loop_proximity_check_R.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "import csv\n",
    "import os\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import sklearn.metrics as mm\n",
    "import sys\n",
    "# sir_inference imports\n",
    "from sir_model import FastProximityModel, patient_zeros_states\n",
    "from ranking import csr_to_list\n",
    "import os.path\n",
    "from os import path\n",
    "N=50000\n",
    "## new try with 100 spreaders\n",
    "N_patient_zero = 20;\n",
    "lamb = 0.03;\n",
    "mu = 0.05;\n",
    "scale=1.0; # Easy Case\n",
    "T=100;\n",
    "seed=2\n",
    "location=\"networks\"\n",
    "# SIR parameters\n",
    "t1 = 10;\n",
    "#seed=int();"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "seed = 2\n",
      "Loading model from networks/interactions_proximity_N50K_s1.0_T100_lamb0.03_s2.csv\n",
      "Load Proximity model\n",
      "Loading transmissions from networks/interactions_proximity_N50K_s1.0_T100_lamb0.03_s2.csv\n",
      "Loading took 28.8s\n",
      "Running SIR simulation\n",
      "t = 0 / 100\n",
      "t = 50 / 100\n",
      "Save plain dynamics\n"
     ]
    }
   ],
   "source": [
    "## import sys\n",
    "from time import time\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import os.path\n",
    "from os import path\n",
    "from scenario import Scenario_check_R\n",
    "from sir_model import EpidemicModel, patient_zeros_states, symptomatic_individuals\n",
    "from ranking import RANKINGS\n",
    "log_fname=\"interactions_proximity_N%dK_s%.1f_T%d_lamb%.2f_s%d.csv\"%(N/1000,scale,T,lamb,seed)\n",
    "csv_file=location+\"/\"+log_fname\n",
    "print(\"seed = %d\"%seed, flush=True)\n",
    "np.random.seed(seed);\n",
    "if path.exists(csv_file): print(\"Loading model from %s\"%csv_file)\n",
    "else:\n",
    "    print(\"Could not find the file! Was looking for \\n \"+csv_file+\"\\n Bye-Bye\")\n",
    "    sys.exit()\n",
    "print(\"Load Proximity model\", flush=True)\n",
    "tic = time()\n",
    "model = EpidemicModel(initial_states=np.zeros(N), x_pos=np.zeros(N), y_pos=np.zeros(N))\n",
    "model.load_transmissions(csv_file)\n",
    "model.recover_probas = mu*np.ones(N)\n",
    "print(f\"Loading took {time()-tic:.1f}s\",flush=True)\n",
    "model.initial_states = patient_zeros_states(N, N_patient_zero)\n",
    "model.time_evolution(model.recover_probas, model.transmissions, print_every=50)\n",
    "t_max = len(model.transmissions)\n",
    "print(\"Save plain dynamics\", flush=True)\n",
    "db = pd.DataFrame()\n",
    "db[\"S\"] = np.sum(model.states==0,axis=1)\n",
    "db[\"I\"] = np.sum(model.states==1,axis=1)\n",
    "db[\"R\"] = np.sum(model.states==2,axis=1)\n",
    "db.to_csv(\"csv/Proximity_N%dK_T%d_s1_pz%d_mu%.2f_l%.2f_seed%d.csv\"%(N/1000,T,N_patient_zero,mu,lamb,seed),\n",
    "          index=False, sep=\"\\t\")\n",
    "del db\n",
    "model.initial_states = model.states[t1]\n",
    "model.states = model.states[t1:]\n",
    "model.transmissions = model.transmissions[t1:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "# trac parameters\n",
    "trac_tau = 5;\n",
    "# MF parameters\n",
    "MF_tau = 5;\n",
    "MF_delta = 15;\n",
    "# observation parameters\n",
    "n_ranking = 100\n",
    "p_untracked=0\n",
    "#seed = int(sys.argv[2]);\n",
    "#seeds for running [32,123,456]\n",
    "#seed=int(sys.argv[1]);\n",
    "################################################\n",
    "\n",
    "intervention_options=dict(quarantine_time=T-t1)\n",
    "observation_options=dict(n_random=0,n_infected=0,n_ranking=n_ranking, p_symptomatic=0.5, tau=5, p_untracked=p_untracked)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using ranking_random to rank\n",
      "Using seed=3\n",
      "Selecting 0/50000 untracked individuals\n",
      "t = 0 / 90\n",
      "state: S:49924, I:60, R:16 I+R:76\n",
      "obser: S:100, I:0, R:0, I+R:0\n",
      "free birds: 60\n",
      "t = 1 / 90\n",
      "state: S:49916, I:66, R:18 I+R:84\n",
      "obser: S:200, I:0, R:0, I+R:0\n",
      "free birds: 66\n",
      "t = 2 / 90\n",
      "state: S:49911, I:69, R:20 I+R:89\n",
      "obser: S:300, I:0, R:0, I+R:0\n",
      "free birds: 69\n",
      "t = 3 / 90\n",
      "state: S:49904, I:73, R:23 I+R:96\n",
      "obser: S:400, I:0, R:0, I+R:0\n",
      "free birds: 73\n",
      "t = 4 / 90\n",
      "state: S:49890, I:84, R:26 I+R:110\n",
      "obser: S:500, I:0, R:0, I+R:0\n",
      "free birds: 84\n",
      "t = 5 / 90\n",
      "state: S:49875, I:97, R:28 I+R:125\n",
      "obser: S:600, I:0, R:0, I+R:0\n",
      "free birds: 97\n",
      "t = 6 / 90\n",
      "state: S:49861, I:104, R:35 I+R:139\n",
      "obser: S:700, I:3, R:1, I+R:4\n",
      "free birds: 101\n",
      "t = 7 / 90\n",
      "state: S:49842, I:118, R:40 I+R:158\n",
      "obser: S:800, I:5, R:1, I+R:6\n",
      "free birds: 113\n",
      "t = 8 / 90\n",
      "state: S:49821, I:134, R:45 I+R:179\n",
      "obser: S:899, I:9, R:1, I+R:10\n",
      "free birds: 125\n",
      "t = 9 / 90\n",
      "state: S:49804, I:144, R:52 I+R:196\n",
      "obser: S:999, I:13, R:4, I+R:17\n",
      "free birds: 131\n",
      "t = 10 / 90\n",
      "state: S:49788, I:153, R:59 I+R:212\n",
      "obser: S:1099, I:18, R:5, I+R:23\n",
      "free birds: 136\n",
      "t = 11 / 90\n",
      "state: S:49769, I:165, R:66 I+R:231\n",
      "obser: S:1197, I:23, R:9, I+R:32\n",
      "free birds: 143\n",
      "t = 12 / 90\n",
      "state: S:49758, I:164, R:78 I+R:242\n",
      "obser: S:1297, I:28, R:13, I+R:41\n",
      "free birds: 139\n",
      "t = 13 / 90\n",
      "state: S:49736, I:178, R:86 I+R:264\n",
      "obser: S:1396, I:36, R:16, I+R:52\n",
      "free birds: 148\n",
      "t = 14 / 90\n",
      "state: S:49725, I:181, R:94 I+R:275\n",
      "obser: S:1496, I:43, R:17, I+R:60\n",
      "free birds: 146\n",
      "t = 15 / 90\n",
      "state: S:49710, I:188, R:102 I+R:290\n",
      "obser: S:1595, I:49, R:19, I+R:68\n",
      "free birds: 148\n",
      "t = 16 / 90\n",
      "state: S:49692, I:192, R:116 I+R:308\n",
      "obser: S:1694, I:55, R:22, I+R:77\n",
      "free birds: 148\n",
      "t = 17 / 90\n",
      "state: S:49676, I:199, R:125 I+R:324\n",
      "obser: S:1793, I:60, R:23, I+R:83\n",
      "free birds: 151\n",
      "t = 18 / 90\n",
      "state: S:49661, I:201, R:138 I+R:339\n",
      "obser: S:1893, I:69, R:25, I+R:94\n",
      "free birds: 148\n",
      "t = 19 / 90\n",
      "state: S:49642, I:204, R:154 I+R:358\n",
      "obser: S:1991, I:71, R:30, I+R:101\n",
      "free birds: 150\n",
      "t = 20 / 90\n",
      "state: S:49618, I:219, R:163 I+R:382\n",
      "obser: S:2090, I:76, R:33, I+R:109\n",
      "free birds: 162\n",
      "t = 21 / 90\n",
      "state: S:49596, I:229, R:175 I+R:404\n",
      "obser: S:2190, I:81, R:37, I+R:118\n",
      "free birds: 170\n",
      "t = 22 / 90\n",
      "state: S:49585, I:229, R:186 I+R:415\n",
      "obser: S:2289, I:87, R:40, I+R:127\n",
      "free birds: 166\n",
      "t = 23 / 90\n",
      "state: S:49563, I:238, R:199 I+R:437\n",
      "obser: S:2389, I:93, R:41, I+R:134\n",
      "free birds: 173\n",
      "t = 24 / 90\n",
      "state: S:49542, I:247, R:211 I+R:458\n",
      "obser: S:2489, I:101, R:42, I+R:143\n",
      "free birds: 178\n",
      "t = 25 / 90\n",
      "state: S:49518, I:265, R:217 I+R:482\n",
      "obser: S:2589, I:109, R:46, I+R:155\n",
      "free birds: 190\n",
      "t = 26 / 90\n",
      "state: S:49494, I:273, R:233 I+R:506\n",
      "obser: S:2687, I:122, R:46, I+R:168\n",
      "free birds: 190\n",
      "t = 27 / 90\n",
      "state: S:49472, I:281, R:247 I+R:528\n",
