUM | CHEMISTRY | BLOOD | 808489\n",
        "                            -- 50824, -- SODIUM, WHOLE BLOOD | BLOOD GAS | BLOOD | 71503\n",
        "                            51006, -- UREA NITROGEN | CHEMISTRY | BLOOD | 791925\n",
        "                            51301, -- WHITE BLOOD CELLS | HEMATOLOGY | BLOOD | 753301\n",
        "                            51300  -- WBC COUNT | HEMATOLOGY | BLOOD | 2371\n",
        "                        )\n",
        "                        AND valuenum IS NOT NULL\n",
        "                        AND valuenum > 0 -- lab values cannot be 0 and cannot be negative\n",
        "                ),\n",
        "                le_avg AS (\n",
        "                    SELECT\n",
        "                        le.subject_id,\n",
        "                        le.charttime,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ANION GAP' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ANIONGAP,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'ALBUMIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS ALBUMIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BANDS' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BANDS,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BICARBONATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BICARBONATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BILIRUBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BILIRUBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CREATININE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CREATININE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'CHLORIDE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS CHLORIDE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'GLUCOSE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS GLUCOSE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMATOCRIT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMATOCRIT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'HEMOGLOBIN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS HEMOGLOBIN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'LACTATE' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS LACTATE,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PLATELET' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PLATELET,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'POTASSIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS POTASSIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PTT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PTT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'INR' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS INR,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'PT' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS PT,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'SODIUM' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS SODIUM,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'BUN' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS BUN,\n",
        "                        avg(\n",
        "                            CASE\n",
        "                                WHEN label = 'WBC' THEN valuenum\n",
        "                                ELSE NULL\n",
        "                            END\n",
        "                        ) AS WBC\n",
        "                    FROM\n",
        "                        le\n",
        "                    GROUP BY\n",
        "                        le.subject_id,\n",
        "                        le.charttime\n",
        "                )\n",
        "                SELECT\n",
        "                    iid.icustay_id,\n",
        "                    adm.hadm_id,\n",
        "                    le_avg.*\n",
        "                FROM\n",
        "                    le_avg\n",
        "                    LEFT JOIN adm ON le_avg.subject_id = adm.subject_id\n",
        "                    AND le_avg.charttime >= adm.data_start\n",
        "                    AND le_avg.charttime < adm.data_end\n",
        "                    LEFT JOIN iid_assign iid ON le_avg.subject_id = iid.subject_id\n",
        "                    AND le_avg.charttime >= iid.data_start\n",
        "                    AND le_avg.charttime < iid.data_end\n",
        "                ORDER BY\n",
        "                    le_avg.subject_id,\n",
        "                    le_avg.charttime\n",
        "            )\n",
        "            SELECT\n",
        "                *\n",
        "            FROM\n",
        "                pivoted_lab\n",
        "        ) AS pl\n",
        "        LEFT JOIN first_adm_offset f ON pl.icustay_id = f.id\n",
        "        AND pl.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "),\n",
        "mechvent AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        charttime -- case statement determining whether it is an instance of mech vent\n",
        ",\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN itemid IS NULL\n",
        "                OR value IS NULL THEN 0 -- can't have null values\n",
        "                WHEN itemid = 720\n",
        "                AND value != 'Other/Remarks' THEN 1 -- VentTypeRecorded\n",
        "                WHEN itemid = 223848\n",
        "                AND value != 'Other' THEN 1\n",
        "                WHEN itemid = 223849 THEN 1 -- ventilator mode\n",
        "                WHEN itemid = 467\n",
        "                AND value = 'Ventilator' THEN 1 -- O2 delivery device == ventilator\n",
        "                WHEN itemid IN(\n",
        "                    445,\n",
        "                    448,\n",
        "                    449,\n",
        "                    450,\n",
        "                    1340,\n",
        "                    1486,\n",
        "                    1600,\n",
        "                    224687 -- minute volume\n",
        ",\n",
        "                    639,\n",
        "                    654,\n",
        "                    681,\n",
        "                    682,\n",
        "                    683,\n",
        "                    684,\n",
        "                    224685,\n",
        "                    224684,\n",
        "                    224686 -- tidal volume\n",
        ",\n",
        "                    218,\n",
        "                    436,\n",
        "                    535,\n",
        "                    444,\n",
        "                    459,\n",
        "                    224697,\n",
        "                    224695,\n",
        "                    224696,\n",
        "                    224746,\n",
        "                    224747 -- High/Low/Peak/Mean/Neg insp force (\"RespPressure\")\n",
        ",\n",
        "                    221,\n",
        "                    1,\n",
        "                    1211,\n",
        "                    1655,\n",
        "                    2000,\n",
        "                    226873,\n",
        "                    224738,\n",
        "                    224419,\n",
        "                    224750,\n",
        "                    227187 -- Insp pressure\n",
        ",\n",
        "                    543 -- PlateauPressure\n",
        ",\n",
        "                    5865,\n",
        "                    5866,\n",
        "                    224707,\n",
        "                    224709,\n",
        "                    224705,\n",
        "                    224706 -- APRV pressure\n",
        ",\n",
        "                    60,\n",
        "                    437,\n",
        "                    505,\n",
        "                    506,\n",
        "                    686,\n",
        "                    220339,\n",
        "                    224700 -- PEEP\n",
        ",\n",
        "                    3459 -- high pressure relief\n",
        ",\n",
        "                    501,\n",
        "                    502,\n",
        "                    503,\n",
        "                    224702 -- PCV\n",
        ",\n",
        "                    223,\n",
        "                    667,\n",
        "                    668,\n",
        "                    669,\n",
        "                    670,\n",
        "                    671,\n",
        "                    672 -- TCPCV\n",
        ",\n",
        "                    224701 -- PSVlevel\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS ventmarker\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.chartevents` ce\n",
        "        LEFT JOIN first_adm_offset f ON ce.icustay_id = f.id\n",
        "        AND ce.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "    WHERE\n",
        "        ce.value IS NOT NULL -- exclude rows marked as error\n",
        "        AND ce.error != 1 -- the below are settings used to indicate ventilation\n",
        "        AND itemid IN(\n",
        "            720,\n",
        "            223849 -- vent mode\n",
        ",\n",
        "            223848 -- vent type\n",
        ",\n",
        "            445,\n",
        "            448,\n",
        "            449,\n",
        "            450,\n",
        "            1340,\n",
        "            1486,\n",
        "            1600,\n",
        "            224687 -- minute volume\n",
        ",\n",
        "            639,\n",
        "            654,\n",
        "            681,\n",
        "            682,\n",
        "            683,\n",
        "            684,\n",
        "            224685,\n",
        "            224684,\n",
        "            224686 -- tidal volume\n",
        ",\n",
        "            218,\n",
        "            436,\n",
        "            535,\n",
        "            444,\n",
        "            224697,\n",
        "            224695,\n",
        "            224696,\n",
        "            224746,\n",
        "            224747 -- High/Low/Peak/Mean (\"RespPressure\")\n",
