From 608928f1ac8286282a63b42b6e8844832e180ff7 Mon Sep 17 00:00:00 2001 From: jreps Date: Tue, 8 Oct 2024 13:33:33 -0400 Subject: [PATCH] char documentation update - updating characterization markdown description - updating website - updating develop version number --- DESCRIPTION | 2 +- docs/404.html | 22 +- docs/articles/AddingShinyModules.html | 31 +- docs/articles/Characterization.html | 182 ++-- docs/articles/CohortDiagnostics.html | 31 +- docs/articles/Cohorts.html | 31 +- docs/articles/DataSources.html | 31 +- docs/articles/Estimation.html | 31 +- docs/articles/Prediction.html | 31 +- docs/articles/ReportGenerator.html | 31 +- docs/articles/index.html | 22 +- docs/authors.html | 38 +- docs/index.html | 22 +- docs/news/index.html | 24 +- docs/pkgdown.yml | 7 +- docs/reference/LargeDataTable.html | 26 +- docs/reference/OhdsiShinyModules.html | 24 +- docs/reference/aboutHelperFile.html | 30 +- docs/reference/aboutServer.html | 40 +- docs/reference/aboutViewer.html | 34 +- .../reference/characterizationHelperFile.html | 30 +- .../characterizationIncidenceServer.html | 46 +- .../characterizationIncidenceViewer.html | 34 +- docs/reference/characterizationServer.html | 38 +- docs/reference/characterizationViewer.html | 34 +- docs/reference/cohortCountsModule.html | 42 +- docs/reference/cohortCountsView.html | 30 +- docs/reference/cohortDefinitionsModule.html | 40 +- docs/reference/cohortDefinitionsView.html | 30 +- .../cohortDiagCharacterizationView.html | 30 +- .../cohortDiagnosticsHelperFile.html | 30 +- docs/reference/cohortDiagnosticsServer.html | 36 +- docs/reference/cohortDiagnosticsView.html | 34 +- docs/reference/cohortGeneratorHelperFile.html | 30 +- docs/reference/cohortGeneratorServer.html | 38 +- docs/reference/cohortGeneratorViewer.html | 34 +- .../cohortMethodAttritionServer.html | 40 +- .../cohortMethodAttritionViewer.html | 34 +- .../cohortMethodCovariateBalanceServer.html | 42 +- .../cohortMethodCovariateBalanceViewer.html | 34 +- .../cohortMethodKaplanMeierServer.html | 40 +- .../cohortMethodKaplanMeierViewer.html | 34 +- ...MethodPopulationCharacteristicsServer.html | 40 +- ...MethodPopulationCharacteristicsViewer.html | 34 +- docs/reference/cohortMethodPowerServer.html | 40 +- docs/reference/cohortMethodPowerViewer.html | 34 +- .../cohortMethodPropensityModelServer.html | 40 +- .../cohortMethodPropensityModelViewer.html | 34 +- ...cohortMethodPropensityScoreDistServer.html | 42 +- ...cohortMethodPropensityScoreDistViewer.html | 34 +- .../cohortMethodSystematicErrorServer.html | 40 +- .../cohortMethodSystematicErrorViewer.html | 34 +- docs/reference/cohortOverlapView.html | 30 +- .../compareCohortCharacterizationView.html | 32 +- docs/reference/conceptsInDataSourceView.html | 30 +- .../reference/createCdDatabaseDataSource.html | 42 +- docs/reference/createCustomColDefList.html | 48 +- docs/reference/createLargeSqlQueryDt.html | 36 +- docs/reference/dataDiagnosticDrillServer.html | 38 +- docs/reference/dataDiagnosticDrillViewer.html | 34 +- docs/reference/dataDiagnosticHelperFile.html | 30 +- docs/reference/dataDiagnosticServer.html | 38 +- .../dataDiagnosticSummaryServer.html | 38 +- .../dataDiagnosticSummaryViewer.html | 34 +- docs/reference/dataDiagnosticViewer.html | 34 +- docs/reference/databaseInformationView.html | 30 +- docs/reference/datasourcesHelperFile.html | 32 +- docs/reference/datasourcesServer.html | 40 +- docs/reference/datasourcesViewer.html | 36 +- docs/reference/estimationHelperFile.html | 30 +- docs/reference/estimationServer.html | 38 +- docs/reference/estimationViewer.html | 34 +- .../reference/getCirceRenderedExpression.html | 38 +- docs/reference/getEnabledCdReports.html | 30 +- .../getExampleConnectionDetails.html | 30 +- docs/reference/getLogoImage.html | 28 +- docs/reference/homeHelperFile.html | 30 +- docs/reference/homeServer.html | 38 +- docs/reference/homeViewer.html | 34 +- docs/reference/incidenceRatesView.html | 30 +- docs/reference/inclusionRulesView.html | 30 +- docs/reference/index.html | 30 +- docs/reference/indexEventBreakdownView.html | 30 +- docs/reference/largeTableServer.html | 40 +- docs/reference/largeTableView.html | 36 +- docs/reference/makeButtonLabel.html | 36 +- docs/reference/orpahanConceptsView.html | 32 +- ...tientLevelPredictionCalibrationServer.html | 42 +- ...tientLevelPredictionCalibrationViewer.html | 34 +- ...LevelPredictionCovariateSummaryServer.html | 46 +- ...LevelPredictionCovariateSummaryViewer.html | 34 +- .../patientLevelPredictionCutoffServer.html | 42 +- .../patientLevelPredictionCutoffViewer.html | 34 +- ...entLevelPredictionDesignSummaryServer.html | 38 +- ...entLevelPredictionDesignSummaryViewer.html | 34 +- ...tientLevelPredictionDiagnosticsServer.html | 40 +- ...tientLevelPredictionDiagnosticsViewer.html | 34 +- ...ntLevelPredictionDiscriminationServer.html | 42 +- ...ntLevelPredictionDiscriminationViewer.html | 34 +- .../patientLevelPredictionHelperFile.html | 30 +- ...ientLevelPredictionModelSummaryServer.html | 40 +- ...ientLevelPredictionModelSummaryViewer.html | 34 +- .../patientLevelPredictionNbServer.html | 42 +- .../patientLevelPredictionNbViewer.html | 34 +- .../patientLevelPredictionServer.html | 38 +- .../patientLevelPredictionSettingsServer.html | 46 +- .../patientLevelPredictionSettingsViewer.html | 34 +- ...atientLevelPredictionValidationServer.html | 46 +- ...atientLevelPredictionValidationViewer.html | 34 +- .../patientLevelPredictionViewer.html | 34 +- docs/reference/phevaluatorHelperFile.html | 32 +- docs/reference/phevaluatorServer.html | 40 +- docs/reference/phevaluatorViewer.html | 36 +- docs/reference/reportHelperFile.html | 30 +- docs/reference/reportServer.html | 46 +- docs/reference/reportViewer.html | 34 +- docs/reference/resultTableServer.html | 54 +- docs/reference/resultTableViewer.html | 40 +- docs/reference/timeDistributionsView.html | 30 +- docs/reference/visitContextView.html | 30 +- docs/sitemap.xml | 832 +++++++++++++----- vignettes/Characterization.Rmd | 37 +- 122 files changed, 2826 insertions(+), 2319 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 02eff0e2..9e6d2f81 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: OhdsiShinyModules Type: Package Title: Repository of Shiny Modules for OHDSI Result Viewers -Version: 3.1.0 +Version: 3.1.0.9000 Authors@R: c( person("Jenna", "Reps", email = "jreps@its.jnj.com", role = c("aut", "cre")), person("Nathan", "Hall", role = c("aut")), diff --git a/docs/404.html b/docs/404.html index 8ad319b3..56e1c2db 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • OhdsiShinyModules - + @@ -18,7 +18,7 @@ - +
@@ -41,7 +41,7 @@
  • - +
  • @@ -53,7 +53,7 @@
  • @@ -105,7 +105,7 @@
    • - +
    @@ -133,16 +133,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/AddingShinyModules.html b/docs/articles/AddingShinyModules.html index fdeff052..131b2db3 100644 --- a/docs/articles/AddingShinyModules.html +++ b/docs/articles/AddingShinyModules.html @@ -6,19 +6,20 @@ Adding Shiny Modules • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,7 +106,7 @@
    • - +
    @@ -114,9 +115,9 @@