      "obser: S:2786, I:126, R:48, I+R:174\n",
      "free birds: 200\n",
      "t = 28 / 90\n",
      "state: S:49439, I:301, R:260 I+R:561\n",
      "obser: S:2886, I:135, R:50, I+R:185\n",
      "free birds: 213\n",
      "t = 29 / 90\n",
      "state: S:49418, I:312, R:270 I+R:582\n",
      "obser: S:2985, I:144, R:52, I+R:196\n",
      "free birds: 218\n",
      "t = 30 / 90\n",
      "state: S:49402, I:315, R:283 I+R:598\n",
      "obser: S:3085, I:155, R:53, I+R:208\n",
      "free birds: 211\n",
      "t = 31 / 90\n",
      "state: S:49375, I:323, R:302 I+R:625\n",
      "obser: S:3184, I:166, R:55, I+R:221\n",
      "free birds: 217\n",
      "t = 32 / 90\n",
      "state: S:49352, I:334, R:314 I+R:648\n",
      "obser: S:3284, I:175, R:57, I+R:232\n",
      "free birds: 225\n",
      "t = 33 / 90\n",
      "state: S:49332, I:342, R:326 I+R:668\n",
      "obser: S:3382, I:190, R:60, I+R:250\n",
      "free birds: 220\n",
      "t = 34 / 90\n",
      "state: S:49306, I:351, R:343 I+R:694\n",
      "obser: S:3481, I:197, R:63, I+R:260\n",
      "free birds: 230\n",
      "t = 35 / 90\n",
      "state: S:49274, I:365, R:361 I+R:726\n",
      "obser: S:3581, I:202, R:66, I+R:268\n",
      "free birds: 243\n",
      "t = 36 / 90\n",
      "state: S:49253, I:369, R:378 I+R:747\n",
      "obser: S:3679, I:212, R:70, I+R:282\n",
      "free birds: 244\n",
      "t = 37 / 90\n",
      "state: S:49226, I:386, R:388 I+R:774\n",
      "obser: S:3777, I:224, R:71, I+R:295\n",
      "free birds: 251\n",
      "t = 38 / 90\n",
      "state: S:49200, I:392, R:408 I+R:800\n",
      "obser: S:3873, I:229, R:80, I+R:309\n",
      "free birds: 256\n",
      "t = 39 / 90\n",
      "state: S:49171, I:403, R:426 I+R:829\n",
      "obser: S:3971, I:238, R:86, I+R:324\n",
      "free birds: 262\n",
      "t = 40 / 90\n",
      "state: S:49132, I:423, R:445 I+R:868\n",
      "obser: S:4068, I:252, R:91, I+R:343\n",
      "free birds: 273\n",
      "t = 41 / 90\n",
      "state: S:49108, I:415, R:477 I+R:892\n",
      "obser: S:4168, I:259, R:93, I+R:352\n",
      "free birds: 271\n",
      "t = 42 / 90\n",
      "state: S:49083, I:421, R:496 I+R:917\n",
      "obser: S:4268, I:271, R:94, I+R:365\n",
      "free birds: 273\n",
      "t = 43 / 90\n",
      "state: S:49061, I:424, R:515 I+R:939\n",
      "obser: S:4366, I:277, R:103, I+R:380\n",
      "free birds: 275\n",
      "t = 44 / 90\n",
      "state: S:49041, I:423, R:536 I+R:959\n",
      "obser: S:4465, I:287, R:108, I+R:395\n",
      "free birds: 273\n",
      "t = 45 / 90\n",
      "state: S:49012, I:434, R:554 I+R:988\n",
      "obser: S:4561, I:302, R:116, I+R:418\n",
      "free birds: 274\n",
      "t = 46 / 90\n",
      "state: S:48988, I:436, R:576 I+R:1012\n",
      "obser: S:4659, I:315, R:117, I+R:432\n",
      "free birds: 271\n",
      "t = 47 / 90\n",
      "state: S:48959, I:444, R:597 I+R:1041\n",
      "obser: S:4758, I:324, R:121, I+R:445\n",
      "free birds: 283\n",
      "t = 48 / 90\n",
      "state: S:48921, I:466, R:613 I+R:1079\n",
      "obser: S:4856, I:332, R:126, I+R:458\n",
      "free birds: 301\n",
      "t = 49 / 90\n",
      "state: S:48899, I:464, R:637 I+R:1101\n",
      "obser: S:4953, I:343, R:128, I+R:471\n",
      "free birds: 298\n",
      "t = 50 / 90\n",
      "state: S:48870, I:465, R:665 I+R:1130\n",
      "obser: S:5051, I:355, R:132, I+R:487\n",
      "free birds: 297\n",
      "t = 51 / 90\n",
      "state: S:48836, I:472, R:692 I+R:1164\n",
      "obser: S:5147, I:365, R:138, I+R:503\n",
      "free birds: 306\n",
      "t = 52 / 90\n",
      "state: S:48797, I:494, R:709 I+R:1203\n",
      "obser: S:5245, I:376, R:143, I+R:519\n",
      "free birds: 320\n",
      "t = 53 / 90\n",
      "state: S:48759, I:508, R:733 I+R:1241\n",
      "obser: S:5344, I:389, R:149, I+R:538\n",
      "free birds: 326\n",
      "t = 54 / 90\n",
      "state: S:48726, I:515, R:759 I+R:1274\n",
      "obser: S:5444, I:396, R:153, I+R:549\n",
      "free birds: 335\n",
      "t = 55 / 90\n",
      "state: S:48684, I:530, R:786 I+R:1316\n",
      "obser: S:5540, I:411, R:156, I+R:567\n",
      "free birds: 340\n",
      "t = 56 / 90\n",
      "state: S:48638, I:554, R:808 I+R:1362\n",
      "obser: S:5636, I:427, R:161, I+R:588\n",
      "free birds: 358\n",
      "t = 57 / 90\n",
      "state: S:48603, I:559, R:838 I+R:1397\n",
      "obser: S:5735, I:438, R:169, I+R:607\n",
      "free birds: 357\n",
      "t = 58 / 90\n",
      "state: S:48573, I:564, R:863 I+R:1427\n",
      "obser: S:5834, I:452, R:175, I+R:627\n",
      "free birds: 356\n",
      "t = 59 / 90\n",
      "state: S:48535, I:569, R:896 I+R:1465\n",
      "obser: S:5933, I:464, R:180, I+R:644\n",
      "free birds: 356\n",
      "t = 60 / 90\n",
      "state: S:48498, I:577, R:925 I+R:1502\n",
      "obser: S:6031, I:480, R:187, I+R:667\n",
      "free birds: 360\n",
      "t = 61 / 90\n",
      "state: S:48453, I:597, R:950 I+R:1547\n",
      "obser: S:6129, I:497, R:195, I+R:692\n",
      "free birds: 376\n",
      "t = 62 / 90\n",
      "state: S:48419, I:599, R:982 I+R:1581\n",
      "obser: S:6229, I:508, R:201, I+R:709\n",
      "free birds: 377\n",
      "t = 63 / 90\n",
      "state: S:48369, I:625, R:1006 I+R:1631\n",
      "obser: S:6328, I:515, R:210, I+R:725\n",
      "free birds: 405\n",
      "t = 64 / 90\n",
      "state: S:48333, I:630, R:1037 I+R:1667\n",
      "obser: S:6426, I:530, R:216, I+R:746\n",
      "free birds: 409\n",
      "t = 65 / 90\n",
      "state: S:48302, I:632, R:1066 I+R:1698\n",
      "obser: S:6525, I:547, R:218, I+R:765\n",
      "free birds: 400\n",
      "t = 66 / 90\n",
      "state: S:48270, I:622, R:1108 I+R:1730\n",
      "obser: S:6624, I:562, R:226, I+R:788\n",
      "free birds: 388\n",
      "t = 67 / 90\n",
      "state: S:48230, I:636, R:1134 I+R:1770\n",
      "obser: S:6722, I:574, R:233, I+R:807\n",
      "free birds: 396\n",
      "t = 68 / 90\n",
      "state: S:48191, I:652, R:1157 I+R:1809\n",
      "obser: S:6821, I:592, R:241, I+R:833\n",
      "free birds: 401\n",
      "t = 69 / 90\n",
      "state: S:48156, I:653, R:1191 I+R:1844\n",
      "obser: S:6919, I:606, R:247, I+R:853\n",
      "free birds: 399\n",
      "t = 70 / 90\n",
      "state: S:48131, I:641, R:1228 I+R:1869\n",
      "obser: S:7016, I:616, R:255, I+R:871\n",
      "free birds: 388\n",
      "t = 71 / 90\n",
      "state: S:48081, I:655, R:1264 I+R:1919\n",
      "obser: S:7112, I:630, R:261, I+R:891\n",
      "free birds: 404\n",
      "t = 72 / 90\n",
      "state: S:48034, I:674, R:1292 I+R:1966\n",
      "obser: S:7209, I:650, R:264, I+R:914\n",
      "free birds: 419\n",
      "t = 73 / 90\n",
      "state: S:47990, I:680, R:1330 I+R:2010\n",
      "obser: S:7307, I:664, R:271, I+R:935\n",
      "free birds: 428\n",
      "t = 74 / 90\n",
      "state: S:47955, I:678, R:1367 I+R:2045\n",
      "obser: S:7405, I:676, R:278, I+R:954\n",
      "free birds: 422\n",
      "t = 75 / 90\n",
      "state: S:47915, I:678, R:1407 I+R:2085\n",
      "obser: S:7504, I:683, R:284, I+R:967\n",
      "free birds: 431\n",
      "t = 76 / 90\n",
      "state: S:47882, I:671, R:1447 I+R:2118\n",
      "obser: S:7604, I:700, R:292, I+R:992\n",
      "free birds: 420\n",
      "t = 77 / 90\n",
      "state: S:47849, I:673, R:1478 I+R:2151\n",
      "obser: S:7700, I:713, R:306, I+R:1019\n",
      "free birds: 418\n",
      "t = 78 / 90\n",
      "state: S:47807, I:680, R:1513 I+R:2193\n",
      "obser: S:7797, I:733, R:311, I+R:1044\n",
      "free birds: 418\n",
      "t = 79 / 90\n",
      "state: S:47763, I:688, R:1549 I+R:2237\n",
      "obser: S:7894, I:747, R:317, I+R:1064\n",