        ",\n",
        "            221,\n",
        "            1,\n",
        "            1211,\n",
        "            1655,\n",
        "            2000,\n",
        "            226873,\n",
        "            224738,\n",
        "            224419,\n",
        "            224750,\n",
        "            227187 -- Insp pressure\n",
        ",\n",
        "            543 -- PlateauPressure\n",
        ",\n",
        "            5865,\n",
        "            5866,\n",
        "            224707,\n",
        "            224709,\n",
        "            224705,\n",
        "            224706 -- APRV pressure\n",
        ",\n",
        "            60,\n",
        "            437,\n",
        "            505,\n",
        "            506,\n",
        "            686,\n",
        "            220339,\n",
        "            224700 -- PEEP\n",
        ",\n",
        "            3459 -- high pressure relief\n",
        ",\n",
        "            501,\n",
        "            502,\n",
        "            503,\n",
        "            224702 -- PCV\n",
        ",\n",
        "            223,\n",
        "            667,\n",
        "            668,\n",
        "            669,\n",
        "            670,\n",
        "            671,\n",
        "            672 -- TCPCV\n",
        ",\n",
        "            224701 -- PSVlevel\n",
        "            -- the below are settings used to indicate extubation\n",
        ",\n",
        "            640 -- extubated\n",
        "            -- the below indicate oxygen/NIV, i.e. the end of a mechanical vent event\n",
        ",\n",
        "            468 -- O2 Delivery Device#2\n",
        ",\n",
        "            469 -- O2 Delivery Mode\n",
        ",\n",
        "            470 -- O2 Flow (lpm)\n",
        ",\n",
        "            471 -- O2 Flow (lpm) #2\n",
        ",\n",
        "            227287 -- O2 Flow (additional cannula)\n",
        ",\n",
        "            226732 -- O2 Delivery Device(s)\n",
        ",\n",
        "            223834 -- O2 Flow\n",
        "            -- used in both oxygen + vent calculation\n",
        ",\n",
        "            467 -- O2 Delivery Device\n",
        "        )\n",
        "    GROUP BY\n",
        "        icustay_id,\n",
        "        charttime\n",
        "),\n",
        "sepsis AS (\n",
        "    -- ICD-9 codes for Angus criteria of sepsis\n",
        "    SELECT\n",
        "        hadm_id,\n",
        "        MAX(\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd9_code, 1, 3) IN (\n",
        "                    '001','002','003','004','005',\n",
        "                    '008','009','010','011','012',\n",
        "                    '013','014','015','016','017',\n",
        "                    '018','020','021','022','023',\n",
        "                    '024','025','026','027','030',\n",
        "                    '031','032','033','034','035',\n",
        "                    '036','037','038','039','040',\n",
        "                    '041','090','091','092','093',\n",
        "                    '094','095','096','097','098',\n",
        "                    '100','101','102','103','104',\n",
        "                    '110','111','112','114','115',\n",
        "                    '116','117','118','320','322',\n",
        "                    '324','325','420','421','451',\n",
        "                    '461','462','463','464','465',\n",
        "                    '481','482','485','486','494',\n",
        "                    '510','513','540','541','542',\n",
        "                    '566','567','590','597','601',\n",
        "                    '614','615','616','681','682',\n",
        "                    '683','686','730'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd9_code, 1, 4) IN (\n",
        "                    '5695','5720','5721','5750',\n",
        "                    '5990','7110','7907','9966',\n",
        "                    '9985','9993'\n",
        "                ) THEN 1\n",
        "                WHEN SUBSTR(icd9_code, 1, 5) IN (\n",
        "                    '49121','56201','56203',\n",
        "                    '56211','56213','56983'\n",
        "                ) THEN 1\n",
        "                ELSE 0\n",
        "            END\n",
        "        ) AS sepsisflag\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.diagnoses_icd`\n",
        "    GROUP BY\n",
        "        hadm_id\n",
        "),\n",
        "vasopressor_duration AS (\n",
        "    SELECT\n",
        "        *\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_derived.vasopressordurations`\n",
        "),\n",
        "premorbid AS (\n",
        "    WITH icd AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            CAST(icd9_code AS STRING) AS icd9_code\n",
        "        FROM\n",
        "            `physionet-data.mimiciii_clinical.diagnoses_icd`\n",
        "    ),\n",
        "    eliflg AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            seq_num,\n",
        "            icd9_code -- note that these codes will seem incomplete at first\n",
        "            -- for example, CHF is missing a lot of codes referenced in the literature (402.11, 402.91, etc)\n",
        "            -- these codes are captured by hypertension flags instead\n",
        "            -- later there are some complicated rules which confirm/reject those codes as CHF\n",
        ",\n",
        "            CASE\n",
        "                WHEN SUBSTR(icd9_code, 1, 3) IN(\n",
        "                    '410', --Acute myocardial infarction\n",
        "                    '411', --Other acute and subacute forms of ischemic heart disease\n",
        "                    '412', --Old myocardial infarction\n",
        "                    '413', --Angina pectoris\n",
        "                    '414'  --Other forms of chronic ischemic heart disease\n",
        "                ) THEN 1\n",
        "            END AS IHD,\n",
        "            CASE\n",
        "                WHEN icd9_code = '39891' THEN 1\n",
        "                WHEN icd9_code BETWEEN '4280 '\n",
        "                AND '4289 ' THEN 1\n",
        "            END AS CHF\n",
        "            /* Congestive heart failure */\n",
        "            -- cardiac arrhythmias is removed in up to date versions\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code BETWEEN '4400 '\n",
        "                AND '4409 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '44100'\n",
        "                AND '4419 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '4420 '\n",
        "                AND '4429 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '4431 '\n",
        "                AND '4439 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN '44421'\n",
        "                AND '44422' THEN 1\n",
        "                WHEN icd9_code = '4471 ' THEN 1\n",
        "                WHEN icd9_code = '449  ' THEN 1\n",
        "                WHEN icd9_code = '5571 ' THEN 1\n",
        "                WHEN icd9_code = '5579 ' THEN 1\n",
        "                WHEN icd9_code = 'V434 ' THEN 1\n",
        "            END AS PERIVASC\n",
        "            /* Peripheral vascular disorder */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40200' THEN 1\n",
        "                WHEN icd9_code = '40210' THEN 1\n",
        "                WHEN icd9_code = '40290' THEN 1\n",
        "                WHEN icd9_code = '40509' THEN 1\n",
        "                WHEN icd9_code = '40519' THEN 1\n",
        "                WHEN icd9_code = '40599' THEN 1\n",
        "            END AS HTNWOCHF\n",
        "            /* Hypertensive heart disease without heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40201' THEN 1\n",
        "                WHEN icd9_code = '40211' THEN 1\n",
        "                WHEN icd9_code = '40291' THEN 1\n",
        "            END AS HTNWCHF\n",
        "            /* Hypertensive heart disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40301' THEN 1\n",
        "                WHEN icd9_code = '40311' THEN 1\n",
        "                WHEN icd9_code = '40391' THEN 1\n",
        "            END AS HRENWRF\n",
        "            /* Hypertensive renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40401' THEN 1\n",
        "                WHEN icd9_code = '40411' THEN 1\n",
        "                WHEN icd9_code = '40491' THEN 1\n",
        "            END AS HHRWCHF\n",
        "            /* Hypertensive heart and renal disease with heart failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40402' THEN 1\n",
        "                WHEN icd9_code = '40412' THEN 1\n",
        "                WHEN icd9_code = '40492' THEN 1\n",
        "            END AS HHRWRF\n",
        "            /* Hypertensive heart and renal disease with renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '40403' THEN 1\n",
        "                WHEN icd9_code = '40413' THEN 1\n",
        "                WHEN icd9_code = '40493' THEN 1\n",
        "            END AS HHRWHRF\n",
        "            /* Hypertensive heart and renal disease with heart and renal failure */\n",
        ",\n",
        "            CASE\n",
        "                WHEN icd9_code = '585  ' THEN 1 -- discontinued code\n",
        "                WHEN icd9_code = '5853 ' THEN 1\n",
        "                WHEN icd9_code = '5854 ' THEN 1\n",
        "                WHEN icd9_code = '5855 ' THEN 1\n",
        "                WHEN icd9_code = '5856 ' THEN 1\n",
        "                WHEN icd9_code = '5859 ' THEN 1\n",
        "                WHEN icd9_code = '586  ' THEN 1\n",
        "                WHEN icd9_code = 'V420 ' THEN 1\n",
        "                WHEN icd9_code = 'V451 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN 'V560 '\n",
        "                AND 'V5632' THEN 1\n",