    Adding Shiny Modules

    Jenna Reps, Jamie Gilbert, Josh Ide

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -366,7 +367,9 @@

    Dependencies -

    + +
    @@ -379,16 +382,16 @@

    Dependencies

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/Characterization.html b/docs/articles/Characterization.html index 28cde0ee..449844fe 100644 --- a/docs/articles/Characterization.html +++ b/docs/articles/Characterization.html @@ -6,19 +6,20 @@ Characterization • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,18 +106,18 @@
    • - +

    Characterization

    -

    Nathan -Hall

    +

    Nathan Hall and +Jenna Reps

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -130,56 +131,105 @@

    2024-10-07

    Introduction

    -

    Characterization, a fundamental aspect of observational health data -research, serves as a cornerstone for understanding and analyzing -populations based on a myriad of characteristics. The methodologies of -characterization play a pivotal role in generating hypotheses about the -determinants of health and disease by providing descriptive insights -into population demographics, medical history, treatment patterns, and -incidence rates of outcomes. There are various methods for -characterization, including database-level characterization, cohort -characterization, treatment pathways analysis, and incidence -measurement. Each of these methods aims to describe populations relative -to an event known as the index date, which anchors the analysis of -baseline, pre-index, and post-index time periods. Through the lens of -use-cases such as disease natural history, treatment utilization, and -quality improvement, characterizing cohorts of patients empowers -researchers to glean actionable insights from observational healthcare -databases.

    +

    The OHDSI Characterization package lets users extract descriptive +analyses from observational healthcare data sets mapped to the OMOP CDM. +There are currently four different types of characterizations analyses +(incidence rates, time-to-event, dechallenge-rechallenge and various +aggregate covariate cohort comparisons).

    +

    The Characterization package currently lets users answer the +following questions:

    +
      +
    • +Incidence Rate: How often does +<add outcome> occur within +<add time-at-risk> after first record of +<add exposure/indication>?
      • +
    • +Time-to-event: When does +<add outcome> occur relative to the first recorded of +<add exposure/indication>? Is it more common before +or after <add exposure>?
      • +
    • +Dechallenge-rechallenge: Is there any evidence of +<add outcome> causing +<add exposure> to be discontinued and then +<add outcome> re-occurring once +<add exposure> restarts?
      • +
    • +Cohort Comparison: What is different at index +between patients in <add exposure/outcome/indication> +and patients in +<add different exposure/outcome/indication>?
      • +
    • +Database Comparison: What is different at index +between patients in <add exposure/outcome/indication> +across two or more OMOP CDM databases?
      • +
    • +Risk factors: What are the risk factors of +<add outcome> occurring within +<add time-at-risk> for those exposed to +<add exposure>?
      • +
    • +Case-series: What happens to cases (those exposure +to <add exposure> who have +<add outcome> during +<add time-at-risk>) before exposure, between exposure +and outcome start and after outcome start? How bad are the cases +prognosis?
      • +

    Features and Functionalities

    -

    The Characterization module is dedicated to investigating these -factors within and between cohorts, and it contains several useful -features that allow for this exploration, including:

    +

    Defining a target cohort as a set of patients with +an exposure or interest and/or with evidence of having an indication of +interest and an outcome cohort as a set of patients +with evidence of the outcome of interest, we run the following +analyses:

    1. -Target Viewer: Computes detailed results for target -cohorts, offering a granular view of the cohort’s demographics, -conditions, drug exposures, and more. This enables a deeper -understanding of the cohort’s characteristics at various time points at -or relative to the index date.
      2. +Cohort Summary - computes aggregate covariate +summaries for cohorts (targets and/or outcomes), offering a granular +view of the cohort’s demographics, conditions, drug exposures, and more. +This enables a deeper understanding of the cohort’s characteristics at +various time points at or relative to the index date.: +
      • -Outcome Stratified: For both target and outcome -cohorts, the package calculates binary features during the designated -time at risk. This analysis helps in identifying specific attributes or -exposures that are present or absent in the cohort members, aiding in -the differentiation/comparability between cohorts.
        • +Database Comparison Lets you compare the same +cohort across two or more databases and adds in the standardized mean +different calculation when exactly two databases are selected. This is a +measure of association between the feature and the cohort, therefore +identifying which features differ across databases.
        +
      • -Incidence Rate: Utilizing the CohortIncidence R package, this set of -analyses computes incidence rates for both target and outcome cohorts -during the time at risk selected. This feature is essential for -assessing the frequency of outcomes or conditions within the specified -timeframe, providing a quantitative measure of risk or occurrence. -Incidence measures are provided in both tabular and graphical form, and -can be stratified across calendar year, age, and sex.
        • +Cohort Comparison Lets you compare two or more +cohorts across a database and adds in the standardized mean different +calculation when exactly two cohort are selected. This is a measure of +association between the feature and the cohort, therefore identifying +which features differ across databases. +
      +
    2. -Time to Event: Generates plots for the number of -events across different time periods (1, 30, or 365 days) for the -selected target and outcome cohorts. These plots visualize the temporal -distribution of events, allowing researchers to observe patterns over -time and make temporal comparisons between cohorts.
      3. +Exposed Case Series - characterizations that look +at people in the target cohort who have the outcome during some +specified time-at-risk: +
        +
      • +Risk Factor Compares aggregate covariate summaries +for patients in the target who have the outcome during the time-at-risk +period vs patients in the target who do not have the outcome during the +time-at-risk period. The standardized mean difference is added to +identify covariates that differ between the cohorts.
        • +
      • +Case Series Compares aggregate covariate summaries +before target start, between target start up to outcome start and after +outcome start for people in the target cohort who have the outcome +during some specified time-at-risk. This lets you see covariates that +are common before exposure and what happens afterwards.
        • +
      • +Time to Event: Shows the distribution of when the +outcome occurs relative to the target start. This can show you whether +the outcome occurs more after or before target exposure.
      • Dechallenge Rechallenge: Offers the ability to compute dechallenge (withdrawal of a drug or treatment) and rechallenge @@ -187,6 +237,16 @@