      "free birds: 429\n",
      "t = 80 / 90\n",
      "state: S:47720, I:695, R:1585 I+R:2280\n",
      "obser: S:7991, I:764, R:323, I+R:1087\n",
      "free birds: 434\n",
      "t = 81 / 90\n",
      "state: S:47672, I:717, R:1611 I+R:2328\n",
      "obser: S:8090, I:778, R:326, I+R:1104\n",
      "free birds: 452\n",
      "t = 82 / 90\n",
      "state: S:47631, I:716, R:1653 I+R:2369\n",
      "obser: S:8187, I:793, R:330, I+R:1123\n",
      "free birds: 450\n",
      "t = 83 / 90\n",
      "state: S:47591, I:727, R:1682 I+R:2409\n",
      "obser: S:8282, I:812, R:337, I+R:1149\n",
      "free birds: 451\n",
      "t = 84 / 90\n",
      "state: S:47557, I:719, R:1724 I+R:2443\n",
      "obser: S:8380, I:830, R:343, I+R:1173\n",
      "free birds: 437\n",
      "t = 85 / 90\n",
      "state: S:47513, I:721, R:1766 I+R:2487\n",
      "obser: S:8478, I:840, R:356, I+R:1196\n",
      "free birds: 445\n",
      "t = 86 / 90\n",
      "state: S:47480, I:727, R:1793 I+R:2520\n",
      "obser: S:8573, I:861, R:363, I+R:1224\n",
      "free birds: 440\n",
      "t = 87 / 90\n",
      "state: S:47447, I:724, R:1829 I+R:2553\n",
      "obser: S:8669, I:875, R:373, I+R:1248\n",
      "free birds: 439\n",
      "t = 88 / 90\n",
      "state: S:47417, I:718, R:1865 I+R:2583\n",
      "obser: S:8768, I:890, R:378, I+R:1268\n",
      "free birds: 433\n",
      "t = 89 / 90\n",
      "state: S:47392, I:709, R:1899 I+R:2608\n",
      "obser: S:8862, I:904, R:387, I+R:1291\n",
      "free birds: 423\n",
      "Save random strategy\n"
     ]
    }
   ],
   "source": [
    "import imp\n",
    "import scenario\n",
    "imp.reload(scenario)\n",
    "from scenario import Scenario_check_R\n",
    "##### RANDOM SCENARIO #######\n",
    "scenario_rnd = Scenario_check_R(\n",
    "    model, seed=seed+1, \n",
    "    ranking_options=dict(ranking=RANKINGS[\"random\"]),\n",
    "    observation_options=observation_options,\n",
    "    intervention_options=intervention_options\n",
    ")\n",
    "scenario_rnd.run(t_max-t1,  print_every = 1)\n",
    "print(\"Save random strategy\", flush=True)\n",
    "scenario_rnd.counts.to_csv(\"csv/Proximity_N%dK_T%d_s1_ti%d_pz%d_mu%.2f_l%.2f_seed%d_obs%d_rnd.csv\"%(N/1000,T,t1,N_patient_zero,mu,lamb,seed,n_ranking),\n",
    "          index=False, sep=\"\\t\")\n",
    "del scenario_rnd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using ranking_tracing to rank\n",
      "Using seed=3\n",
      "Selecting 0/50000 untracked individuals\n",
      "t = 0 / 90\n",
      "state: S:49924, I:60, R:16 I+R:76\n",
      "obser: S:100, I:0, R:0, I+R:0\n",
      "free birds: 60\n",
      "t = 1 / 90\n",
      "state: S:49916, I:66, R:18 I+R:84\n",
      "obser: S:200, I:0, R:0, I+R:0\n",
      "free birds: 66\n",
      "t = 2 / 90\n",
      "state: S:49911, I:69, R:20 I+R:89\n",
      "obser: S:300, I:0, R:0, I+R:0\n",
      "free birds: 69\n",
      "t = 3 / 90\n",
      "state: S:49904, I:73, R:23 I+R:96\n",
      "obser: S:400, I:0, R:0, I+R:0\n",
      "free birds: 73\n",
      "t = 4 / 90\n",
      "state: S:49890, I:84, R:26 I+R:110\n",
      "obser: S:500, I:0, R:0, I+R:0\n",
      "free birds: 84\n",
      "t = 5 / 90\n",
      "state: S:49875, I:97, R:28 I+R:125\n",
      "obser: S:600, I:0, R:0, I+R:0\n",
      "free birds: 97\n",
      "t = 6 / 90\n",
      "state: S:49862, I:104, R:34 I+R:138\n",
      "obser: S:700, I:4, R:0, I+R:4\n",
      "free birds: 100\n",
      "t = 7 / 90\n",
      "state: S:49853, I:109, R:38 I+R:147\n",
      "obser: S:788, I:12, R:6, I+R:18\n",
      "free birds: 97\n",
      "t = 8 / 90\n",
      "state: S:49829, I:127, R:44 I+R:171\n",
      "obser: S:876, I:19, R:14, I+R:33\n",
      "free birds: 108\n",
      "t = 9 / 90\n",
      "state: S:49811, I:140, R:49 I+R:189\n",
      "obser: S:958, I:34, R:24, I+R:58\n",
      "free birds: 106\n",
      "t = 10 / 90\n",
      "state: S:49797, I:143, R:60 I+R:203\n",
      "obser: S:1033, I:53, R:35, I+R:88\n",
      "free birds: 92\n",
      "t = 11 / 90\n",
      "state: S:49785, I:140, R:75 I+R:215\n",
      "obser: S:1108, I:69, R:47, I+R:116\n",
      "free birds: 81\n",
      "t = 12 / 90\n",
      "state: S:49768, I:152, R:80 I+R:232\n",
      "obser: S:1187, I:79, R:61, I+R:140\n",
      "free birds: 85\n",
      "t = 13 / 90\n",
      "state: S:49757, I:155, R:88 I+R:243\n",
      "obser: S:1268, I:86, R:80, I+R:166\n",
      "free birds: 84\n",
      "t = 14 / 90\n",
      "state: S:49746, I:156, R:98 I+R:254\n",
      "obser: S:1349, I:94, R:95, I+R:189\n",
      "free birds: 82\n",
      "t = 15 / 90\n",
      "state: S:49730, I:166, R:104 I+R:270\n",
      "obser: S:1434, I:102, R:107, I+R:209\n",
      "free birds: 87\n",
      "t = 16 / 90\n",
      "state: S:49721, I:162, R:117 I+R:279\n",
      "obser: S:1523, I:109, R:116, I+R:225\n",
      "free birds: 82\n",
      "t = 17 / 90\n",
      "state: S:49710, I:166, R:124 I+R:290\n",
      "obser: S:1613, I:121, R:121, I+R:242\n",
      "free birds: 78\n",
      "t = 18 / 90\n",
      "state: S:49697, I:170, R:133 I+R:303\n",
      "obser: S:1703, I:129, R:128, I+R:257\n",
      "free birds: 80\n",
      "t = 19 / 90\n",
      "state: S:49686, I:176, R:138 I+R:314\n",
      "obser: S:1796, I:134, R:133, I+R:267\n",
      "free birds: 82\n",
      "t = 20 / 90\n",
      "state: S:49673, I:181, R:146 I+R:327\n",
      "obser: S:1888, I:142, R:138, I+R:280\n",
      "free birds: 86\n",
      "t = 21 / 90\n",
      "state: S:49661, I:189, R:150 I+R:339\n",
      "obser: S:1972, I:153, R:146, I+R:299\n",
      "free birds: 85\n",
      "t = 22 / 90\n",
      "state: S:49647, I:195, R:158 I+R:353\n",
      "obser: S:2057, I:162, R:155, I+R:317\n",
      "free birds: 85\n",
      "t = 23 / 90\n",
      "state: S:49637, I:196, R:167 I+R:363\n",
      "obser: S:2139, I:177, R:164, I+R:341\n",
      "free birds: 76\n",
      "t = 24 / 90\n",
      "state: S:49630, I:193, R:177 I+R:370\n",
      "obser: S:2222, I:187, R:173, I+R:360\n",
      "free birds: 69\n",
      "t = 25 / 90\n",
      "state: S:49624, I:189, R:187 I+R:376\n",
      "obser: S:2302, I:196, R:189, I+R:385\n",
      "free birds: 60\n",
      "t = 26 / 90\n",
      "state: S:49611, I:193, R:196 I+R:389\n",
      "obser: S:2381, I:204, R:205, I+R:409\n",
      "free birds: 64\n",
      "t = 27 / 90\n",
      "state: S:49600, I:197, R:203 I+R:400\n",
      "obser: S:2456, I:213, R:227, I+R:440\n",
      "free birds: 64\n",
      "t = 28 / 90\n",
      "state: S:49591, I:197, R:212 I+R:409\n",
      "obser: S:2540, I:216, R:241, I+R:457\n",
      "free birds: 69\n",
      "t = 29 / 90\n",
      "state: S:49574, I:203, R:223 I+R:426\n",
      "obser: S:2621, I:219, R:258, I+R:477\n",
      "free birds: 78\n",
      "t = 30 / 90\n",
      "state: S:49563, I:202, R:235 I+R:437\n",
      "obser: S:2707, I:224, R:270, I+R:494\n",
      "free birds: 77\n",
      "t = 31 / 90\n",
      "state: S:49550, I:210, R:240 I+R:450\n",
      "obser: S:2792, I:234, R:281, I+R:515\n",
      "free birds: 78\n",
      "t = 32 / 90\n",
      "state: S:49537, I:215, R:248 I+R:463\n",
      "obser: S:2872, I:249, R:289, I+R:538\n",
      "free birds: 72\n",
      "t = 33 / 90\n",
      "state: S:49527, I:211, R:262 I+R:473\n",
      "obser: S:2954, I:258, R:300, I+R:558\n",
      "free birds: 71\n",
      "t = 34 / 90\n",
      "state: S:49512, I:212, R:276 I+R:488\n",
      "obser: S:3039, I:267, R:312, I+R:579\n",
      "free birds: 74\n",
      "t = 35 / 90\n",
      "state: S:49501, I:213, R:286 I+R:499\n",
      "obser: S:3123, I:276, R:321, I+R:597\n",
      "free birds: 69\n",
      "t = 36 / 90\n",