        "                WHEN icd9_code = 'V568 ' THEN 1\n",
        "                WHEN icd9_code BETWEEN 'V4511'\n",
        "                AND 'V4512' THEN 1\n",
        "            END AS RENLFAIL\n",
        "            /* Renal failure */\n",
        "        FROM\n",
        "            icd\n",
        "    ),\n",
        "    eligrp AS (\n",
        "        SELECT\n",
        "            hadm_id,\n",
        "            MAX(ihd) AS ihd,\n",
        "            MAX(chf) AS chf,\n",
        "            MAX(perivasc) AS perivasc,\n",
        "            MAX(htnwchf) AS htnwchf,\n",
        "            MAX(hrenwrf) AS hrenwrf,\n",
        "            MAX(hhrwchf) AS hhrwchf,\n",
        "            MAX(hhrwrf) AS hhrwrf,\n",
        "            MAX(hhrwhrf) AS hhrwhrf,\n",
        "            MAX(renlfail) AS renlfail\n",
        "        FROM\n",
        "            eliflg\n",
        "        GROUP BY\n",
        "            hadm_id\n",
        "    )\n",
        "    SELECT\n",
        "        adm.subject_id,\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN ihd = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS ISCHEMIC_HEART_DISEASE,\n",
        "        CASE\n",
        "            WHEN chf = 1 THEN 1\n",
        "            WHEN htnwchf = 1 THEN 1\n",
        "            WHEN hhrwchf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS CONGESTIVE_HEART_FAILURE,\n",
        "        CASE\n",
        "            WHEN perivasc = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS PERIPHERAL_VASCULAR,\n",
        "        CASE\n",
        "            WHEN renlfail = 1 THEN 1\n",
        "            WHEN hrenwrf = 1 THEN 1\n",
        "            WHEN hhrwrf = 1 THEN 1\n",
        "            WHEN hhrwhrf = 1 THEN 1\n",
        "            ELSE 0\n",
        "        END AS RENAL_FAILURE\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.admissions` adm\n",
        "        LEFT JOIN eligrp eli ON adm.hadm_id = eli.hadm_id\n",
        "    ORDER BY\n",
        "        adm.hadm_id\n",
        "),\n",
        "surgflag AS (\n",
        "    SELECT\n",
        "        adm.hadm_id,\n",
        "        CASE\n",
        "            WHEN LOWER(curr_service) LIKE '%surg%' THEN 1\n",
        "            ELSE 0\n",
        "        END AS surgical,\n",
        "        ROW_NUMBER() OVER(\n",
        "            PARTITION BY adm.HADM_ID\n",
        "            ORDER BY\n",
        "                TRANSFERTIME\n",
        "        ) AS serviceOrder\n",
        "    FROM\n",
        "        `physionet-data.mimiciii_clinical.admissions` adm\n",
        "        LEFT JOIN `physionet-data.mimiciii_clinical.services` se ON adm.hadm_id = se.hadm_id\n",
        "),\n",
        "tx_raw AS (\n",
        "    -- BLOOD TRANSFUSED in mL\n",
        "    WITH carevue AS (\n",
        "        SELECT\n",
        "            cv.icustay_id,\n",
        "            cv.charttime,\n",
        "            -- carevue always has units in millilitres (or null)\n",
        "            ROUND(cv.amount) AS amount\n",
        "        FROM\n",
        "            `physionet-data.mimiciii_clinical.inputevents_cv` cv\n",
        "        WHERE\n",
        "            cv.itemid IN(\n",
        "                30001,  -- Packed RBC's\n",
        "                30002,  -- Whole Blood\n",
        "                30004,  -- Washed PRBC's\n",
        "                30104,  -- OR Packed RBC's\n",
        "                30179,  -- PRBC's\n",
        "                42588,  -- VICU PRBC\n",
        "                42239,  -- CC7 PRBC\n",
        "                42186,\t-- Pre admit PRBC\n",
        "                42239,\t-- CC7 PRBC\n",
        "                42324,\t-- er prbc\n",
        "                42588,\t-- VICU PRBC\n",
        "                42740,\t-- prbc in er\n",
        "                43010,\t-- packed cells pacu\n",
        "                45020,\t-- RBC waste\n",
        "                46124,\t-- er in prbc\n",
        "                46407,\t-- ED PRBC\n",
        "                46612\t  -- E.R. prbc\n",
        "            )\n",
        "            AND amount > 100 --do not count any transfusions events <100mls\n",
        "    )\n",
        "    SELECT\n",
        "        cv.icustay_id,\n",
        "        charttime,\n",
        "        sum(amount) AS rbc_volume,\n",
        "    FROM\n",
        "        carevue cv\n",
        "        LEFT JOIN first_adm_offset f ON cv.icustay_id = f.id\n",
        "        AND cv.charttime < DATETIME_ADD(f.outtime, INTERVAL 1 HOUR)\n",
        "    GROUP BY\n",
        "        cv.icustay_id,\n",
        "        cv.charttime\n",
        "),\n",
        "tx AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        TIMESTAMP_SECONDS(60 * DIV(UNIX_SECONDS(TIMESTAMP(charttime)), 60)) AS episode,\n",
        "        --some samples have duplicate readings every 15 minutes - we take an hourly window and average the volume across this window\n",
        "        --doing so reduces errors significantly\n",
        "        MIN(charttime) AS charttime,\n",
        "        --get the first timestamp of each window\n",
        "        AVG(rbc_volume) AS rbc_volume\n",
        "    FROM tx_raw\n",
        "    GROUP BY icustay_id, episode\n",
        "    ORDER BY icustay_id, episode\n",
        "),\n",
        "tx_counts AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        COUNT(charttime) AS tx_episodes,\n",
        "        SUM(rbc_volume) AS rbc_volume,\n",
        "        CEIL(SUM(rbc_volume) / 350) AS rbc_units\n",
        "    FROM tx\n",
        "    WHERE\n",
        "        icustay_id IS NOT NULL\n",
        "    GROUP BY\n",
        "        icustay_id\n",
        "),\n",
        "pivoted_hemoglobin AS (\n",
        "    SELECT\n",
        "        icustay_id,\n",
        "        charttime,\n",
        "        hemoglobin\n",
        "    FROM\n",
        "        pivoted_lab\n",
        "    WHERE\n",
        "        icustay_id IS NOT NULL\n",
        "        AND charttime IS NOT NULL\n",
        "        AND hemoglobin IS NOT NULL\n",
        "    ORDER BY\n",
        "        icustay_id\n",
        ")\n",
        ", tx_hgb_paired AS (\n",
        "        SELECT\n",
        "            w.icustay_id,\n",
        "            w.last_hb_in_window,\n",
        "            MIN(p.hemoglobin) AS hemoglobin,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume,\n",
        "            DATETIME_DIFF(w.tx_offset, w.last_hb_in_window, SECOND) AS delta_tx_hgb_seconds,\n",
        "        FROM\n",
        "            (\n",
        "                SELECT\n",
        "                    p.icustay_id,\n",
        "                    t.charttime AS tx_offset,\n",
        "                    t.rbc_volume,\n",
        "                    MAX(p.charttime) AS last_hb_in_window,\n",
        "                    p.hemoglobin\n",
        "                FROM tx t --`arctic-welder-307905.blood_transfusion.tx` t\n",
        "                    INNER JOIN pivoted_hemoglobin p ON p.icustay_id = t.icustay_id\n",
        "                    AND p.charttime BETWEEN DATETIME_SUB(t.charttime, INTERVAL 6 HOUR)\n",
        "                    AND t.charttime --we search the 6 hours prior to transfusion for minimum hemoglobin levels associated with that transfusion\n",
        "                GROUP BY\n",
        "                    p.icustay_id,\n",
        "                    t.charttime,\n",
        "                    t.rbc_volume,\n",
        "                    p.hemoglobin\n",
        "                ORDER BY\n",
        "                    icustay_id,\n",
        "                    last_hb_in_window\n",
        "            ) w\n",
        "            INNER JOIN pivoted_hemoglobin p ON p.icustay_id = w.icustay_id\n",
        "            AND p.charttime = w.last_hb_in_window\n",
        "        GROUP BY\n",
        "            w.icustay_id,\n",
        "            w.last_hb_in_window,\n",
        "            w.tx_offset,\n",
        "            w.rbc_volume\n",
        "        ORDER BY\n",
        "            icustay_id,\n",
        "             last_hb_in_window,\n",
        "             tx_offset\n",
        ")\n",
        ", tx_hgb_filtered AS (\n",
        "        SELECT\n",
        "            *,\n",
        "            ROW_NUMBER() OVER(x) AS event_number\n",
        "        FROM tx_hgb_paired\n",
        "        WINDOW x AS(\n",
        "                PARTITION BY icustay_id\n",
        "                ORDER BY tx_offset\n",
        "            )\n",
        "        ORDER BY icustay_id\n",
        "\n",
        "),\n",
        "\n",
        "tx_mimic_control AS (SELECT icustay_id, hadm_id, subject_id, charttime, HEMOGLOBIN\n",
        "FROM pivoted_lab\n",
        "WHERE icustay_id NOT IN ((SELECT DISTINCT(icustay_id) FROM tx_hgb_filtered))),\n",
        "\n",
        "tx_mimic_control_hb_not_null AS (SELECT * FROM tx_mimic_control\n",
        "WHERE HEMOGLOBIN IS NOT NULL\n",
        "ORDER BY icustay_id, HEMOGLOBIN),\n",
        "\n",
        "tx_mimic_control_hb_min_all_columns AS (SELECT *,\n",
        "ROW_NUMBER() OVER(PARTITION BY icustay_id ORDER BY HEMOGLOBIN, charttime ASC) AS RowRank\n",
        "FROM tx_mimic_control_hb_not_null),\n",
        "\n",
        " tx_mimic_control_hb_min AS (SELECT icustay_id, MIN(HEMOGLOBIN) as min_hemoglobin\n",
        "  FROM tx_mimic_control_hb_not_null\n",
        "  GROUP BY icustay_id)\n",
        "\n",
        "SELECT icustay_id, subject_id, charttime, HEMOGLOBIN FROM tx_mimic_control_hb_min_all_columns\n",
        "Where RowRank=1\n",
        "ORDER BY icustay_id\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "Hir4kS1_xZER"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Hemoglobins level for control group - mimic3\n",
        "control_mimic3.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 206
        },
        "id": "__uOIrkNy0T_",