        Features and FunctionalitiesCohortIncidence R package, this set of +analyses computes incidence rates for both target and outcome cohorts +during the time at risk selected. This feature is essential for +assessing the frequency of outcomes or conditions within the specified +timeframe, providing a quantitative measure of risk or occurrence. +Incidence measures are provided in both tabular and graphical form, and +can be stratified across calendar year, age, and sex.

    @@ -200,14 +260,18 @@

    Utility and Applicationhere.

    +evidence-based medicine.

    +

    To find out more about the analyses execution details and see +examples, please see here.

    +

    To see the code behind the Characterization R package, please see here.

    + +
    @@ -220,16 +284,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/CohortDiagnostics.html b/docs/articles/CohortDiagnostics.html index 2dcc2fd6..d95aa1be 100644 --- a/docs/articles/CohortDiagnostics.html +++ b/docs/articles/CohortDiagnostics.html @@ -6,19 +6,20 @@ Cohort Diagnostics • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
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    • - +
    @@ -114,9 +115,9 @@

    Cohort Diagnostics

    Nathan Hall

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -263,7 +264,9 @@

    Utility and Application -

    + + @@ -276,16 +279,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/Cohorts.html b/docs/articles/Cohorts.html index c8e7199b..2fd096d9 100644 --- a/docs/articles/Cohorts.html +++ b/docs/articles/Cohorts.html @@ -6,19 +6,20 @@ Cohorts • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,7 +106,7 @@
    • - +
    @@ -114,9 +115,9 @@

    Cohorts

    Nathan Hall

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -221,7 +222,9 @@

    Tools for Cohort Creation & + +

    @@ -234,16 +237,16 @@

    Tools for Cohort Creation &

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/DataSources.html b/docs/articles/DataSources.html index 39d24a82..6d43f341 100644 --- a/docs/articles/DataSources.html +++ b/docs/articles/DataSources.html @@ -6,19 +6,20 @@ Data Sources • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,7 +106,7 @@
    • - +
    @@ -114,9 +115,9 @@

    Data Sources

    Nathan Hall

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -217,7 +218,9 @@

    Example OMOP-mapped Datasets -

    + + @@ -230,16 +233,16 @@

    Example OMOP-mapped Datasets

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/Estimation.html b/docs/articles/Estimation.html index bc5e8ebd..ccb61c81 100644 --- a/docs/articles/Estimation.html +++ b/docs/articles/Estimation.html @@ -6,19 +6,20 @@ Estimation • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,7 +106,7 @@
    • - +
    @@ -114,9 +115,9 @@

    Estimation

    Nathan Hall

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -483,7 +484,9 @@

    Utility and Application -

    + + @@ -496,16 +499,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/Prediction.html b/docs/articles/Prediction.html index bf31d92e..e2c1d9ec 100644 --- a/docs/articles/Prediction.html +++ b/docs/articles/Prediction.html @@ -6,19 +6,20 @@ Prediction • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,7 +106,7 @@
    • - +
    @@ -114,9 +115,9 @@

    Prediction

    Nathan Hall

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -207,7 +208,9 @@

    Utility and Application -

    + + @@ -220,16 +223,16 @@

    Utility and Application

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/ReportGenerator.html b/docs/articles/ReportGenerator.html index 2a703391..facb80e0 100644 --- a/docs/articles/ReportGenerator.html +++ b/docs/articles/ReportGenerator.html @@ -6,19 +6,20 @@ Report Generator • OhdsiShinyModules - + + - +
    @@ -41,7 +42,7 @@
  • - +
  • @@ -53,7 +54,7 @@
  • @@ -105,7 +106,7 @@
    • - +
    @@ -114,9 +115,9 @@

    Report Generator

    Nathan Hall

    -

    2024-10-07

    +

    2024-10-08

    + -
    @@ -156,7 +157,9 @@

    Notes + +

    @@ -169,16 +172,16 @@

    Notes

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/articles/index.html b/docs/articles/index.html index 48d06b34..b7245041 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,9 +1,9 @@ -Articles • OhdsiShinyModulesArticles • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +
    @@ -119,15 +119,15 @@

    All vignettes

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/authors.html b/docs/authors.html index bec37db2..c1a98ba8 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • OhdsiShinyModulesAuthors and Citation • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +
    -

    Authors and Citation

    +

    Authors

    - +
    • -

      Jenna Reps. Author, maintainer. +

      Jenna Reps. Author, maintainer.

    • -

      Nathan Hall. Author. +

      Nathan Hall. Author.

    • -

      Jamie Gibert. Author. +

      Jamie Gibert. Author.

    Citation

    - +

    Reps J, Hall N, Gibert J (2024). OhdsiShinyModules: Repository of Shiny Modules for OHDSI Result Viewers. -R package version 3.1.0. +R package version 3.1.0.9000. 

    @Manual{,
   title = {OhdsiShinyModules: Repository of Shiny Modules for OHDSI Result Viewers},
   author = {Jenna Reps and Nathan Hall and Jamie Gibert},
   year = {2024},
-  note = {R package version 3.1.0},
+  note = {R package version 3.1.0.9000},
 }
    @@ -134,15 +134,15 @@

    Citation

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/index.html b/docs/index.html index 600565e8..d252dba7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@ Repository of Shiny Modules for OHDSI Result Viewers • OhdsiShinyModules - + @@ -19,7 +19,7 @@ - +
    @@ -42,7 +42,7 @@
  • - +
  • @@ -54,7 +54,7 @@
  • @@ -106,7 +106,7 @@
    • - +
    @@ -239,16 +239,16 @@

    Developers

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/news/index.html b/docs/news/index.html index 15ccf1a7..ba0891b3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,9 +1,9 @@ -Changelog • OhdsiShinyModulesChangelog • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Changelog