      "state: S:49494, I:211, R:295 I+R:506\n",
      "obser: S:3206, I:285, R:334, I+R:619\n",
      "free birds: 65\n",
      "t = 37 / 90\n",
      "state: S:49480, I:219, R:301 I+R:520\n",
      "obser: S:3292, I:291, R:345, I+R:636\n",
      "free birds: 73\n",
      "t = 38 / 90\n",
      "state: S:49473, I:213, R:314 I+R:527\n",
      "obser: S:3369, I:303, R:359, I+R:662\n",
      "free birds: 63\n",
      "t = 39 / 90\n",
      "state: S:49457, I:212, R:331 I+R:543\n",
      "obser: S:3447, I:311, R:375, I+R:686\n",
      "free birds: 61\n",
      "t = 40 / 90\n",
      "state: S:49452, I:209, R:339 I+R:548\n",
      "obser: S:3528, I:316, R:393, I+R:709\n",
      "free birds: 61\n",
      "t = 41 / 90\n",
      "state: S:49447, I:205, R:348 I+R:553\n",
      "obser: S:3602, I:327, R:409, I+R:736\n",
      "free birds: 54\n",
      "t = 42 / 90\n",
      "state: S:49436, I:202, R:362 I+R:564\n",
      "obser: S:3675, I:332, R:434, I+R:766\n",
      "free birds: 54\n",
      "t = 43 / 90\n",
      "state: S:49431, I:199, R:370 I+R:569\n",
      "obser: S:3748, I:337, R:456, I+R:793\n",
      "free birds: 51\n",
      "t = 44 / 90\n",
      "state: S:49426, I:197, R:377 I+R:574\n",
      "obser: S:3821, I:351, R:474, I+R:825\n",
      "free birds: 41\n",
      "t = 45 / 90\n",
      "state: S:49419, I:198, R:383 I+R:581\n",
      "obser: S:3894, I:362, R:491, I+R:853\n",
      "free birds: 37\n",
      "t = 46 / 90\n",
      "state: S:49416, I:192, R:392 I+R:584\n",
      "obser: S:3976, I:366, R:505, I+R:871\n",
      "free birds: 36\n",
      "t = 47 / 90\n",
      "state: S:49415, I:185, R:400 I+R:585\n",
      "obser: S:4060, I:367, R:520, I+R:887\n",
      "free birds: 36\n",
      "t = 48 / 90\n",
      "state: S:49413, I:177, R:410 I+R:587\n",
      "obser: S:4147, I:371, R:530, I+R:901\n",
      "free birds: 34\n",
      "t = 49 / 90\n",
      "state: S:49405, I:180, R:415 I+R:595\n",
      "obser: S:4241, I:372, R:535, I+R:907\n",
      "free birds: 41\n",
      "t = 50 / 90\n",
      "state: S:49395, I:184, R:421 I+R:605\n",
      "obser: S:4336, I:375, R:538, I+R:913\n",
      "free birds: 45\n",
      "t = 51 / 90\n",
      "state: S:49389, I:179, R:432 I+R:611\n",
      "obser: S:4431, I:377, R:541, I+R:918\n",
      "free birds: 46\n",
      "t = 52 / 90\n",
      "state: S:49380, I:178, R:442 I+R:620\n",
      "obser: S:4527, I:379, R:543, I+R:922\n",
      "free birds: 49\n",
      "t = 53 / 90\n",
      "state: S:49375, I:173, R:452 I+R:625\n",
      "obser: S:4623, I:381, R:546, I+R:927\n",
      "free birds: 49\n",
      "t = 54 / 90\n",
      "state: S:49368, I:170, R:462 I+R:632\n",
      "obser: S:4717, I:383, R:554, I+R:937\n",
      "free birds: 50\n",
      "t = 55 / 90\n",
      "state: S:49364, I:167, R:469 I+R:636\n",
      "obser: S:4803, I:387, R:568, I+R:955\n",
      "free birds: 49\n",
      "t = 56 / 90\n",
      "state: S:49355, I:165, R:480 I+R:645\n",
      "obser: S:4883, I:395, R:583, I+R:978\n",
      "free birds: 46\n",
      "t = 57 / 90\n",
      "state: S:49346, I:163, R:491 I+R:654\n",
      "obser: S:4960, I:406, R:597, I+R:1003\n",
      "free birds: 41\n",
      "t = 58 / 90\n",
      "state: S:49336, I:167, R:497 I+R:664\n",
      "obser: S:5039, I:414, R:611, I+R:1025\n",
      "free birds: 42\n",
      "t = 59 / 90\n",
      "state: S:49331, I:167, R:502 I+R:669\n",
      "obser: S:5122, I:420, R:624, I+R:1044\n",
      "free birds: 39\n",
      "t = 60 / 90\n",
      "state: S:49325, I:163, R:512 I+R:675\n",
      "obser: S:5205, I:426, R:637, I+R:1063\n",
      "free birds: 37\n",
      "t = 61 / 90\n",
      "state: S:49315, I:164, R:521 I+R:685\n",
      "obser: S:5292, I:431, R:647, I+R:1078\n",
      "free birds: 40\n",
      "t = 62 / 90\n",
      "state: S:49308, I:164, R:528 I+R:692\n",
      "obser: S:5379, I:440, R:654, I+R:1094\n",
      "free birds: 37\n",
      "t = 63 / 90\n",
      "state: S:49304, I:158, R:538 I+R:696\n",
      "obser: S:5459, I:451, R:666, I+R:1117\n",
      "free birds: 29\n",
      "t = 64 / 90\n",
      "state: S:49302, I:152, R:546 I+R:698\n",
      "obser: S:5538, I:460, R:678, I+R:1138\n",
      "free birds: 21\n",
      "t = 65 / 90\n",
      "state: S:49302, I:135, R:563 I+R:698\n",
      "obser: S:5622, I:465, R:690, I+R:1155\n",
      "free birds: 15\n",
      "t = 66 / 90\n",
      "state: S:49302, I:128, R:570 I+R:698\n",
      "obser: S:5714, I:469, R:698, I+R:1167\n",
      "free birds: 10\n",
      "t = 67 / 90\n",
      "state: S:49300, I:124, R:576 I+R:700\n",
      "obser: S:5801, I:472, R:710, I+R:1182\n",
      "free birds: 8\n",
      "t = 68 / 90\n",
      "state: S:49300, I:119, R:581 I+R:700\n",
      "obser: S:5890, I:474, R:720, I+R:1194\n",
      "free birds: 5\n",
      "t = 69 / 90\n",
      "state: S:49300, I:115, R:585 I+R:700\n",
      "obser: S:5980, I:474, R:730, I+R:1204\n",
      "free birds: 4\n",
      "t = 70 / 90\n",
      "state: S:49300, I:108, R:592 I+R:700\n",
      "obser: S:6072, I:474, R:738, I+R:1212\n",
      "free birds: 4\n",
      "t = 71 / 90\n",
      "state: S:49299, I:102, R:599 I+R:701\n",
      "obser: S:6166, I:474, R:744, I+R:1218\n",
      "free birds: 5\n",
      "t = 72 / 90\n",
      "state: S:49297, I:100, R:603 I+R:703\n",
      "obser: S:6262, I:474, R:748, I+R:1222\n",
      "free birds: 7\n",
      "t = 73 / 90\n",
      "state: S:49297, I:94, R:609 I+R:703\n",
      "obser: S:6362, I:474, R:748, I+R:1222\n",
      "free birds: 6\n",
      "t = 74 / 90\n",
      "state: S:49297, I:89, R:614 I+R:703\n",
      "obser: S:6462, I:474, R:748, I+R:1222\n",
      "free birds: 5\n",
      "t = 75 / 90\n",
      "state: S:49297, I:84, R:619 I+R:703\n",
      "obser: S:6562, I:474, R:748, I+R:1222\n",
      "free birds: 5\n",
      "t = 76 / 90\n",
      "state: S:49294, I:83, R:623 I+R:706\n",
      "obser: S:6661, I:474, R:749, I+R:1223\n",
      "free birds: 8\n",
      "t = 77 / 90\n",
      "state: S:49294, I:77, R:629 I+R:706\n",
      "obser: S:6760, I:475, R:750, I+R:1225\n",
      "free birds: 7\n",
      "t = 78 / 90\n",
      "state: S:49294, I:72, R:634 I+R:706\n",
      "obser: S:6857, I:477, R:751, I+R:1228\n",
      "free birds: 5\n",
      "t = 79 / 90\n",
      "state: S:49294, I:71, R:635 I+R:706\n",
      "obser: S:6951, I:479, R:755, I+R:1234\n",
      "free birds: 3\n",
      "t = 80 / 90\n",
      "state: S:49294, I:70, R:636 I+R:706\n",
      "obser: S:7047, I:480, R:758, I+R:1238\n",
      "free birds: 2\n",
      "t = 81 / 90\n",
      "state: S:49293, I:66, R:641 I+R:707\n",
      "obser: S:7142, I:480, R:763, I+R:1243\n",
      "free birds: 3\n",
      "t = 82 / 90\n",
      "state: S:49293, I:62, R:645 I+R:707\n",
      "obser: S:7239, I:480, R:766, I+R:1246\n",
      "free birds: 2\n",
      "t = 83 / 90\n",
      "state: S:49293, I:60, R:647 I+R:707\n",
      "obser: S:7336, I:480, R:769, I+R:1249\n",
      "free birds: 2\n",
      "t = 84 / 90\n",
      "state: S:49293, I:57, R:650 I+R:707\n",
      "obser: S:7435, I:480, R:770, I+R:1250\n",
      "free birds: 2\n",
      "t = 85 / 90\n",
      "state: S:49293, I:54, R:653 I+R:707\n",
      "obser: S:7535, I:480, R:770, I+R:1250\n",
      "free birds: 2\n",
      "t = 86 / 90\n",
      "state: S:49293, I:51, R:656 I+R:707\n",
      "obser: S:7635, I:480, R:770, I+R:1250\n",
      "free birds: 2\n",
      "t = 87 / 90\n",
      "state: S:49293, I:51, R:656 I+R:707\n",
      "obser: S:7733, I:480, R:772, I+R:1252\n",
      "free birds: 2\n",
      "t = 88 / 90\n",
      "state: S:49293, I:46, R:661 I+R:707\n",
      "obser: S:7831, I:480, R:774, I+R:1254\n",
      "free birds: 2\n",