        "outputId": "5a30e361-1a5d-4dc5-cee0-99339bc9afb1"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "   icustay_id  subject_id           charttime  HEMOGLOBIN\n",
              "0      200001       55973 2181-11-26 05:36:00         7.3\n",
              "1      200003       27513 2199-08-08 01:41:00         9.6\n",
              "2      200006       10950 2159-09-04 05:21:00         8.7\n",
              "3      200007       20707 2109-02-18 15:22:00        12.8\n",
              "4      200010       11861 2132-08-05 02:22:00         8.6"
            ],
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              "      <th>icustay_id</th>\n",
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              "      <th>HEMOGLOBIN</th>\n",
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              "  <tbody>\n",
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              "      <th>0</th>\n",
              "      <td>200001</td>\n",
              "      <td>55973</td>\n",
              "      <td>2181-11-26 05:36:00</td>\n",
              "      <td>7.3</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>200003</td>\n",
              "      <td>27513</td>\n",
              "      <td>2199-08-08 01:41:00</td>\n",
              "      <td>9.6</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>200006</td>\n",
              "      <td>10950</td>\n",
              "      <td>2159-09-04 05:21:00</td>\n",
              "      <td>8.7</td>\n",
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              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>200007</td>\n",
              "      <td>20707</td>\n",
              "      <td>2109-02-18 15:22:00</td>\n",
              "      <td>12.8</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>200010</td>\n",
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              "      <td>2132-08-05 02:22:00</td>\n",
              "      <td>8.6</td>\n",
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            ]
          },
          "metadata": {},
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        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# MIMIC 4 Control Sepsis"
      ],
      "metadata": {
        "id": "CsuGmjaZ59Il"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "sepsis_mimic4 = client.query(\"\"\"\n",
        "SELECT *\n",
        "FROM `physionet-data.mimic_derived.sepsis3`\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "02862Ns8zfdQ"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "control_mimic4_septic=pd.merge(control_mimic4,sepsis_mimic4,how='inner',on='stay_id')\n",
        "#Septic control mimic 4\n",
        "control_mimic4_septic.head()"
      ],
      "metadata": {
        "id": "mukFj1vmzfdQ",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 444
        },
        "outputId": "1a1b8022-713d-4181-9eba-0aedeb1c8421"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    stay_id  subject_id_x           charttime  HEMOGLOBIN  subject_id_y  \\\n",
              "0  30000484      18421337 2136-01-15 04:28:00         8.1      18421337   \n",
              "1  30000646      12207593 2194-04-29 02:33:00        12.9      12207593   \n",
              "2  30002415      17921898 2126-12-17 10:04:00        10.4      17921898   \n",
              "3  30002654      15978672 2154-10-19 03:34:00         9.4      15978672   \n",
              "4  30002925      10208468 2134-06-06 07:00:00         9.7      10208468   \n",
              "\n",
              "      antibiotic_time        culture_time suspected_infection_time  \\\n",
              "0 2136-01-14 21:00:00 2136-01-14 18:10:00      2136-01-14 18:10:00   \n",
              "1 2194-04-29 07:00:00 2194-04-29 01:00:00      2194-04-29 01:00:00   \n",
              "2 2126-12-17 12:00:00 2126-12-16 15:05:00      2126-12-16 15:05:00   \n",
              "3 2154-10-18 03:00:00 2154-10-17 11:15:00      2154-10-17 11:15:00   \n",
              "4 2134-06-05 04:00:00 2134-06-04 23:17:00      2134-06-04 23:17:00   \n",
              "\n",
              "            sofa_time  sofa_score  respiration  coagulation  liver  \\\n",
              "0 2136-01-14 19:00:00           3            0            0      0   \n",
              "1 2194-04-29 11:00:00           3            2            0      0   \n",
              "2 2126-12-17 12:00:00           4            2            2      0   \n",
              "3 2154-10-18 03:00:00           4            0            0      0   \n",
              "4 2134-06-05 04:00:00           3            0            0      0   \n",
              "\n",
              "   cardiovascular  cns  renal  sepsis3  \n",
              "0               0    3      0     True  \n",
              "1               1    0      0     True  \n",
              "2               0    0      0     True  \n",
              "3               4    0      0     True  \n",
              "4               1    0      2     True  "
            ],
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              "\n",
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              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>stay_id</th>\n",
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              "      <th>HEMOGLOBIN</th>\n",
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              "      <th>respiration</th>\n",
              "      <th>coagulation</th>\n",
              "      <th>liver</th>\n",
              "      <th>cardiovascular</th>\n",
              "      <th>cns</th>\n",
              "      <th>renal</th>\n",
              "      <th>sepsis3</th>\n",
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              "      <th>0</th>\n",
              "      <td>30000484</td>\n",
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              "      <td>2136-01-15 04:28:00</td>\n",
              "      <td>8.1</td>\n",
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              "      <td>2136-01-14 21:00:00</td>\n",
              "      <td>2136-01-14 18:10:00</td>\n",
              "      <td>2136-01-14 18:10:00</td>\n",
              "      <td>2136-01-14 19:00:00</td>\n",
              "      <td>3</td>\n",
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              "      <td>3</td>\n",
              "      <td>0</td>\n",
              "      <td>True</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>30000646</td>\n",
              "      <td>12207593</td>\n",
              "      <td>2194-04-29 02:33:00</td>\n",
              "      <td>12.9</td>\n",
              "      <td>12207593</td>\n",
              "      <td>2194-04-29 07:00:00</td>\n",
              "      <td>2194-04-29 01:00:00</td>\n",
              "      <td>2194-04-29 01:00:00</td>\n",
              "      <td>2194-04-29 11:00:00</td>\n",
              "      <td>3</td>\n",
              "      <td>2</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>1</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>True</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>30002415</td>\n",
              "      <td>17921898</td>\n",
              "      <td>2126-12-17 10:04:00</td>\n",
              "      <td>10.4</td>\n",
              "      <td>17921898</td>\n",
              "      <td>2126-12-17 12:00:00</td>\n",
              "      <td>2126-12-16 15:05:00</td>\n",
              "      <td>2126-12-16 15:05:00</td>\n",
              "      <td>2126-12-17 12:00:00</td>\n",
              "      <td>4</td>\n",
              "      <td>2</td>\n",
              "      <td>2</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>True</td>\n",
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              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>30002654</td>\n",
              "      <td>15978672</td>\n",
              "      <td>2154-10-19 03:34:00</td>\n",
              "      <td>9.4</td>\n",
              "      <td>15978672</td>\n",
              "      <td>2154-10-18 03:00:00</td>\n",
              "      <td>2154-10-17 11:15:00</td>\n",
              "      <td>2154-10-17 11:15:00</td>\n",
              "      <td>2154-10-18 03:00:00</td>\n",
              "      <td>4</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>0</td>\n",
              "      <td>4</td>\n",
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              "      <td>0</td>\n",
              "      <td>True</td>\n",
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              "      <th>4</th>\n",
              "      <td>30002925</td>\n",
              "      <td>10208468</td>\n",
              "      <td>2134-06-06 07:00:00</td>\n",
              "      <td>9.7</td>\n",
              "      <td>10208468</td>\n",
              "      <td>2134-06-05 04:00:00</td>\n",
              "      <td>2134-06-04 23:17:00</td>\n",
              "      <td>2134-06-04 23:17:00</td>\n",
              "      <td>2134-06-05 04:00:00</td>\n",
              "      <td>3</td>\n",
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              "      <td>1</td>\n",
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              "\n",
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              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-0b300a90-f29b-43ce-ad6b-8c8640bcc7f0');\n",
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              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
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              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 18
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#MIMIC 3 Control Sepsis"
      ],
      "metadata": {
        "id": "nNv5EGq2z_9o"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "control_mimic3.rename(columns = {'icustay_id':'stay_id'}, inplace = True)\n",
        "control_mimic3_carevue_septic=pd.merge(control_mimic3,sepsis_mimiciii,how='inner',on='stay_id')\n",
        "#Septic control mimic3\n",