    - +
    @@ -212,15 +212,15 @@

    OhdsiS

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9449d457..0ef782e9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: '3.2' -pkgdown: 2.1.0 +pandoc: 3.1.11 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: AddingShinyModules: AddingShinyModules.html @@ -10,4 +10,5 @@ articles: Estimation: Estimation.html Prediction: Prediction.html ReportGenerator: ReportGenerator.html -last_built: 2024-10-07T15:13Z +last_built: 2024-10-08T17:31Z + diff --git a/docs/reference/LargeDataTable.html b/docs/reference/LargeDataTable.html index 13f6b753..0dd62454 100644 --- a/docs/reference/LargeDataTable.html +++ b/docs/reference/LargeDataTable.html @@ -1,5 +1,5 @@ -Large Data Table — LargeDataTable • OhdsiShinyModulesLarge Data Table — LargeDataTable • OhdsiShinyModules - +
    @@ -32,7 +32,7 @@
    - +

    Large Data Table

    - +
    @@ -129,7 +129,7 @@

    Public fields

    Methods

    - +

    Public methods

    @@ -273,15 +273,15 @@

    Arguments -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/OhdsiShinyModules.html b/docs/reference/OhdsiShinyModules.html index a205f06b..608325cd 100644 --- a/docs/reference/OhdsiShinyModules.html +++ b/docs/reference/OhdsiShinyModules.html @@ -1,9 +1,9 @@ -OhdsiShinyModules — OhdsiShinyModules • OhdsiShinyModulesOhdsiShinyModules — OhdsiShinyModules • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    OhdsiShinyModules

    - +
    @@ -115,15 +115,15 @@

    Author

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/aboutHelperFile.html b/docs/reference/aboutHelperFile.html index 278c0bdc..438eacc9 100644 --- a/docs/reference/aboutHelperFile.html +++ b/docs/reference/aboutHelperFile.html @@ -1,9 +1,9 @@ -The location of the about module helper file — aboutHelperFile • OhdsiShinyModulesThe location of the about module helper file — aboutHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the about module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the about module helper file

    Value

    -

    string location of the about helper file

    + + +

    string location of the about helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other About: +

    Other About: aboutServer(), aboutViewer()

    @@ -126,15 +128,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/aboutServer.html b/docs/reference/aboutServer.html index e917e216..e206b59d 100644 --- a/docs/reference/aboutServer.html +++ b/docs/reference/aboutServer.html @@ -1,9 +1,9 @@ -The module server for the shiny app home — aboutServer • OhdsiShinyModulesThe module server for the shiny app home — aboutServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the shiny app home

    - +
    @@ -106,27 +106,27 @@

    The module server for the shiny app home

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    -
    config
    +
    config

    the config from the app.R file that contains a list of which modules to include

    Value

    -

    The server for the shiny app home

    + + +

    The server for the shiny app home

    Details

    @@ -134,7 +134,7 @@

    Details

    See also

    -

    Other About: +

    Other About: aboutHelperFile(), aboutViewer()

    @@ -151,15 +151,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/aboutViewer.html b/docs/reference/aboutViewer.html index 183dca7e..27e92841 100644 --- a/docs/reference/aboutViewer.html +++ b/docs/reference/aboutViewer.html @@ -1,9 +1,9 @@ -The module viewer for the shiny app home — aboutViewer • OhdsiShinyModulesThe module viewer for the shiny app home — aboutViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for the shiny app home

    - +
    @@ -101,15 +101,15 @@

    The module viewer for the shiny app home

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the home page module

    + + +

    The user interface to the home page module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other About: +

    Other About: aboutHelperFile(), aboutServer()

    @@ -134,15 +134,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/characterizationHelperFile.html b/docs/reference/characterizationHelperFile.html index ed7edb25..730fe4cd 100644 --- a/docs/reference/characterizationHelperFile.html +++ b/docs/reference/characterizationHelperFile.html @@ -1,9 +1,9 @@ -The location of the characterization module helper file — characterizationHelperFile • OhdsiShinyModulesThe location of the characterization module helper file — characterizationHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the characterization module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the characterization module helper file

    Value

    -

    string location of the characterization helper file

    + + +

    string location of the characterization helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationIncidenceServer(), characterizationIncidenceViewer(), characterizationServer(), @@ -128,15 +130,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/characterizationIncidenceServer.html b/docs/reference/characterizationIncidenceServer.html index 60470985..4fd2d02a 100644 --- a/docs/reference/characterizationIncidenceServer.html +++ b/docs/reference/characterizationIncidenceServer.html @@ -1,9 +1,9 @@ -The module server for exploring incidence results — characterizationIncidenceServer • OhdsiShinyModulesThe module server for exploring incidence results — characterizationIncidenceServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring incidence results

    - +
    @@ -109,39 +109,39 @@

    The module server for exploring incidence results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    -
    parents
    +
    parents

    a list of parent cohorts

    -
    parentIndex
    +
    parentIndex

    an integer specifying the parent index of interest

    -
    outcomes
    +
    outcomes

    a reactive object specifying the outcomes of interest

    -
    targetIds
    +
    targetIds

    a reactive vector of integer specifying the targetIds of interest

    Value

    -

    The server to the prediction incidence module

    + + +

    The server to the prediction incidence module

    Details

    @@ -149,7 +149,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceViewer(), characterizationServer(), @@ -168,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/characterizationIncidenceViewer.html b/docs/reference/characterizationIncidenceViewer.html index ad3bd6f1..2005853c 100644 --- a/docs/reference/characterizationIncidenceViewer.html +++ b/docs/reference/characterizationIncidenceViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring incidence results — characterizationIncidenceViewer • OhdsiShinyModulesThe module viewer for exploring incidence results — characterizationIncidenceViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring incidence results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring incidence results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the description incidence module

    + + +

    The user interface to the description incidence module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceServer(), characterizationServer(), @@ -136,15 +136,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/characterizationServer.html b/docs/reference/characterizationServer.html index 64d74634..608d0627 100644 --- a/docs/reference/characterizationServer.html +++ b/docs/reference/characterizationServer.html @@ -1,9 +1,9 @@ -The module server for exploring characterization studies — characterizationServer • OhdsiShinyModulesThe module server for exploring characterization studies — characterizationServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring characterization studies

    - +
    @@ -105,23 +105,23 @@

    The module server for exploring characterization studies

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    Value

    -

    The server for the characterization module

    + + +

    The server for the characterization module

    Details

    @@ -129,7 +129,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceServer(), characterizationIncidenceViewer(), @@ -148,15 +148,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/characterizationViewer.html b/docs/reference/characterizationViewer.html index 37f2b12d..af3d405e 100644 --- a/docs/reference/characterizationViewer.html +++ b/docs/reference/characterizationViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring characterization studies — characterizationViewer • OhdsiShinyModulesThe module viewer for exploring characterization studies — characterizationViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring characterization studies

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring characterization studies