      "t = 89 / 90\n",
      "state: S:49293, I:42, R:665 I+R:707\n",
      "obser: S:7930, I:480, R:775, I+R:1255\n",
      "free birds: 1\n",
      "Save tracing strategy\n"
     ]
    }
   ],
   "source": [
    "##### TRACING SCENARIO #######\n",
    "scenario_trac = Scenario_check_R( model, seed=seed+1, \n",
    "    ranking_options=dict(ranking=RANKINGS[\"tracing\"], tau=5),\n",
    "    observation_options=observation_options,\n",
    "    intervention_options=intervention_options\n",
    ")\n",
    "scenario_trac.run(t_max-t1, print_every = 1)\n",
    "print(\"Save tracing strategy\", flush=True)\n",
    "scenario_trac.counts.to_csv(\"csv/Proximity_N%dK_T%d_s1_ti%d_pz%d_mu%.2f_l%.2f_seed%d_obs%d_trac_t%d.csv\"%(N/1000,T,t1,N_patient_zero,mu,lamb,seed,n_ranking,trac_tau),\n",
    "                  index=False, sep=\"\\t\")\n",
    "del scenario_trac"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using ranking_backtrack to rank\n",
      "Using seed=3\n",
      "Selecting 0/50000 untracked individuals\n",
      "t = 0 / 90\n",
      "state: S:49900, I:96, R:4 I+R:100\n",
      "obser: S:100, I:0, R:0, I+R:0\n",
      "free birds: 96\n",
      "t = 1 / 90\n",
      "state: S:49882, I:113, R:5 I+R:118\n",
      "obser: S:198, I:2, R:0, I+R:2\n",
      "free birds: 111\n",
      "t = 2 / 90\n",
      "state: S:49861, I:134, R:5 I+R:139\n",
      "obser: S:298, I:2, R:0, I+R:2\n",
      "free birds: 132\n",
      "t = 3 / 90\n",
      "state: S:49839, I:154, R:7 I+R:161\n",
      "obser: S:398, I:2, R:0, I+R:2\n",
      "free birds: 152\n",
      "t = 4 / 90\n",
      "state: S:49822, I:170, R:8 I+R:178\n",
      "obser: S:498, I:2, R:0, I+R:2\n",
      "free birds: 168\n",
      "t = 5 / 90\n",
      "state: S:49792, I:198, R:10 I+R:208\n",
      "obser: S:598, I:2, R:0, I+R:2\n",
      "free birds: 196\n",
      "t = 6 / 90\n",
      "state: S:49762, I:226, R:12 I+R:238\n",
      "obser: S:698, I:10, R:1, I+R:11\n",
      "free birds: 216\n",
      "t = 7 / 90\n",
      "state: S:49733, I:252, R:15 I+R:267\n",
      "obser: S:797, I:21, R:1, I+R:22\n",
      "free birds: 232\n",
      "t = 8 / 90\n",
      "state: S:49702, I:278, R:20 I+R:298\n",
      "obser: S:896, I:33, R:1, I+R:34\n",
      "free birds: 246\n",
      "t = 9 / 90\n",
      "state: S:49673, I:306, R:21 I+R:327\n",
      "obser: S:995, I:42, R:1, I+R:43\n",
      "free birds: 265\n",
      "t = 10 / 90\n",
      "state: S:49635, I:340, R:25 I+R:365\n",
      "obser: S:1057, I:92, R:4, I+R:96\n",
      "free birds: 250\n",
      "t = 11 / 90\n",
      "state: S:49610, I:358, R:32 I+R:390\n",
      "obser: S:1101, I:150, R:11, I+R:161\n",
      "free birds: 212\n",
      "t = 12 / 90\n",
      "state: S:49587, I:378, R:35 I+R:413\n",
      "obser: S:1152, I:200, R:16, I+R:216\n",
      "free birds: 182\n",
      "t = 13 / 90\n",
      "state: S:49561, I:397, R:42 I+R:439\n",
      "obser: S:1233, I:224, R:18, I+R:242\n",
      "free birds: 182\n",
      "t = 14 / 90\n",
      "state: S:49531, I:424, R:45 I+R:469\n",
      "obser: S:1304, I:254, R:23, I+R:277\n",
      "free birds: 180\n",
      "t = 15 / 90\n",
      "state: S:49504, I:448, R:48 I+R:496\n",
      "obser: S:1376, I:289, R:27, I+R:316\n",
      "free birds: 169\n",
      "t = 16 / 90\n",
      "state: S:49494, I:454, R:52 I+R:506\n",
      "obser: S:1459, I:308, R:30, I+R:338\n",
      "free birds: 159\n",
      "t = 17 / 90\n",
      "state: S:49463, I:478, R:59 I+R:537\n",
      "obser: S:1540, I:335, R:30, I+R:365\n",
      "free birds: 160\n",
      "t = 18 / 90\n",
      "state: S:49438, I:496, R:66 I+R:562\n",
      "obser: S:1615, I:365, R:35, I+R:400\n",
      "free birds: 153\n",
      "t = 19 / 90\n",
      "state: S:49414, I:515, R:71 I+R:586\n",
      "obser: S:1683, I:403, R:35, I+R:438\n",
      "free birds: 138\n",
      "t = 20 / 90\n",
      "state: S:49397, I:528, R:75 I+R:603\n",
      "obser: S:1762, I:427, R:39, I+R:466\n",
      "free birds: 128\n",
      "t = 21 / 90\n",
      "state: S:49378, I:543, R:79 I+R:622\n",
      "obser: S:1835, I:454, R:41, I+R:495\n",
      "free birds: 120\n",
      "t = 22 / 90\n",
      "state: S:49366, I:550, R:84 I+R:634\n",
      "obser: S:1921, I:471, R:43, I+R:514\n",
      "free birds: 113\n",
      "t = 23 / 90\n",
      "state: S:49356, I:553, R:91 I+R:644\n",
      "obser: S:2007, I:486, R:44, I+R:530\n",
      "free birds: 107\n",
      "t = 24 / 90\n",
      "state: S:49341, I:559, R:100 I+R:659\n",
      "obser: S:2098, I:498, R:45, I+R:543\n",
      "free birds: 108\n",
      "t = 25 / 90\n",
      "state: S:49324, I:571, R:105 I+R:676\n",
      "obser: S:2184, I:517, R:46, I+R:563\n",
      "free birds: 105\n",
      "t = 26 / 90\n",
      "state: S:49306, I:586, R:108 I+R:694\n",
      "obser: S:2268, I:540, R:46, I+R:586\n",
      "free birds: 99\n",
      "t = 27 / 90\n",
      "state: S:49298, I:591, R:111 I+R:702\n",
      "obser: S:2359, I:550, R:46, I+R:596\n",
      "free birds: 96\n",
      "t = 28 / 90\n",
      "state: S:49287, I:597, R:116 I+R:713\n",
      "obser: S:2439, I:569, R:49, I+R:618\n",
      "free birds: 88\n",
      "t = 29 / 90\n",
      "state: S:49271, I:611, R:118 I+R:729\n",
      "obser: S:2531, I:580, R:52, I+R:632\n",
      "free birds: 93\n",
      "t = 30 / 90\n",
      "state: S:49261, I:617, R:122 I+R:739\n",
      "obser: S:2619, I:597, R:52, I+R:649\n",
      "free birds: 86\n",
      "t = 31 / 90\n",
      "state: S:49248, I:625, R:127 I+R:752\n",
      "obser: S:2696, I:623, R:53, I+R:676\n",
      "free birds: 71\n",
      "t = 32 / 90\n",
      "state: S:49231, I:638, R:131 I+R:769\n",
      "obser: S:2785, I:634, R:54, I+R:688\n",
      "free birds: 77\n",
      "t = 33 / 90\n",
      "state: S:49222, I:642, R:136 I+R:778\n",
      "obser: S:2875, I:647, R:54, I+R:701\n",
      "free birds: 73\n",
      "t = 34 / 90\n",
      "state: S:49210, I:648, R:142 I+R:790\n",
      "obser: S:2961, I:663, R:55, I+R:718\n",
      "free birds: 68\n",
      "t = 35 / 90\n",
      "state: S:49202, I:644, R:154 I+R:798\n",
      "obser: S:3053, I:673, R:55, I+R:728\n",
      "free birds: 66\n",
      "t = 36 / 90\n",
      "state: S:49192, I:648, R:160 I+R:808\n",
      "obser: S:3145, I:682, R:56, I+R:738\n",
      "free birds: 66\n",
      "t = 37 / 90\n",
      "state: S:49180, I:654, R:166 I+R:820\n",
      "obser: S:3233, I:695, R:59, I+R:754\n",
      "free birds: 64\n",
      "t = 38 / 90\n",
      "state: S:49171, I:659, R:170 I+R:829\n",
      "obser: S:3314, I:714, R:59, I+R:773\n",
      "free birds: 54\n",
      "t = 39 / 90\n",
      "state: S:49167, I:657, R:176 I+R:833\n",
      "obser: S:3397, I:734, R:59, I+R:793\n",
      "free birds: 38\n",
      "t = 40 / 90\n",
      "state: S:49161, I:658, R:181 I+R:839\n",
      "obser: S:3491, I:740, R:60, I+R:800\n",
      "free birds: 38\n",
      "t = 41 / 90\n",
      "state: S:49157, I:658, R:185 I+R:843\n",
      "obser: S:3583, I:750, R:61, I+R:811\n",
      "free birds: 31\n",
      "t = 42 / 90\n",
      "state: S:49153, I:662, R:185 I+R:847\n",
      "obser: S:3673, I:761, R:61, I+R:822\n",
      "free birds: 24\n",
      "t = 43 / 90\n",
      "state: S:49147, I:660, R:193 I+R:853\n",
      "obser: S:3767, I:767, R:61, I+R:828\n",
      "free birds: 24\n",
      "t = 44 / 90\n",
      "state: S:49138, I:665, R:197 I+R:862\n",
      "obser: S:3863, I:771, R:61, I+R:832\n",
      "free birds: 29\n",
      "t = 45 / 90\n",
      "state: S:49133, I:662, R:205 I+R:867\n",
      "obser: S:3960, I:776, R:61, I+R:837\n",
      "free birds: 28\n",
      "t = 46 / 90\n",
      "state: S:49133, I:655, R:212 I+R:867\n",