        "control_mimic3_carevue_septic.head()"
      ],
      "metadata": {
        "id": "F2sIwa-l1KJp",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 490
        },
        "outputId": "b75134dd-567d-43b8-fb09-9816f66d06b9"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "   stay_id  subject_id           charttime  HEMOGLOBIN  hadm_id  excluded  \\\n",
              "0   200019       21789 2178-07-10 08:20:00        10.8   112486         1   \n",
              "1   200047       26135 2190-01-31 05:07:00        12.2   159741         1   \n",
              "2   200067       85350 2126-07-01 02:10:00        12.8   122992         1   \n",
              "3   200081       51698 2142-03-04 05:23:00         8.3   190004         1   \n",
              "4   200099       52619 2163-06-22 02:10:00         9.8   175374         1   \n",
              "\n",
              "               intime             outtime    dbsource  \\\n",
              "0 2178-07-08 09:03:12 2178-07-11 10:28:40     carevue   \n",
              "1 2190-01-30 21:47:36 2190-01-31 15:06:57     carevue   \n",
              "2 2126-06-29 18:45:37 2126-07-02 16:00:28  metavision   \n",
              "3 2142-03-01 16:46:10 2142-03-04 18:29:57  metavision   \n",
              "4 2163-06-21 19:49:09 2163-06-23 20:23:11  metavision   \n",
              "\n",
              "  suspected_infection_time_poe  ...  vent sofa  lods sirs qsofa  \\\n",
              "0          2178-07-08 21:51:00  ...     0    5     7    3     2   \n",
              "1          2190-01-30 21:30:00  ...     0    5     1    1     0   \n",
              "2          2126-06-29 20:20:00  ...     0    6     7    3     2   \n",
              "3          2142-02-27 16:00:00  ...     0    2     2    3     2   \n",
              "4          2163-06-21 20:39:00  ...     0    7     1    2     2   \n",
              "\n",
              "   qsofa_sysbp_score  qsofa_gcs_score qsofa_resprate_score  suspicion_poe  \\\n",
              "0                0.0              1.0                  1.0           True   \n",
              "1                NaN              NaN                  NaN           True   \n",
              "2                1.0              NaN                  1.0           True   \n",
              "3                1.0              NaN                  1.0           True   \n",
              "4                1.0              NaN                  1.0           True   \n",
              "\n",
              "  sepsis-3  \n",
              "0        1  \n",
              "1        1  \n",
              "2        1  \n",
              "3        1  \n",
              "4        1  \n",
              "\n",
              "[5 rows x 53 columns]"
            ],
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              "                                                     [key], {});\n",
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              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 19
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# SEPTIC Joining MIMIC 4 (METAVISION) with Mimic 3 (carevue) - FULL SEPTIC COHORT CONTROL"
      ],
      "metadata": {
        "id": "QBjuOx420ahW"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "control_group_septic_full = pd.concat([control_mimic3_carevue_septic,control_mimic4_septic])\n",
        "#FULL SEPTIC GROUP CONTROL\n",
        "control_group_septic_full.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 473
        },
        "outputId": "02414009-67c5-4965-b1b9-50238daf8d60",
        "id": "Z5F3UJVU0ahW"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "   stay_id  subject_id           charttime  HEMOGLOBIN   hadm_id  excluded  \\\n",
              "0   200019     21789.0 2178-07-10 08:20:00        10.8  112486.0       1.0   \n",
              "1   200047     26135.0 2190-01-31 05:07:00        12.2  159741.0       1.0   \n",
              "2   200067     85350.0 2126-07-01 02:10:00        12.8  122992.0       1.0   \n",
              "3   200081     51698.0 2142-03-04 05:23:00         8.3  190004.0       1.0   \n",
              "4   200099     52619.0 2163-06-22 02:10:00         9.8  175374.0       1.0   \n",
              "\n",
              "               intime             outtime    dbsource  \\\n",
              "0 2178-07-08 09:03:12 2178-07-11 10:28:40     carevue   \n",
              "1 2190-01-30 21:47:36 2190-01-31 15:06:57     carevue   \n",
              "2 2126-06-29 18:45:37 2126-07-02 16:00:28  metavision   \n",
              "3 2142-03-01 16:46:10 2142-03-04 18:29:57  metavision   \n",
              "4 2163-06-21 19:49:09 2163-06-23 20:23:11  metavision   \n",
              "\n",
              "  suspected_infection_time_poe  ...  suspected_infection_time sofa_time  \\\n",
              "0          2178-07-08 21:51:00  ...                       NaT       NaT   \n",
              "1          2190-01-30 21:30:00  ...                       NaT       NaT   \n",
              "2          2126-06-29 20:20:00  ...                       NaT       NaT   \n",
              "3          2142-02-27 16:00:00  ...                       NaT       NaT   \n",
              "4          2163-06-21 20:39:00  ...                       NaT       NaT   \n",
              "\n",
              "   sofa_score respiration coagulation  liver  cardiovascular cns  renal  \\\n",
              "0         NaN         NaN         NaN    NaN             NaN NaN    NaN   \n",
              "1         NaN         NaN         NaN    NaN             NaN NaN    NaN   \n",
              "2         NaN         NaN         NaN    NaN             NaN NaN    NaN   \n",
              "3         NaN         NaN         NaN    NaN             NaN NaN    NaN   \n",
              "4         NaN         NaN         NaN    NaN             NaN NaN    NaN   \n",
              "\n",
              "  sepsis3  \n",
              "0     NaN  \n",
              "1     NaN  \n",
              "2     NaN  \n",
              "3     NaN  \n",
              "4     NaN  \n",
              "\n",
              "[5 rows x 67 columns]"
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              "      <td>2126-06-29 20:20:00</td>\n",
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              "      </button>\n",
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              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
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              "          element.innerHTML = '';\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 20
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Next Steps - from here"
      ],
      "metadata": {
        "id": "R2Vomj782h7F"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "- Check all variables in paper\n",
        "- Looking at the probability of transfusion over time ??\n",
        "- Probability of transfusion across gender and across race-ethnicity because those are the ones that we will have to consider when we start looking at the question does transfusion help or not\n",
        "-Use casual inference methodology (TMLE) and multiply robust estimation to estimate the causal effect of transfusion among non bleeding patients with sepsis\n"
      ],
      "metadata": {
        "id": "n_qGwcFQ2l3A"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "#MIMIC 4 ethnicities"
      ],
      "metadata": {
        "id": "J-ZsIQTqU3-u"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "mimic4_ethnicities = client.query(\"\"\"\n",
        "SELECT hadm_id, ethnicity\n",
        "FROM `physionet-data.mimic_core.admissions`\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "cxLXlcz5U1y9"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "mimic4_ethnicities.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 206
        },
        "id": "5iLAOrScWg0q",
        "outputId": "6f007435-a47e-4c28-d886-1fecbff62ac2"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    hadm_id                      ethnicity\n",
              "0  21292863  AMERICAN INDIAN/ALASKA NATIVE\n",
              "1  25693393  AMERICAN INDIAN/ALASKA NATIVE\n",
              "2  25137562  AMERICAN INDIAN/ALASKA NATIVE\n",
              "3  23443808  AMERICAN INDIAN/ALASKA NATIVE\n",
              "4  23324841  AMERICAN INDIAN/ALASKA NATIVE"
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              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
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              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 43
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#MIMIC 3 ethnicities"
      ],
      "metadata": {
        "id": "CmfxSEd9WSwk"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "mimic3_ethnicities = client.query(\"\"\"\n",
        "SELECT hadm_id,ethnicity\n",
        "FROM `physionet-data.mimiciii_clinical.admissions`\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "QNqQtvV5WTW2"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "mimic3_ethnicities.head()"
      ],
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        "colab": {
          "base_uri": "https://localhost:8080/",
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        },
        "id": "CMAcHp3gWZUi",
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      "execution_count": null,
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        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "   hadm_id                       ethnicity\n",
              "0   180546  HISPANIC/LATINO - PUERTO RICAN\n",
              "1   149469  HISPANIC/LATINO - PUERTO RICAN\n",
              "2   153826  HISPANIC/LATINO - PUERTO RICAN\n",
              "3   192349                 ASIAN - CHINESE\n",
              "4   191209  HISPANIC/LATINO - PUERTO RICAN"
            ],
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              "    <tr>\n",
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              "      <td>HISPANIC/LATINO - PUERTO RICAN</td>\n",