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the characterization viewer module

    + + +

    The user interface to the characterization viewer module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other Characterization: +

    Other Characterization: characterizationHelperFile(), characterizationIncidenceServer(), characterizationIncidenceViewer(), @@ -136,15 +136,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortCountsModule.html b/docs/reference/cohortCountsModule.html index 220c27a4..482732cd 100644 --- a/docs/reference/cohortCountsModule.html +++ b/docs/reference/cohortCountsModule.html @@ -1,9 +1,9 @@ -Shiny module for cohort counts — cohortCountsModule • OhdsiShinyModulesShiny module for cohort counts — cohortCountsModule • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Shiny module for cohort counts

    - +
    @@ -109,39 +109,37 @@

    Shiny module for cohort counts

    Arguments

    - - -
    id
    +
    id

    namespace id

    -
    dataSource
    +
    dataSource

    Backend Data source (DatabaseConnection)

    -
    cohortTable
    +
    cohortTable

    data.frame of all cohorts

    -
    databaseTable
    +
    databaseTable

    data.frame of all databases

    -
    selectedCohorts
    +
    selectedCohorts

    shiny::reactive - should return cohorts selected or NULL

    -
    selectedDatabaseIds
    +
    selectedDatabaseIds

    shiny::reactive - should return cohorts selected or NULL

    -
    cohortIds
    +
    cohortIds

    shiny::reactive - should return cohorts selected integers or NULL

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsView(), cohortDefinitionsModule(), cohortDefinitionsView(), @@ -176,15 +174,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortCountsView.html b/docs/reference/cohortCountsView.html index 44efb217..c6886b27 100644 --- a/docs/reference/cohortCountsView.html +++ b/docs/reference/cohortCountsView.html @@ -1,9 +1,9 @@ -Cohort Counts View — cohortCountsView • OhdsiShinyModulesCohort Counts View — cohortCountsView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Counts View

    - +
    @@ -101,15 +101,13 @@

    Cohort Counts View

    Arguments

    - - -
    id
    +
    id

    Namespace id

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortDefinitionsModule(), cohortDefinitionsView(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortDefinitionsModule.html b/docs/reference/cohortDefinitionsModule.html index ab312d7b..d1e61cca 100644 --- a/docs/reference/cohortDefinitionsModule.html +++ b/docs/reference/cohortDefinitionsModule.html @@ -1,9 +1,9 @@ -Cohort Definition module — cohortDefinitionsModule • OhdsiShinyModulesCohort Definition module — cohortDefinitionsModule • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Definition module

    - +
    @@ -108,35 +108,33 @@

    Cohort Definition module

    Arguments

    - - -
    id
    +
    id

    Namespace id

    -
    dataSource
    +
    dataSource

    DatabaseConnection

    -
    cohortDefinitions
    +
    cohortDefinitions

    reactive of cohort definitions to display

    -
    cohortTable
    +
    cohortTable

    data.frame of cohorts, cohortId, cohortName

    -
    cohortCountTable
    +
    cohortCountTable

    data.frame of cohortCounts, cohortId, subjects records

    -
    databaseTable
    +
    databaseTable

    data.frame of databasese, databaseId, name

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsView(), @@ -171,15 +169,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortDefinitionsView.html b/docs/reference/cohortDefinitionsView.html index e4da463d..863b92f1 100644 --- a/docs/reference/cohortDefinitionsView.html +++ b/docs/reference/cohortDefinitionsView.html @@ -1,9 +1,9 @@ -Cohort Definitions View — cohortDefinitionsView • OhdsiShinyModulesCohort Definitions View — cohortDefinitionsView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Definitions View

    - +
    @@ -101,15 +101,13 @@

    Cohort Definitions View

    Arguments

    - - -
    id
    +
    id

    Namespace id for module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortDiagCharacterizationView.html b/docs/reference/cohortDiagCharacterizationView.html index 824baec8..5ccb96fd 100644 --- a/docs/reference/cohortDiagCharacterizationView.html +++ b/docs/reference/cohortDiagCharacterizationView.html @@ -1,9 +1,9 @@ -characterization — cohortDiagCharacterizationView • OhdsiShinyModulescharacterization — cohortDiagCharacterizationView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    characterization

    - +
    @@ -101,15 +101,13 @@

    characterization

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("characterization") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortDiagnosticsHelperFile.html b/docs/reference/cohortDiagnosticsHelperFile.html index 0c576e76..6458b35f 100644 --- a/docs/reference/cohortDiagnosticsHelperFile.html +++ b/docs/reference/cohortDiagnosticsHelperFile.html @@ -1,9 +1,9 @@ -The location of the description module helper file — cohortDiagnosticsHelperFile • OhdsiShinyModulesThe location of the description module helper file — cohortDiagnosticsHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the description module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the description module helper file

    Value

    -

    string location of the description helper file

    + + +

    string location of the description helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortDiagnosticsServer.html b/docs/reference/cohortDiagnosticsServer.html index 4e60cb44..c763d619 100644 --- a/docs/reference/cohortDiagnosticsServer.html +++ b/docs/reference/cohortDiagnosticsServer.html @@ -1,9 +1,9 @@ -Cohort Diagnostics Explorer main module — cohortDiagnosticsServer • OhdsiShinyModulesCohort Diagnostics Explorer main module — cohortDiagnosticsServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Diagnostics Explorer main module

    - +
    @@ -106,27 +106,25 @@

    Cohort Diagnostics Explorer main module

    Arguments

    - - -
    id
    +
    id

    module Id

    -
    connectionHandler
    +
    connectionHandler

    ResultModelManager ConnectionHander instance

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    results database settings

    -
    dataSource
    +
    dataSource

    dataSource optionally created with createCdDatabaseDataSource

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -161,15 +159,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortDiagnosticsView.html b/docs/reference/cohortDiagnosticsView.html index a9754916..7b9f3ca8 100644 --- a/docs/reference/cohortDiagnosticsView.html +++ b/docs/reference/cohortDiagnosticsView.html @@ -1,9 +1,9 @@ -View for cohort diagnostics module — cohortDiagnosticsView • OhdsiShinyModulesView for cohort diagnostics module — cohortDiagnosticsView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    View for cohort diagnostics module

    - +
    @@ -101,15 +101,15 @@

    View for cohort diagnostics module

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort diagnostics viewer module

    + + +

    The user interface to the cohort diagnostics viewer module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -152,15 +152,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortGeneratorHelperFile.html b/docs/reference/cohortGeneratorHelperFile.html index 1dfd9e06..c7d00825 100644 --- a/docs/reference/cohortGeneratorHelperFile.html +++ b/docs/reference/cohortGeneratorHelperFile.html @@ -1,9 +1,9 @@ -The location of the cohort-generator module helper file — cohortGeneratorHelperFile • OhdsiShinyModulesThe location of the cohort-generator module helper file — cohortGeneratorHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the cohort-generator module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the cohort-generator module helper file