      "obser: S:4057, I:779, R:61, I+R:840\n",
      "free birds: 25\n",
      "t = 47 / 90\n",
      "state: S:49131, I:652, R:217 I+R:869\n",
      "obser: S:4154, I:782, R:61, I+R:843\n",
      "free birds: 24\n",
      "t = 48 / 90\n",
      "state: S:49128, I:646, R:226 I+R:872\n",
      "obser: S:4254, I:784, R:61, I+R:845\n",
      "free birds: 25\n",
      "t = 49 / 90\n",
      "state: S:49125, I:645, R:230 I+R:875\n",
      "obser: S:4347, I:792, R:63, I+R:855\n",
      "free birds: 20\n",
      "t = 50 / 90\n",
      "state: S:49122, I:640, R:238 I+R:878\n",
      "obser: S:4439, I:799, R:64, I+R:863\n",
      "free birds: 15\n",
      "t = 51 / 90\n",
      "state: S:49118, I:640, R:242 I+R:882\n",
      "obser: S:4534, I:804, R:64, I+R:868\n",
      "free birds: 14\n",
      "t = 52 / 90\n",
      "state: S:49117, I:628, R:255 I+R:883\n",
      "obser: S:4630, I:808, R:64, I+R:872\n",
      "free birds: 11\n",
      "t = 53 / 90\n",
      "state: S:49116, I:623, R:261 I+R:884\n",
      "obser: S:4730, I:808, R:65, I+R:873\n",
      "free birds: 12\n",
      "t = 54 / 90\n",
      "state: S:49116, I:618, R:266 I+R:884\n",
      "obser: S:4830, I:809, R:65, I+R:874\n",
      "free birds: 11\n",
      "t = 55 / 90\n",
      "state: S:49116, I:612, R:272 I+R:884\n",
      "obser: S:4928, I:811, R:65, I+R:876\n",
      "free birds: 9\n",
      "t = 56 / 90\n",
      "state: S:49115, I:607, R:278 I+R:885\n",
      "obser: S:5028, I:811, R:65, I+R:876\n",
      "free birds: 10\n",
      "t = 57 / 90\n",
      "state: S:49115, I:601, R:284 I+R:885\n",
      "obser: S:5128, I:811, R:65, I+R:876\n",
      "free birds: 9\n",
      "t = 58 / 90\n",
      "state: S:49114, I:596, R:290 I+R:886\n",
      "obser: S:5228, I:811, R:65, I+R:876\n",
      "free birds: 10\n",
      "t = 59 / 90\n",
      "state: S:49114, I:589, R:297 I+R:886\n",
      "obser: S:5328, I:811, R:65, I+R:876\n",
      "free birds: 9\n",
      "t = 60 / 90\n",
      "state: S:49113, I:584, R:303 I+R:887\n",
      "obser: S:5428, I:811, R:65, I+R:876\n",
      "free birds: 10\n",
      "t = 61 / 90\n",
      "state: S:49111, I:582, R:307 I+R:889\n",
      "obser: S:5528, I:811, R:65, I+R:876\n",
      "free birds: 12\n",
      "t = 62 / 90\n",
      "state: S:49111, I:577, R:312 I+R:889\n",
      "obser: S:5627, I:811, R:66, I+R:877\n",
      "free birds: 12\n",
      "t = 63 / 90\n",
      "state: S:49108, I:571, R:321 I+R:892\n",
      "obser: S:5727, I:811, R:66, I+R:877\n",
      "free birds: 14\n",
      "t = 64 / 90\n",
      "state: S:49106, I:565, R:329 I+R:894\n",
      "obser: S:5827, I:811, R:66, I+R:877\n",
      "free birds: 15\n",
      "t = 65 / 90\n",
      "state: S:49106, I:560, R:334 I+R:894\n",
      "obser: S:5926, I:811, R:67, I+R:878\n",
      "free birds: 15\n",
      "t = 66 / 90\n",
      "state: S:49104, I:555, R:341 I+R:896\n",
      "obser: S:6026, I:812, R:67, I+R:879\n",
      "free birds: 16\n",
      "t = 67 / 90\n",
      "state: S:49102, I:553, R:345 I+R:898\n",
      "obser: S:6123, I:812, R:70, I+R:882\n",
      "free birds: 18\n",
      "t = 68 / 90\n",
      "state: S:49099, I:547, R:354 I+R:901\n",
      "obser: S:6223, I:813, R:70, I+R:883\n",
      "free birds: 20\n",
      "t = 69 / 90\n",
      "state: S:49098, I:540, R:362 I+R:902\n",
      "obser: S:6315, I:821, R:70, I+R:891\n",
      "free birds: 13\n",
      "t = 70 / 90\n",
      "state: S:49097, I:531, R:372 I+R:903\n",
      "obser: S:6413, I:822, R:71, I+R:893\n",
      "free birds: 13\n",
      "t = 71 / 90\n",
      "state: S:49094, I:530, R:376 I+R:906\n",
      "obser: S:6513, I:822, R:71, I+R:893\n",
      "free birds: 16\n",
      "t = 72 / 90\n",
      "state: S:49092, I:528, R:380 I+R:908\n",
      "obser: S:6613, I:822, R:71, I+R:893\n",
      "free birds: 18\n",
      "t = 73 / 90\n",
      "state: S:49090, I:525, R:385 I+R:910\n",
      "obser: S:6713, I:822, R:71, I+R:893\n",
      "free birds: 20\n",
      "t = 74 / 90\n",
      "state: S:49088, I:521, R:391 I+R:912\n",
      "obser: S:6813, I:822, R:71, I+R:893\n",
      "free birds: 21\n",
      "t = 75 / 90\n",
      "state: S:49084, I:521, R:395 I+R:916\n",
      "obser: S:6913, I:822, R:71, I+R:893\n",
      "free birds: 23\n",
      "t = 76 / 90\n",
      "state: S:49082, I:514, R:404 I+R:918\n",
      "obser: S:7013, I:823, R:71, I+R:894\n",
      "free birds: 24\n",
      "t = 77 / 90\n",
      "state: S:49080, I:513, R:407 I+R:920\n",
      "obser: S:7103, I:832, R:73, I+R:905\n",
      "free birds: 17\n",
      "t = 78 / 90\n",
      "state: S:49077, I:512, R:411 I+R:923\n",
      "obser: S:7190, I:843, R:75, I+R:918\n",
      "free birds: 9\n",
      "t = 79 / 90\n",
      "state: S:49076, I:510, R:414 I+R:924\n",
      "obser: S:7283, I:850, R:75, I+R:925\n",
      "free birds: 3\n",
      "t = 80 / 90\n",
      "state: S:49075, I:505, R:420 I+R:925\n",
      "obser: S:7381, I:852, R:75, I+R:927\n",
      "free birds: 2\n",
      "t = 81 / 90\n",
      "state: S:49075, I:503, R:422 I+R:925\n",
      "obser: S:7481, I:852, R:75, I+R:927\n",
      "free birds: 2\n",
      "t = 82 / 90\n",
      "state: S:49074, I:500, R:426 I+R:926\n",
      "obser: S:7581, I:852, R:75, I+R:927\n",
      "free birds: 3\n",
      "t = 83 / 90\n",
      "state: S:49074, I:493, R:433 I+R:926\n",
      "obser: S:7681, I:852, R:75, I+R:927\n",
      "free birds: 3\n",
      "t = 84 / 90\n",
      "state: S:49074, I:490, R:436 I+R:926\n",
      "obser: S:7781, I:852, R:75, I+R:927\n",
      "free birds: 3\n",
      "t = 85 / 90\n",
      "state: S:49073, I:482, R:445 I+R:927\n",
      "obser: S:7880, I:852, R:76, I+R:928\n",
      "free birds: 4\n",
      "t = 86 / 90\n",
      "state: S:49072, I:482, R:446 I+R:928\n",
      "obser: S:7980, I:852, R:76, I+R:928\n",
      "free birds: 5\n",
      "t = 87 / 90\n",
      "state: S:49072, I:479, R:449 I+R:928\n",
      "obser: S:8079, I:852, R:77, I+R:929\n",
      "free birds: 5\n",
      "t = 88 / 90\n",
      "state: S:49072, I:475, R:453 I+R:928\n",
      "obser: S:8179, I:852, R:77, I+R:929\n",
      "free birds: 5\n",
      "t = 89 / 90\n",
      "state: S:49072, I:466, R:462 I+R:928\n",
      "obser: S:8279, I:852, R:77, I+R:929\n",
      "free birds: 5\n",
      "Save MF strategy\n",
      "End seed\n"
     ]
    }
   ],
   "source": [
    "##### MF SCENARIO #######\n",
    "import imp\n",
    "import scenario\n",
    "imp.reload(scenario)\n",
    "from scenario import Scenario_check_R\n",
    "scenario_MF = Scenario_check_R(\n",
    "    model, seed=seed+1, \n",
    "    ranking_options=dict(ranking=RANKINGS[\"backtrack\"], \n",
    "                         algo=\"MF\", init=\"all_S\", tau=5, delta=10), \n",
    "    observation_options=observation_options,\n",
    "    intervention_options=intervention_options,\n",
    ")\n",
    "scenario_MF.run(t_max-t1, print_every = 1)\n",
    "print(\"Save MF strategy\", flush=True)\n",
    "scenario_MF.counts.to_csv(\"csv/Proximity_N%dK_T%d_s1_ti%d_pz%d_mu%.2f_l%.2f_seed%d_obs%d_MF_t%d_d%d.csv\"%(N/1000,T,t1,N_patient_zero,mu,lamb,seed,n_ranking,MF_tau,MF_delta),\n",
    "                  index=False, sep=\"\\t\")\n",
    "del scenario_MF\n",
    "# 1h01min per round\n",
    "print(\"End seed\", flush=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using step_scenario to rank\n",
      "Using seed=2\n",
      "Selecting 0/50000 untracked individuals\n",
      "SCENARIO BP\n",
      "winBP: (S,I,R): (49909.3, 86.4, 4.3), seeds: 90.7, ll: -29801.0\n",
      "t = 0 / 90\n",
      "state: S:49900, I:96, R:4 I+R:100\n",
      "obser: S:98, I:2, R:0, I+R:2\n",
      "free birds: 94\n",