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              "    <tr>\n",
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              "      <td>192349</td>\n",
              "      <td>ASIAN - CHINESE</td>\n",
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              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>191209</td>\n",
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              "                                                     [key], {});\n",
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              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 45
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#Merge ethnicities to obtain a full cohort"
      ],
      "metadata": {
        "id": "K-H8Bdz8Wt8j"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "ethnicities = pd.concat([mimic4_ethnicities,mimic3_ethnicities])\n",
        "ethnicities.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 206
        },
        "id": "g0DA1k5PWtXm",
        "outputId": "7a26471f-10d6-427e-b66f-030371e7d9da"
      },
      "execution_count": null,
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        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    hadm_id                      ethnicity\n",
              "0  21292863  AMERICAN INDIAN/ALASKA NATIVE\n",
              "1  25693393  AMERICAN INDIAN/ALASKA NATIVE\n",
              "2  25137562  AMERICAN INDIAN/ALASKA NATIVE\n",
              "3  23443808  AMERICAN INDIAN/ALASKA NATIVE\n",
              "4  23324841  AMERICAN INDIAN/ALASKA NATIVE"
            ],
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              "    <tr>\n",
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              "      <td>AMERICAN INDIAN/ALASKA NATIVE</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>23324841</td>\n",
              "      <td>AMERICAN INDIAN/ALASKA NATIVE</td>\n",
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              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
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              "            + ' to learn more about interactive tables.';\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 46
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "treatment_group_septic_w_ethnicity=treatment_group_septic.merge(ethnicities, on='hadm_id', how='inner')\n",
        "control_group_septic_w_ethnicity=control_group_septic_full.merge(ethnicities, on='hadm_id', how='inner')"
      ],
      "metadata": {
        "id": "UsxDSyF0lBh1"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "len(treatment_group_septic)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Fcw5BIfXpceE",
        "outputId": "c1f7ba42-ee67-4c5d-a5d3-4aa455206ed8"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "8641"
            ]
          },
          "metadata": {},
          "execution_count": 74
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#OLD STUFF TO CHECK"
      ],
      "metadata": {
        "id": "hnfP1CD_ff0S"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Mimic 4 Subject id of patients with more than one ethnicity"
      ],
      "metadata": {
        "id": "9tDOFKG4qW6m"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_multiple_ethnicity_mimic4= client.query(\"\"\"\n",
        "with patients_more_ethnicity as (with t1 as (SELECT DISTINCT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimic_core.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>1)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "distinct_ethnicity_subject_id as (SELECT distinct subject_id, ethnicity FROM `physionet-data.mimic_core.admissions`\n",
        "WHERE subject_id in (Select subject_id from patients_more_ethnicity)\n",
        "order by subject_id),\n",
        "\n",
        "subject_id_more_one_ethnicity as (Select distinct subject_id\n",
        "from distinct_ethnicity_subject_id)\n",
        "\n",
        "Select * from Subject_id_more_one_ethnicity\n",
        "\"\"\").to_dataframe()\n"
      ],
      "metadata": {
        "id": "orhQ6OShqVsv"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#List of subjects id that have listed more ethnicities in the db\n",
        "len(Subject_id_multiple_ethnicity_mimic4)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "jjdvxtBpqvpc",
        "outputId": "2398f44c-376c-42c9-d84b-3953dc24f5d0"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "6333"
            ]
          },
          "metadata": {},
          "execution_count": 44
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_ethnicity_mimic4= client.query(\"\"\"\n",
        "with patients_more_ethnicity as (with t1 as (SELECT DISTINCT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimic_core.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>1)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "distinct_subjectid_ethnicity as (SELECT distinct subject_id, ethnicity FROM `physionet-data.mimic_core.admissions`\n",
        "WHERE subject_id in (Select subject_id from patients_more_ethnicity)\n",
        "order by subject_id)\n",
        "\n",
        "Select * from distinct_subjectid_ethnicity\n",
        "\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "BcUA1RyTsCo_"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_ethnicity_mimic4)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
        },
        "id": "Eftil6EBsZZX",
        "outputId": "8acdd2db-4507-4f74-c99e-19c7cecd9cac"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "       subject_id               ethnicity\n",
              "0        10002013                   WHITE\n",
              "1        10002013                   OTHER\n",
              "2        10002869                 UNKNOWN\n",
              "3        10002869                   WHITE\n",
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    {
      "cell_type": "code",
      "source": [
        "import pandas as pd\n",
        "control_group_septic_full.merge(Subject_id_multiple_ethnicity, on= 'subject_id', how= 'inner' )"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 183
        },
        "id": "2gJxeuSlt1wB",
        "outputId": "08f14c00-1a78-472c-85b6-9e70492f809a"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "error",
          "ename": "NameError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-50-4f2d7e1d6863>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mcontrol_group_septic_full\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmerge\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSubject_id_more_one_ethnicity\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mon\u001b[0m\u001b[0;34m=\u001b[0m \u001b[0;34m'subject_id'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhow\u001b[0m\u001b[0;34m=\u001b[0m \u001b[0;34m'inner'\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m: name 'Subject_id_more_one_ethnicity' is not defined"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd\n",
        "treatment_group_septic.merge(Subject_id_multiple_ethnicity, on= 'subject_id', how= 'inner' )"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
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        "id": "60-LLjVVx1Zo",
        "outputId": "4d13a5e0-86dd-4bef-f7cf-d01c4f264d25"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "error",
          "ename": "NameError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-51-b968c7ea5d90>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mtreatment_group_septic\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmerge\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSubject_id_more_one_ethnicity\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mon\u001b[0m\u001b[0;34m=\u001b[0m \u001b[0;34m'subject_id'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhow\u001b[0m\u001b[0;34m=\u001b[0m \u001b[0;34m'inner'\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m: name 'Subject_id_more_one_ethnicity' is not defined"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#Patients with majority ethnicity tied\n",
        "majority_ethjnicity_tied_mimic4= client.query(\"\"\"\n",
        "with t as (with t1 as (SELECT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimic_core.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>2)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "\n",
        "subjectid_ethnicity as (SELECT subject_id, ethnicity FROM `physionet-data.mimic_core.admissions`\n",
        "WHERE subject_id in (Select subject_id from t)\n",
        "order by subject_id)\n",
        ",\n",
        "subjectid_ethnicity_frequency as (SELECT subject_id, ethnicity, COUNT(*)  as frequency,\n",
        "FROM subjectid_ethnicity\n",
        "GROUP BY subject_id, ethnicity\n",
        "ORDER BY subject_id, frequency)\n",
        ",\n",
        "subjectid_ethnicity_ranked as (SELECT subject_id, ethnicity, frequency,\n",
        "DENSE_RANK() OVER(PARTITION BY subject_id ORDER BY frequency DESC) as most_common_ethnicity\n",
        "FROM subjectid_ethnicity_frequency\n",
        "ORDER BY subject_id, most_common_ethnicity)\n",
        ",\n",
        "duplicate_ethnicity_subjects as (SELECT subject_id, COUNT(*) as duplicate\n",
        "FROM subjectid_ethnicity_ranked\n",
        "WHERE most_common_ethnicity=1\n",
        "GROUP BY subject_id HAVING COUNT(*)>1\n",
        "ORDER BY subject_id)\n",
        "\n",
        "SELECT *\n",
        "FROM subjectid_ethnicity_ranked a\n",
        "INNER JOIN duplicate_ethnicity_subjects b ON a.subject_id=b.subject_id\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "12VrFrDNZ8bC"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# MIMIC3"
      ],
      "metadata": {
        "id": "slI-DdHezFdC"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_more_one_ethnicity_mimic3= client.query(\"\"\"\n",