    Value

    -

    string location of the cohort-generator helper file

    + + +

    string location of the cohort-generator helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other CohortGenerator: +

    Other CohortGenerator: cohortGeneratorServer(), cohortGeneratorViewer()

    @@ -126,15 +128,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortGeneratorServer.html b/docs/reference/cohortGeneratorServer.html index 7ac888fb..e2981631 100644 --- a/docs/reference/cohortGeneratorServer.html +++ b/docs/reference/cohortGeneratorServer.html @@ -1,9 +1,9 @@ -The module server for the main cohort generator module — cohortGeneratorServer • OhdsiShinyModulesThe module server for the main cohort generator module — cohortGeneratorServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the main cohort generator module

    - +
    @@ -101,27 +101,27 @@

    The module server for the main cohort generator module

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a named list containing the cohort generator results database details (schema, table prefix)

    Value

    -

    the cohort generator results viewer main module server

    + + +

    the cohort generator results viewer main module server

    See also

    -

    Other CohortGenerator: +

    Other CohortGenerator: cohortGeneratorHelperFile(), cohortGeneratorViewer()

    @@ -138,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortGeneratorViewer.html b/docs/reference/cohortGeneratorViewer.html index 92153549..7fa45e40 100644 --- a/docs/reference/cohortGeneratorViewer.html +++ b/docs/reference/cohortGeneratorViewer.html @@ -1,9 +1,9 @@ -The viewer of the main cohort generator module — cohortGeneratorViewer • OhdsiShinyModulesThe viewer of the main cohort generator module — cohortGeneratorViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The viewer of the main cohort generator module

    - +
    @@ -101,19 +101,19 @@

    The viewer of the main cohort generator module

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort generator results viewer

    + + +

    The user interface to the cohort generator results viewer

    See also

    -

    Other CohortGenerator: +

    Other CohortGenerator: cohortGeneratorHelperFile(), cohortGeneratorServer()

    @@ -130,15 +130,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodAttritionServer.html b/docs/reference/cohortMethodAttritionServer.html index 8a4b9fb7..095faab4 100644 --- a/docs/reference/cohortMethodAttritionServer.html +++ b/docs/reference/cohortMethodAttritionServer.html @@ -1,9 +1,9 @@ -The module server for rendering the PLE attrition results — cohortMethodAttritionServer • OhdsiShinyModulesThe module server for rendering the PLE attrition results — cohortMethodAttritionServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the PLE attrition results

    - +
    @@ -106,31 +106,31 @@

    The module server for rendering the PLE attrition results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    the PLE attrition results content server

    + + +

    the PLE attrition results content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), cohortMethodCovariateBalanceViewer(), @@ -163,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodAttritionViewer.html b/docs/reference/cohortMethodAttritionViewer.html index 0af3f67e..c1f59353 100644 --- a/docs/reference/cohortMethodAttritionViewer.html +++ b/docs/reference/cohortMethodAttritionViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE attrition results — cohortMethodAttritionViewer • OhdsiShinyModulesThe module viewer for rendering the PLE attrition results — cohortMethodAttritionViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE attrition results

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE attrition results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method attrition

    + + +

    The user interface to the cohort method attrition

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodCovariateBalanceServer(), cohortMethodCovariateBalanceViewer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodCovariateBalanceServer.html b/docs/reference/cohortMethodCovariateBalanceServer.html index 1a124066..cf039181 100644 --- a/docs/reference/cohortMethodCovariateBalanceServer.html +++ b/docs/reference/cohortMethodCovariateBalanceServer.html @@ -1,9 +1,9 @@ -The module server for rendering the covariate balance plot — cohortMethodCovariateBalanceServer • OhdsiShinyModulesThe module server for rendering the covariate balance plot — cohortMethodCovariateBalanceServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the covariate balance plot

    - +
    @@ -107,35 +107,35 @@

    The module server for rendering the covariate balance plot

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    metaAnalysisDbIds
    +
    metaAnalysisDbIds

    metaAnalysisDbIds

    Value

    -

    the PLE covariate balance content server

    + + +

    the PLE covariate balance content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceViewer(), @@ -168,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodCovariateBalanceViewer.html b/docs/reference/cohortMethodCovariateBalanceViewer.html index bb49b87c..a5a8a7ad 100644 --- a/docs/reference/cohortMethodCovariateBalanceViewer.html +++ b/docs/reference/cohortMethodCovariateBalanceViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE covariate balance analysis — cohortMethodCovariateBalanceViewer • OhdsiShinyModulesThe module viewer for rendering the PLE covariate balance analysis — cohortMethodCovariateBalanceViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE covariate balance analysis

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE covariate balance analysis

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method covariate balance results

    + + +

    The user interface to the cohort method covariate balance results

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodKaplanMeierServer.html b/docs/reference/cohortMethodKaplanMeierServer.html index cc1e00e8..3358725c 100644 --- a/docs/reference/cohortMethodKaplanMeierServer.html +++ b/docs/reference/cohortMethodKaplanMeierServer.html @@ -1,9 +1,9 @@ -The module server for rendering the Kaplan Meier curve — cohortMethodKaplanMeierServer • OhdsiShinyModulesThe module server for rendering the Kaplan Meier curve — cohortMethodKaplanMeierServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the Kaplan Meier curve

    - +
    @@ -106,31 +106,31 @@

    The module server for rendering the Kaplan Meier curve

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    the PLE Kaplain Meier content server

    + + +

    the PLE Kaplain Meier content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -163,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodKaplanMeierViewer.html b/docs/reference/cohortMethodKaplanMeierViewer.html index 8cfeda0e..2aae8d28 100644 --- a/docs/reference/cohortMethodKaplanMeierViewer.html +++ b/docs/reference/cohortMethodKaplanMeierViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE Kaplan Meier curve — cohortMethodKaplanMeierViewer • OhdsiShinyModulesThe module viewer for rendering the PLE Kaplan Meier curve — cohortMethodKaplanMeierViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE Kaplan Meier curve

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE Kaplan Meier curve

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The module viewer for Kaplan Meier objects

    + + +

    The module viewer for Kaplan Meier objects

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPopulationCharacteristicsServer.html b/docs/reference/cohortMethodPopulationCharacteristicsServer.html index 33fdb88e..6ea8456f 100644 --- a/docs/reference/cohortMethodPopulationCharacteristicsServer.html +++ b/docs/reference/cohortMethodPopulationCharacteristicsServer.html @@ -1,9 +1,9 @@ -The module server for rendering the population characteristics — cohortMethodPopulationCharacteristicsServer • OhdsiShinyModulesThe module server for rendering the population characteristics — cohortMethodPopulationCharacteristicsServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the population characteristics