      "SCENARIO BP\n",
      "1 obs 100\n",
      "winBP: (S,I,R): (49898.0, 93.0, 9.0), seeds: 89.8, ll: -29816.7\n",
      "t = 1 / 90\n",
      "state: S:49884, I:112, R:4 I+R:116\n",
      "obser: S:198, I:2, R:0, I+R:2\n",
      "free birds: 110\n",
      "SCENARIO BP\n",
      "2 obs 100\n",
      "winBP: (S,I,R): (49889.2, 97.0, 13.8), seeds: 86.7, ll: -29819.9\n",
      "t = 2 / 90\n",
      "state: S:49861, I:135, R:4 I+R:139\n",
      "obser: S:298, I:2, R:0, I+R:2\n",
      "free birds: 133\n",
      "SCENARIO BP\n",
      "3 obs 100\n",
      "winBP: (S,I,R): (49881.0, 100.4, 18.6), seeds: 83.6, ll: -29833.3\n",
      "t = 3 / 90\n",
      "state: S:49842, I:154, R:4 I+R:158\n",
      "obser: S:397, I:3, R:0, I+R:3\n",
      "free birds: 151\n",
      "SCENARIO BP\n",
      "4 obs 100\n",
      "winBP: (S,I,R): (49872.2, 104.2, 23.6), seeds: 80.9, ll: -29832.0\n",
      "t = 4 / 90\n",
      "state: S:49818, I:176, R:6 I+R:182\n",
      "obser: S:480, I:20, R:0, I+R:20\n",
      "free birds: 156\n",
      "SCENARIO BP\n",
      "5 obs 100\n",
      "winBP: (S,I,R): (49850.1, 120.8, 29.0), seeds: 79.4, ll: -29890.2\n",
      "t = 5 / 90\n",
      "state: S:49788, I:206, R:6 I+R:212\n",
      "obser: S:575, I:25, R:0, I+R:25\n",
      "free birds: 181\n",
      "SCENARIO BP\n",
      "6 obs 100\n",
      "winBP: (S,I,R): (49838.8, 126.4, 34.8), seeds: 77.1, ll: -29912.3\n",
      "t = 6 / 90\n",
      "state: S:49759, I:233, R:8 I+R:241\n",
      "obser: S:667, I:39, R:0, I+R:39\n",
      "free birds: 195\n",
      "SCENARIO BP\n",
      "7 obs 108\n",
      "winBP: (S,I,R): (49809.9, 147.9, 42.3), seeds: 77.2, ll: -29971.2\n",
      "t = 7 / 90\n",
      "state: S:49740, I:250, R:10 I+R:260\n",
      "obser: S:735, I:77, R:1, I+R:78\n",
      "free birds: 174\n",
      "SCENARIO BP\n",
      "8 obs 111\n",
      "winBP: (S,I,R): (49747.3, 198.5, 54.2), seeds: 79.9, ll: -30096.5\n",
      "t = 8 / 90\n",
      "state: S:49711, I:274, R:15 I+R:289\n",
      "obser: S:796, I:114, R:5, I+R:119\n",
      "free birds: 163\n",
      "SCENARIO BP\n",
      "9 obs 109\n",
      "winBP: (S,I,R): (49710.3, 224.0, 65.7), seeds: 79.2, ll: -30193.8\n",
      "t = 9 / 90\n",
      "state: S:49693, I:289, R:18 I+R:307\n",
      "obser: S:863, I:148, R:9, I+R:157\n",
      "free birds: 145\n",
      "SCENARIO BP\n",
      "10 obs 112\n",
      "winBP: (S,I,R): (49666.0, 253.7, 80.3), seeds: 78.9, ll: -30295.1\n",
      "t = 10 / 90\n",
      "state: S:49670, I:307, R:23 I+R:330\n",
      "obser: S:937, I:176, R:10, I+R:186\n",
      "free birds: 136\n",
      "SCENARIO BP\n",
      "11 obs 115\n",
      "winBP: (S,I,R): (49639.0, 271.0, 90.0), seeds: 77.8, ll: -30380.8\n",
      "t = 11 / 90\n",
      "state: S:49654, I:318, R:28 I+R:346\n",
      "obser: S:1018, I:200, R:11, I+R:211\n",
      "free birds: 124\n",
      "SCENARIO BP\n",
      "12 obs 114\n",
      "winBP: (S,I,R): (49609.5, 287.7, 102.8), seeds: 77.1, ll: -30463.8\n",
      "t = 12 / 90\n",
      "state: S:49639, I:328, R:33 I+R:361\n",
      "obser: S:1088, I:229, R:17, I+R:246\n",
      "free birds: 108\n",
      "SCENARIO BP\n",
      "13 obs 109\n",
      "winBP: (S,I,R): (49567.3, 310.5, 122.2), seeds: 77.0, ll: -30558.5\n",
      "t = 13 / 90\n",
      "state: S:49624, I:341, R:35 I+R:376\n",
      "obser: S:1162, I:260, R:20, I+R:280\n",
      "free birds: 91\n",
      "SCENARIO BP\n",
      "14 obs 114\n",
      "winBP: (S,I,R): (49523.8, 336.5, 139.8), seeds: 76.0, ll: -30660.1\n",
      "t = 14 / 90\n",
      "state: S:49616, I:346, R:38 I+R:384\n",
      "obser: S:1233, I:291, R:20, I+R:311\n",
      "free birds: 68\n",
      "SCENARIO BP\n",
      "15 obs 109\n",
      "winBP: (S,I,R): (49504.0, 345.7, 150.4), seeds: 74.4, ll: -30738.9\n",
      "t = 15 / 90\n",
      "state: S:49604, I:354, R:42 I+R:396\n",
      "obser: S:1311, I:313, R:23, I+R:336\n",
      "free birds: 57\n",
      "SCENARIO BP\n",
      "16 obs 111\n",
      "winBP: (S,I,R): (49486.5, 348.6, 164.9), seeds: 72.9, ll: -30812.1\n",
      "t = 16 / 90\n",
      "state: S:49596, I:358, R:46 I+R:404\n",
      "obser: S:1405, I:324, R:23, I+R:347\n",
      "free birds: 52\n",
      "SCENARIO BP\n",
      "17 obs 108\n",
      "winBP: (S,I,R): (49482.0, 341.0, 177.0), seeds: 71.4, ll: -30866.7\n",
      "t = 17 / 90\n",
      "state: S:49592, I:356, R:52 I+R:408\n",
      "obser: S:1494, I:335, R:24, I+R:359\n",
      "free birds: 45\n",
      "SCENARIO BP\n",
      "18 obs 107\n",
      "winBP: (S,I,R): (49485.9, 327.0, 187.1), seeds: 69.6, ll: -30906.4\n",
      "t = 18 / 90\n",
      "state: S:49584, I:361, R:55 I+R:416\n",
      "obser: S:1584, I:347, R:26, I+R:373\n",
      "free birds: 41\n",
      "SCENARIO BP\n",
      "19 obs 107\n",
      "winBP: (S,I,R): (49472.2, 326.9, 200.8), seeds: 68.6, ll: -30960.6\n",
      "t = 19 / 90\n",
      "state: S:49578, I:363, R:59 I+R:422\n",
      "obser: S:1678, I:352, R:28, I+R:380\n",
      "free birds: 42\n",
      "SCENARIO BP\n",
      "20 obs 104\n",
      "winBP: (S,I,R): (49486.3, 303.5, 210.1), seeds: 66.7, ll: -30985.9\n",
      "t = 20 / 90\n",
      "state: S:49574, I:367, R:59 I+R:426\n",
      "obser: S:1772, I:360, R:29, I+R:389\n",
      "free birds: 38\n",
      "SCENARIO BP\n",
      "21 obs 106\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 86.42258969995511\n",
      "winBP: (S,I,R): (49490.0, 298.3, 211.7), seeds: 59.4, ll: -51336.4\n",
      "t = 21 / 90\n",
      "state: S:49572, I:366, R:62 I+R:428\n",
      "obser: S:1868, I:365, R:29, I+R:394\n",
      "free birds: 35\n",
      "SCENARIO BP\n",
      "22 obs 104\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 93.02629342653972\n",
      "winBP: (S,I,R): (49494.5, 284.8, 220.7), seeds: 68.5, ll: -51312.9\n",
      "t = 22 / 90\n",
      "state: S:49571, I:361, R:68 I+R:429\n",
      "obser: S:1956, I:377, R:29, I+R:406\n",
      "free birds: 23\n",
      "SCENARIO BP\n",
      "23 obs 102\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 97.0050068862488\n",
      "winBP: (S,I,R): (49485.0, 283.3, 231.7), seeds: 79.6, ll: -51387.9\n",
      "t = 23 / 90\n",
      "state: S:49570, I:361, R:69 I+R:430\n",
      "obser: S:2053, I:381, R:29, I+R:410\n",
      "free birds: 20\n",
      "SCENARIO BP\n",
      "24 obs 104\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 100.37633439621605\n",
      "winBP: (S,I,R): (49480.5, 276.9, 242.6), seeds: 99.5, ll: -51470.1\n",
      "t = 24 / 90\n",
      "state: S:49567, I:358, R:75 I+R:433\n",
      "obser: S:2152, I:382, R:29, I+R:411\n",
      "free birds: 22\n",
      "SCENARIO BP\n",
      "25 obs 103\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 104.23463338660494\n",
      "winBP: (S,I,R): (49497.6, 258.3, 244.1), seeds: 103.6, ll: -51458.0\n",
      "t = 25 / 90\n",
      "state: S:49565, I:358, R:77 I+R:435\n",
      "obser: S:2247, I:386, R:30, I+R:416\n",
      "free birds: 20\n",
      "SCENARIO BP\n",
      "26 obs 102\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 120.84628666056317\n",
      "winBP: (S,I,R): (49482.6, 260.3, 257.1), seeds: 127.4, ll: -51533.2\n",
      "t = 26 / 90\n",
      "state: S:49563, I:359, R:78 I+R:437\n",
      "obser: S:2343, I:390, R:30, I+R:420\n",
      "free birds: 18\n",
      "SCENARIO BP\n",
      "27 obs 101\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 126.42744427983139\n",
      "winBP: (S,I,R): (49482.1, 256.1, 261.8), seeds: 148.6, ll: -inf\n",
      "t = 27 / 90\n",
      "state: S:49562, I:354, R:84 I+R:438\n",
      "obser: S:2443, I:390, R:30, I+R:420\n",
      "free birds: 19\n",
      "SCENARIO BP\n",
      "28 obs 100\n",