        "with patients_more_ethnicity as (with t1 as (SELECT DISTINCT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimiciii_clinical.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>1)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "distinct_ethnicity_subject_id as (SELECT distinct subject_id, ethnicity FROM `physionet-data.mimiciii_clinical.admissions`\n",
        "WHERE subject_id in (Select subject_id from patients_more_ethnicity)\n",
        "order by subject_id),\n",
        "\n",
        "subject_id_more_one_ethnicity as (Select distinct subject_id\n",
        "from distinct_ethnicity_subject_id)\n",
        "\n",
        "Select * from Subject_id_more_one_ethnicity\"\"\").to_dataframe()\n"
      ],
      "metadata": {
        "id": "uWEJqlnNzHTC"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Subjects with multiple ethnicities\n",
        "Subject_id_more_one_ethnicity_mimic3"
      ],
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        "colab": {
          "base_uri": "https://localhost:8080/",
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        "outputId": "f69e1120-a1e6-4114-8ea9-f9b5d9d7efe5"
      },
      "execution_count": null,
      "outputs": [
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              "..          ...\n",
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              "\n",
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              "          const element = document.querySelector('#df-c953103f-058d-4ecd-8614-e1a6169f1fb0');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
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              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 53
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_ethnicity_mimic3= client.query(\"\"\"with patients_more_ethnicity as (with t1 as (SELECT DISTINCT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimiciii_clinical.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>1)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "distinct_subjectid_ethnicity as (SELECT distinct subject_id, ethnicity FROM `physionet-data.mimiciii_clinical.admissions`\n",
        "WHERE subject_id in (Select subject_id from patients_more_ethnicity)\n",
        "order by subject_id)\n",
        "\n",
        "Select * from distinct_subjectid_ethnicity\n",
        "\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "nx-07sPYzdxZ"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Retrieve the ethnicities for the patients with multiple ethnicities\n",
        "Subject_id_ethnicity_mimic3"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
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        "id": "84x20-Q50qSN",
        "outputId": "d32d77fc-ee7f-4789-9967-902ea23af89b"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "     subject_id              ethnicity\n",
              "0           191                  ASIAN\n",
              "1           191        ASIAN - CHINESE\n",
              "2           426  UNKNOWN/NOT SPECIFIED\n",
              "3           426                  WHITE\n",
              "4           518                  OTHER\n",
              "..          ...                    ...\n",
              "575       97659                  WHITE\n",
              "576       98347  UNKNOWN/NOT SPECIFIED\n",
              "577       98347                  WHITE\n",
              "578       99088        WHITE - RUSSIAN\n",
              "579       99088                  WHITE\n",
              "\n",
              "[580 rows x 2 columns]"
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              "      <td>ASIAN - CHINESE</td>\n",
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              "      <td>WHITE - RUSSIAN</td>\n",
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              "      <td>99088</td>\n",
              "      <td>WHITE</td>\n",
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              "<p>580 rows × 2 columns</p>\n",
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              "                                                     [key], {});\n",
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              "\n",
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    {
      "cell_type": "code",
      "source": [
        "#Split composite ethnicities into its subsets\n",
        "Subject_id_ethnicity_mimic3[['general ethnicity', 'specific']] = Subject_id_ethnicity_mimic3['ethnicity'].str.split('-', expand=True)"
      ],
      "metadata": {
        "id": "LzUb0nY91Rck"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Dataframe with main ethnicity group for patient with multiple ethnicities\n",
        "general_ethnicity= Subject_id_ethnicity_mimic3[['subject_id','general ethnicity']]\n",
        "general_ethnicity"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
        },
        "id": "oDxt4mwD2L-r",
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      "execution_count": null,
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        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "     subject_id      general ethnicity\n",
              "0           191                  ASIAN\n",
              "1           191                 ASIAN \n",
              "2           426  UNKNOWN/NOT SPECIFIED\n",
              "3           426                  WHITE\n",
              "4           518                  OTHER\n",
              "..          ...                    ...\n",
              "575       97659                  WHITE\n",
              "576       98347  UNKNOWN/NOT SPECIFIED\n",
              "577       98347                  WHITE\n",
              "578       99088                 WHITE \n",
              "579       99088                  WHITE\n",
              "\n",
              "[580 rows x 2 columns]"
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              "                                                     [key], {});\n",
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              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
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              "            + ' to learn more about interactive tables.';\n",
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    },
    {
      "cell_type": "code",
      "source": [
        "#Get rid of empty spaces in the string\n",
        "import pandas as pd\n",
        "general_ethnicity['general ethnicity']=general_ethnicity['general ethnicity'].str.replace(' ', '')\n",
        "# convert series to dataframe\n",
        "general_ethnicity= pd.DataFrame(general_ethnicity)"
      ],
      "metadata": {
        "id": "-0KK3WPr6QMB"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
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        "general_ethnicity"
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      "execution_count": null,
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        {
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          "data": {
            "text/plain": [
              "     subject_id     general ethnicity\n",
              "0           191                 ASIAN\n",
              "1           191                 ASIAN\n",
              "2           426  UNKNOWN/NOTSPECIFIED\n",
              "3           426                 WHITE\n",
              "4           518                 OTHER\n",
              "..          ...                   ...\n",
              "575       97659                 WHITE\n",
              "576       98347  UNKNOWN/NOTSPECIFIED\n",
              "577       98347                 WHITE\n",
              "578       99088                 WHITE\n",
              "579       99088                 WHITE\n",
              "\n",
              "[580 rows x 2 columns]"
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              "      <td>191</td>\n",
              "      <td>ASIAN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>426</td>\n",
              "      <td>UNKNOWN/NOTSPECIFIED</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>426</td>\n",
              "      <td>WHITE</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>518</td>\n",
              "      <td>OTHER</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>575</th>\n",
              "      <td>97659</td>\n",
              "      <td>WHITE</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>576</th>\n",
              "      <td>98347</td>\n",
              "      <td>UNKNOWN/NOTSPECIFIED</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>577</th>\n",
              "      <td>98347</td>\n",
              "      <td>WHITE</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>578</th>\n",
              "      <td>99088</td>\n",
              "      <td>WHITE</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>579</th>\n",
              "      <td>99088</td>\n",
              "      <td>WHITE</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>580 rows × 2 columns</p>\n",
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              "                                                     [key], {});\n",
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              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 59
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#general_ethnicity['general ethnicity'].str.strip()"
      ],
      "metadata": {
        "id": "tzK1GIX25EF9"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "general_ethnicity=general_ethnicity.drop_duplicates()"
      ],
      "metadata": {
        "id": "2vv_yzOt3ZET"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Patients with multiple ethnicity in mimic 3\n",
        "general_ethnicity"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 424
        },
        "id": "C8Z8rqer34vk",
        "outputId": "54845c54-077c-486b-a533-a2b79c3f858e"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "     subject_id     general ethnicity\n",
              "0           191                 ASIAN\n",