    - +
    @@ -106,31 +106,31 @@

    The module server for rendering the population characteristics

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    the PLE population characteristics content server

    + + +

    the PLE population characteristics content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -163,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPopulationCharacteristicsViewer.html b/docs/reference/cohortMethodPopulationCharacteristicsViewer.html index e0bb426a..d0687569 100644 --- a/docs/reference/cohortMethodPopulationCharacteristicsViewer.html +++ b/docs/reference/cohortMethodPopulationCharacteristicsViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE population characteristics — cohortMethodPopulationCharacteristicsViewer • OhdsiShinyModulesThe module viewer for rendering the PLE population characteristics — cohortMethodPopulationCharacteristicsViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE population characteristics

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE population characteristics

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method population characteristics objects

    + + +

    The user interface to the cohort method population characteristics objects

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPowerServer.html b/docs/reference/cohortMethodPowerServer.html index 2fa75281..7b1fd7e6 100644 --- a/docs/reference/cohortMethodPowerServer.html +++ b/docs/reference/cohortMethodPowerServer.html @@ -1,9 +1,9 @@ -The module server for rendering the PLE power analysis results — cohortMethodPowerServer • OhdsiShinyModulesThe module server for rendering the PLE power analysis results — cohortMethodPowerServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the PLE power analysis results

    - +
    @@ -106,31 +106,31 @@

    The module server for rendering the PLE power analysis results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    the PLE systematic error power server

    + + +

    the PLE systematic error power server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -163,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPowerViewer.html b/docs/reference/cohortMethodPowerViewer.html index b98cb899..a9c264de 100644 --- a/docs/reference/cohortMethodPowerViewer.html +++ b/docs/reference/cohortMethodPowerViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE power analysis — cohortMethodPowerViewer • OhdsiShinyModulesThe module viewer for rendering the PLE power analysis — cohortMethodPowerViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE power analysis

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE power analysis

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method power calculation results

    + + +

    The user interface to the cohort method power calculation results

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPropensityModelServer.html b/docs/reference/cohortMethodPropensityModelServer.html index fae12a7a..e0ad52c2 100644 --- a/docs/reference/cohortMethodPropensityModelServer.html +++ b/docs/reference/cohortMethodPropensityModelServer.html @@ -1,9 +1,9 @@ -The module server for rendering the propensity score model — cohortMethodPropensityModelServer • OhdsiShinyModulesThe module server for rendering the propensity score model — cohortMethodPropensityModelServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the propensity score model

    - +
    @@ -106,31 +106,31 @@

    The module server for rendering the propensity score model

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    the PLE propensity score model

    + + +

    the PLE propensity score model

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -163,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPropensityModelViewer.html b/docs/reference/cohortMethodPropensityModelViewer.html index a0d9890c..da22d5fe 100644 --- a/docs/reference/cohortMethodPropensityModelViewer.html +++ b/docs/reference/cohortMethodPropensityModelViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE propensity score model covariates/coefficients — cohortMethodPropensityModelViewer • OhdsiShinyModulesThe module viewer for rendering the PLE propensity score model covariates/coefficients — cohortMethodPropensityModelViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE propensity score model covariates/coefficients

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE propensity score model covariates/co

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method propensity score model covariates/coefficients

    + + +

    The user interface to the cohort method propensity score model covariates/coefficients

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPropensityScoreDistServer.html b/docs/reference/cohortMethodPropensityScoreDistServer.html index 96a6da07..e8094b2b 100644 --- a/docs/reference/cohortMethodPropensityScoreDistServer.html +++ b/docs/reference/cohortMethodPropensityScoreDistServer.html @@ -1,9 +1,9 @@ -The module server for rendering a PLE propensity score distribution — cohortMethodPropensityScoreDistServer • OhdsiShinyModulesThe module server for rendering a PLE propensity score distribution — cohortMethodPropensityScoreDistServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@

    - +

    The module server for rendering a PLE propensity score distribution

    - +
    @@ -107,35 +107,35 @@

    The module server for rendering a PLE propensity score distribution

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection to the PLE results database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    metaAnalysisDbIds
    +
    metaAnalysisDbIds

    metaAnalysisDbIds

    Value

    -

    the PLE propensity score distribution content server

    + + +

    the PLE propensity score distribution content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -168,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodPropensityScoreDistViewer.html b/docs/reference/cohortMethodPropensityScoreDistViewer.html index 670c354f..50e5a9a8 100644 --- a/docs/reference/cohortMethodPropensityScoreDistViewer.html +++ b/docs/reference/cohortMethodPropensityScoreDistViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the propensity score distribution — cohortMethodPropensityScoreDistViewer • OhdsiShinyModulesThe module viewer for rendering the propensity score distribution — cohortMethodPropensityScoreDistViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the propensity score distribution

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the propensity score distribution

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method propensity score distribution

    + + +

    The user interface to the cohort method propensity score distribution

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodSystematicErrorServer.html b/docs/reference/cohortMethodSystematicErrorServer.html index cc528fda..3e3827c5 100644 --- a/docs/reference/cohortMethodSystematicErrorServer.html +++ b/docs/reference/cohortMethodSystematicErrorServer.html @@ -1,9 +1,9 @@ -The module server for rendering the systematic error objects — cohortMethodSystematicErrorServer • OhdsiShinyModulesThe module server for rendering the systematic error objects — cohortMethodSystematicErrorServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for rendering the systematic error objects

    - +
    @@ -106,31 +106,31 @@

    The module server for rendering the systematic error objects

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    selectedRow
    +
    selectedRow

    the selected row from the main results table

    -
    connectionHandler
    +
    connectionHandler

    the connection handler to the result databases

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    the PLE systematic error content server

    + + +

    the PLE systematic error content server

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -163,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortMethodSystematicErrorViewer.html b/docs/reference/cohortMethodSystematicErrorViewer.html index cc4eca0e..855355cd 100644 --- a/docs/reference/cohortMethodSystematicErrorViewer.html +++ b/docs/reference/cohortMethodSystematicErrorViewer.html @@ -1,9 +1,9 @@ -The module viewer for rendering the PLE systematic error objects — cohortMethodSystematicErrorViewer • OhdsiShinyModulesThe module viewer for rendering the PLE systematic error objects — cohortMethodSystematicErrorViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for rendering the PLE systematic error objects

    - +
    @@ -101,19 +101,19 @@

    The module viewer for rendering the PLE systematic error objects

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the cohort method systematic error module