      "...adjust prob_i0 and prob_r0\n",
      "...drop first time and reset observations\n",
      "pI at intial time: 147.8794809121469\n",
      "winBP: (S,I,R): (49521.2, 228.3, 250.4), seeds: 168.4, ll: -inf\n",
      "t = 28 / 90\n",
      "state: S:49561, I:351, R:88 I+R:439\n",
      "obser: S:2542, I:391, R:30, I+R:421\n",
      "free birds: 19\n",
      "SCENARIO BP\n",
      "29 obs 100\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-26-b14d90522f55>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     30\u001b[0m                          \u001b[0msave_csv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mname_csv\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     31\u001b[0m )\n\u001b[0;32m---> 32\u001b[0;31m \u001b[0mscenario_bp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt_max\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mt1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprint_every\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     33\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Save bp strategy\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mflush\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     34\u001b[0m scenario_bp.counts.to_csv(name_csv,\n",
      "\u001b[0;32m~/git/sir_inference/scenario.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, t_max, print_every)\u001b[0m\n\u001b[1;32m    269\u001b[0m         \u001b[0;31m# iterate\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    270\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mt\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt_max\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 271\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    272\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mprint_every\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mt\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mprint_every\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    273\u001b[0m                 \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mf\"t = {t} / {t_max}\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/git/sir_inference/scenario.py\u001b[0m in \u001b[0;36mupdate\u001b[0;34m(self, t)\u001b[0m\n\u001b[1;32m    245\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate_states\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    246\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mranking_options\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 247\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate_scores\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    248\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobservation_options\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    249\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate_observations\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/git/sir_inference/scenario.py\u001b[0m in \u001b[0;36mupdate_scores\u001b[0;34m(self, t)\u001b[0m\n\u001b[1;32m    122\u001b[0m         \u001b[0;34m\"Assumes observations[t-1] and transmissions[t-1] computed\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    123\u001b[0m         self.scores[t] = self.ranking(\n\u001b[0;32m--> 124\u001b[0;31m             \u001b[0mt\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobservations\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mranking_options\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    125\u001b[0m         )\n\u001b[1;32m    126\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mscores\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mt\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"t\"\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mt\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/git/sir_inference/bp_ranking.py\u001b[0m in \u001b[0;36mstep_scenario\u001b[0;34m(self, t, model, obs, params)\u001b[0m\n\u001b[1;32m     31\u001b[0m         \u001b[0;31m#print(t, daily_contacts[0])\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     32\u001b[0m         \u001b[0;31m#print(t, daily_obs)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 33\u001b[0;31m         \u001b[0mrank_algo\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrank\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mt\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdaily_contacts\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdaily_obs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     34\u001b[0m         \u001b[0mrank\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msorted\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrank_algo\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mtup\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mtup\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreverse\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     35\u001b[0m         \u001b[0mrank\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtup\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtup\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m  \u001b[0;32mfor\u001b[0m \u001b[0mtup\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrank\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/git/loop_abm/src/loop_ranker/winbp_prob0_rank.py\u001b[0m in \u001b[0;36mrank\u001b[0;34m(self, t_day, daily_contacts, daily_obs, data)\u001b[0m\n\u001b[1;32m     66\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     67\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mc\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdaily_contacts\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 68\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend_contact\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mc\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     69\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     70\u001b[0m         \u001b[0;31m### add fake obs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "import imp\n",
    "import scenario\n",
    "imp.reload(scenario)\n",
    "from scenario import Scenario\n",
    "import bp_ranking\n",
    "imp.reload(bp_ranking)\n",
    "from bp_ranking import bp_ranker_class\n",
    "\n",
    "name_csv = \"csv/Proximity_N%dK_T%d_s1_ti%d_pz%d_mu%.2f_l%.2f_seed%d_obs%d_bp%d.csv\"%(N, T,t1,N_patient_zero,mu,lamb,seed,n_ranking,trac_tau)\n",
    "pseed=50/N\n",
    "psus = 0.55\n",
    "pautoinf = 1e-10\n",
    "bp_ranker = bp_ranker_class(params = sib.Params(\n",
    "                                 prob_r = sib.Exponential(mu=mu_r),\n",
    "                                 pseed = pseed,\n",
    "                                 psus = psus,\n",
    "                                 pautoinf = pautoinf),\n",
    "                 maxit0 = 20,\n",
    "                 maxit1 = 20,\n",
    "                 tol = 1e-3,\n",
    "                 memory_decay = 1e-5,\n",
    "                 window_length = 21,\n",
    "                           )\n",
    "bp_ranker.init(N, T)\n",
    "bp_ranker.__name__ = \"bp\"\n",
    "scenario_bp = Scenario( model, seed=seed, \n",
    "    ranking_options=dict(ranking=bp_ranker.step_scenario),\n",
    "    observation_options=observation_options,\n",
    "    intervention_options=intervention_options,\n",
    "                         save_csv = name_csv\n",
    ")\n",
    "scenario_bp.run(t_max-t1, print_every = 1)\n",
    "print(\"Save bp strategy\", flush=True)\n",
    "scenario_bp.counts.to_csv(name_csv,\n",
    "          index=False, sep=\"\\t\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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