              "2           426  UNKNOWN/NOTSPECIFIED\n",
              "3           426                 WHITE\n",
              "4           518                 OTHER\n",
              "5           518         BLACK/AFRICAN\n",
              "..          ...                   ...\n",
              "574       97659  UNKNOWN/NOTSPECIFIED\n",
              "575       97659                 WHITE\n",
              "576       98347  UNKNOWN/NOTSPECIFIED\n",
              "577       98347                 WHITE\n",
              "578       99088                 WHITE\n",
              "\n",
              "[553 rows x 2 columns]"
            ],
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              "      <td>97659</td>\n",
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              "      <td>98347</td>\n",
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              "      <th>578</th>\n",
              "      <td>99088</td>\n",
              "      <td>WHITE</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>553 rows × 2 columns</p>\n",
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              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
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            ]
          },
          "metadata": {},
          "execution_count": 61
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#Patient with majority ethnicity tied in MIMIC-III\n",
        "majority_ethjnicity_tied_mimic3= client.query(\"\"\"\n",
        "--IF WHITE AND NON-WHITE THEN NON-WHITE, IF WHITE AND UNKNOWN THEN WHITE, IF NON-WHITE AND UNKNOWN THEN NON-WHITE\n",
        "--NO PATIENT WITH 3 DIFFERENT CATEGORIES TIED, JUST TIES BETWEEN MAX 2 CATEGORIES\n",
        "WITH admissions_ethnicity_categorized AS (WITH ethnicity_dictionary as (SELECT DISTINCT ethnicity,\n",
        "CASE\n",
        "  WHEN ethnicity LIKE '%WHITE%' THEN 'WHITE'\n",
        "  --WHEN ethnicity LIKE '%ASIAN%' THEN 'ASIAN'\n",
        "  --WHEN ethnicity LIKE '%HISPANIC%' THEN 'HISPANIC'\n",
        "  --WHEN ethnicity LIKE '%BLACK%' THEN 'BLACK'\n",
        "  WHEN ethnicity IN ('PATIENT DECLINED TO ANSWER','UNKNOWN/NOT SPECIFIED','UNABLE TO OBTAIN') THEN 'UNKNOWN'\n",
        "  ELSE 'NON-WHITE'\n",
        "END\n",
        "as ethnicity_categorization\n",
        "FROM `physionet-data.mimiciii_clinical.admissions`)\n",
        "\n",
        "SELECT adm.*, dic.ethnicity_categorization\n",
        "FROM `physionet-data.mimiciii_clinical.admissions` as adm\n",
        "INNER JOIN ethnicity_dictionary dic ON adm.ethnicity=dic.ethnicity)\n",
        ",\n",
        "t as (with t1 as (SELECT cat.subject_id, cat.ethnicity_categorization\n",
        " FROM admissions_ethnicity_categorized cat),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>2)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "\n",
        "subjectid_ethnicity as (SELECT subject_id, ethnicity_categorization FROM admissions_ethnicity_categorized\n",
        "WHERE subject_id in (Select subject_id from t)\n",
        "order by subject_id)\n",
        ",\n",
        "subjectid_ethnicity_frequency as (SELECT subject_id, ethnicity_categorization, COUNT(*)  as frequency,\n",
        "FROM subjectid_ethnicity\n",
        "GROUP BY subject_id, ethnicity_categorization\n",
        "ORDER BY subject_id, frequency)\n",
        ",\n",
        "subjectid_ethnicity_ranked as (SELECT subject_id, ethnicity_categorization, frequency,\n",
        "DENSE_RANK() OVER(PARTITION BY subject_id ORDER BY frequency DESC) as most_common_ethnicity\n",
        "FROM subjectid_ethnicity_frequency\n",
        "ORDER BY subject_id, most_common_ethnicity)\n",
        ",\n",
        "duplicate_ethnicity_subjects as (SELECT subject_id, COUNT(*) as duplicate\n",
        "FROM subjectid_ethnicity_ranked\n",
        "WHERE most_common_ethnicity=1\n",
        "GROUP BY subject_id HAVING COUNT(*)>1\n",
        "ORDER BY subject_id)\n",
        "\n",
        "SELECT *\n",
        "FROM subjectid_ethnicity_ranked a\n",
        "INNER JOIN duplicate_ethnicity_subjects b ON a.subject_id=b.subject_id\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "ATU1g9dmM3n9"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Solve with the previous rule, to solve ties between the majority ethnicities\n",
        "import pandas as pd\n",
        "import numpy as np\n",
        "length=majority_ethjnicity_tied_mimic3['subject_id'].unique()\n",
        "ethnicity_ties_solved = pd.DataFrame(columns=['subject_id', 'ethnicity'], index=range(length.size))\n",
        "k=0\n",
        "j=0\n",
        "for i in length:\n",
        "  ethnicity_list_temp=majority_ethjnicity_tied_mimic3[majority_ethjnicity_tied_mimic3['subject_id']==i]\n",
        "  ethnicity_ties_solved.iloc[k]['subject_id']=length[k]\n",
        "  if (ethnicity_list_temp['ethnicity_categorization'][j]=='NON-WHITE')|(ethnicity_list_temp['ethnicity_categorization'][j+1]=='NON-WHITE'):\n",
        "    ethnicity_ties_solved.iloc[k]['ethnicity']='NON-WHITE'\n",
        "  else:\n",
        "    ethnicity_ties_solved.iloc[k]['ethnicity']='WHITE'\n",
        "  k=k+1\n",
        "  j=j+2\n",
        "ethnicity_ties_solved"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 300
        },
        "id": "guKw5RuLio2F",
        "outputId": "aef8b5c7-222f-4095-9046-327884c96a31"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "  subject_id  ethnicity\n",
              "0      12110  NON-WHITE\n",
              "1      32447  NON-WHITE\n",
              "2      29866  NON-WHITE\n",
              "3       4268  NON-WHITE\n",
              "4       7029  NON-WHITE\n",
              "5      21734      WHITE\n",
              "6      16275  NON-WHITE\n",
              "7      68127  NON-WHITE"
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              "      <td>NON-WHITE</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>68127</td>\n",
              "      <td>NON-WHITE</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "      <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-85766e54-02a2-4489-8bb4-bd9c7a95bf9b')\"\n",
              "              title=\"Convert this dataframe to an interactive table.\"\n",
              "              style=\"display:none;\">\n",
              "        \n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
              "    <path d=\"M0 0h24v24H0V0z\" fill=\"none\"/>\n",
              "    <path d=\"M18.56 5.44l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94zm-11 1L8.5 8.5l.94-2.06 2.06-.94-2.06-.94L8.5 2.5l-.94 2.06-2.06.94zm10 10l.94 2.06.94-2.06 2.06-.94-2.06-.94-.94-2.06-.94 2.06-2.06.94z\"/><path d=\"M17.41 7.96l-1.37-1.37c-.4-.4-.92-.59-1.43-.59-.52 0-1.04.2-1.43.59L10.3 9.45l-7.72 7.72c-.78.78-.78 2.05 0 2.83L4 21.41c.39.39.9.59 1.41.59.51 0 1.02-.2 1.41-.59l7.78-7.78 2.81-2.81c.8-.78.8-2.07 0-2.86zM5.41 20L4 18.59l7.72-7.72 1.47 1.35L5.41 20z\"/>\n",
              "  </svg>\n",
              "      </button>\n",
              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
              "      width: 32px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
              "    }\n",
              "  </style>\n",
              "\n",
              "      <script>\n",
              "        const buttonEl =\n",
              "          document.querySelector('#df-85766e54-02a2-4489-8bb4-bd9c7a95bf9b button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-85766e54-02a2-4489-8bb4-bd9c7a95bf9b');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 63
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "ar7uF9zFqSqD"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# June 06 2022"
      ],
      "metadata": {
        "id": "_r0eKfQj7YaO"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_ethnicity_mimic3= client.query(\"\"\"with patients_more_ethnicity as (with t1 as (SELECT DISTINCT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimiciii_clinical.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq>1)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "distinct_subjectid_ethnicity as (SELECT distinct subject_id, ethnicity FROM `physionet-data.mimiciii_clinical.admissions`\n",
        "WHERE subject_id in (Select subject_id from patients_more_ethnicity)\n",
        "order by subject_id)\n",
        "\n",
        "Select * from distinct_subjectid_ethnicity\n",
        "\n",
        "\"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "30M-Xm6Q7ZQY"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "Subject_id_one_ethnicity_mimic3= client.query(\"\"\"with patients_one_ethnicity as (with t1 as (SELECT DISTINCT a.subject_id, a.ethnicity\n",
        " FROM `physionet-data.mimiciii_clinical.admissions` a),\n",
        "\n",
        "t3 as (SELECT subject_id, COUNT(*) AS freq\n",
        "from t1\n",
        "group by subject_id\n",
        "having freq=1)\n",
        "\n",
        "Select * from t3),\n",
        "\n",
        "distinct_subjectid_ethnicity as (SELECT distinct subject_id, ethnicity FROM `physionet-data.mimiciii_clinical.admissions`\n",
        "WHERE subject_id in (Select subject_id from patients_one_ethnicity)\n",
        "order by subject_id)\n",
        "\n",
        "Select subject_id,\n",
        "CASE\n",
        "  WHEN ethnicity LIKE '%WHITE%' THEN 'WHITE'\n",
        "  WHEN ethnicity IN ('PATIENT DECLINED TO ANSWER','UNKNOWN/NOT SPECIFIED','UNABLE TO OBTAIN') THEN 'UNKNOWN'\n",
        "  ELSE 'NON-WHITE'\n",
        "END\n",
        "as ethnicity\n",
        " from distinct_subjectid_ethnicity\n",
        " \"\"\").to_dataframe()"
      ],
      "metadata": {
        "id": "bpmgNTysEVk-"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#Uniforming white rows\n",
        "Subject_id_ethnicity_mimic3.loc[Subject_id_ethnicity_mimic3['ethnicity'].str.contains('WHITE'), 'ethnicity'] = 'WHITE'"
      ],
      "metadata": {
        "id": "Z4AG_7x49U5K"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "8bdIpPtk_Qwu"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}