    + + +

    The user interface to the cohort method systematic error module

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/cohortOverlapView.html b/docs/reference/cohortOverlapView.html index 4fa1d93d..1a81528a 100644 --- a/docs/reference/cohortOverlapView.html +++ b/docs/reference/cohortOverlapView.html @@ -1,9 +1,9 @@ -Cohort Overlap View — cohortOverlapView • OhdsiShinyModulesCohort Overlap View — cohortOverlapView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Cohort Overlap View

    - +
    @@ -101,15 +101,13 @@

    Cohort Overlap View

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("cohortOverlap") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/compareCohortCharacterizationView.html b/docs/reference/compareCohortCharacterizationView.html index 4ff5d070..88b36bef 100644 --- a/docs/reference/compareCohortCharacterizationView.html +++ b/docs/reference/compareCohortCharacterizationView.html @@ -1,9 +1,9 @@ -compare characterization view — compareCohortCharacterizationView • OhdsiShinyModulescompare characterization view — compareCohortCharacterizationView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    compare characterization view

    - +
    @@ -104,19 +104,17 @@

    compare characterization view

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("compareCohortCharacterization") inside diagnosticsExplorer module

    -
    title
    +
    title

    Optional string title field

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -151,15 +149,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/conceptsInDataSourceView.html b/docs/reference/conceptsInDataSourceView.html index 55678bdb..95d3d03f 100644 --- a/docs/reference/conceptsInDataSourceView.html +++ b/docs/reference/conceptsInDataSourceView.html @@ -1,9 +1,9 @@ -concepts In DataSource View — conceptsInDataSourceView • OhdsiShinyModulesconcepts In DataSource View — conceptsInDataSourceView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    concepts In DataSource View

    - +
    @@ -101,15 +101,13 @@

    concepts In DataSource View

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("conceptsInDataSource") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/createCdDatabaseDataSource.html b/docs/reference/createCdDatabaseDataSource.html index a3c912c2..f0aa05d2 100644 --- a/docs/reference/createCdDatabaseDataSource.html +++ b/docs/reference/createCdDatabaseDataSource.html @@ -1,11 +1,11 @@ -Create a CD data source from a database — createCdDatabaseDataSource • OhdsiShinyModulesCreate a CD data source from a database — createCdDatabaseDataSource • OhdsiShinyModules - +
    @@ -27,7 +27,7 @@
    - +

    Create a CD data source from a database

    - +
    @@ -113,35 +113,35 @@

    Create a CD data source from a database

    Arguments

    - - -
    connectionHandler
    +
    connectionHandler

    An instance of a ResultModelManager::connectionHander - manages a connection to a database.

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    dataModelSpecificationsPath
    +
    dataModelSpecificationsPath

    The path to a file containing specifications for the data model used by the database.

    -
    dataMigrationsRef
    +
    dataMigrationsRef

    The path to a file listing all migrations for the data model that should have been applied

    -
    displayProgress
    +
    displayProgress

    display a progress messaage (can only be used inside a shiny reactive context)

    Value

    -

    An object of class `CdDataSource`.

    + + +

    An object of class `CdDataSource`.

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -176,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/createCustomColDefList.html b/docs/reference/createCustomColDefList.html index 57f3a577..37b2fe18 100644 --- a/docs/reference/createCustomColDefList.html +++ b/docs/reference/createCustomColDefList.html @@ -1,9 +1,9 @@ -Creating a list of custom column definitions for use in reactables — createCustomColDefList • OhdsiShinyModulesCreating a list of custom column definitions for use in reactables — createCustomColDefList • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Creating a list of custom column definitions for use in reactables

    - +
    @@ -107,47 +107,47 @@

    Creating a list of custom column definitions for use in reactables

    Arguments

    - - -
    rawColNames
    +
    rawColNames

    The raw column names taken directly from the source data table that are to be overwritten in the reactable

    -
    niceColNames
    -

    The formatted column names that will appear as-specified in +

    niceColNames
    +

    The formatted column names that will appear as-specified in the reactable

    -
    tooltipText
    -

    The text to be displayed in a toolTip when hovering over the +

    tooltipText
    +

    The text to be displayed in a toolTip when hovering over the column in the reactable

    -
    case
    +
    case

    Optional argument to convert raw column names to snake or camel case. Defaults to NULL and preserves whatever raw column names are passed in

    -
    customColDefOptions
    +
    customColDefOptions

    A list of lists, where the inner lists are any custom options from reactable::colDef for each column

    Value

    -

    A named list of reactable::colDef objects

    + + +

    A named list of reactable::colDef objects

    See also

    -

    Other Utils: +

    Other Utils: datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), @@ -168,15 +168,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/createLargeSqlQueryDt.html b/docs/reference/createLargeSqlQueryDt.html index 3d0de091..fdffcc5a 100644 --- a/docs/reference/createLargeSqlQueryDt.html +++ b/docs/reference/createLargeSqlQueryDt.html @@ -1,11 +1,11 @@ -Create Large Sql Query Data Table — createLargeSqlQueryDt • OhdsiShinyModulesCreate Large Sql Query Data Table — createLargeSqlQueryDt • OhdsiShinyModules - +
    @@ -27,7 +27,7 @@
    - +

    Create Large Sql Query Data Table

    - +
    @@ -110,28 +110,26 @@

    Create Large Sql Query Data Table

    Arguments

    - - -
    connectionHandler
    +
    connectionHandler

    ResultModelManager connectionHandler instance

    -
    connectionDetails
    +
    connectionDetails

    DatabaseConnector connectionDetails instance

    -
    baseQuery
    +
    baseQuery

    base sql query

    -
    countQuery
    +
    countQuery

    count query string (should match query). Can be auto generated with sub query (default) but this will likely result in slow results

    See also

    -

    Other LargeTables: +

    Other LargeTables: largeTableServer(), largeTableView()

    @@ -148,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticDrillServer.html b/docs/reference/dataDiagnosticDrillServer.html index 6dbb5af7..8c3f5db0 100644 --- a/docs/reference/dataDiagnosticDrillServer.html +++ b/docs/reference/dataDiagnosticDrillServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction summary results — dataDiagnosticDrillServer • OhdsiShinyModulesThe module server for exploring prediction summary results — dataDiagnosticDrillServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction summary results

    - +
    @@ -101,23 +101,23 @@

    The module server for exploring prediction summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the summary module

    + + +

    The server to the summary module

    Details

    @@ -125,7 +125,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), dataDiagnosticServer(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticDrillViewer.html b/docs/reference/dataDiagnosticDrillViewer.html index 1dfb5136..36f2c8ff 100644 --- a/docs/reference/dataDiagnosticDrillViewer.html +++ b/docs/reference/dataDiagnosticDrillViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring data-diagnostic results in more detail — dataDiagnosticDrillViewer • OhdsiShinyModulesThe module viewer for exploring data-diagnostic results in more detail — dataDiagnosticDrillViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring data-diagnostic results in more detail

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring data-diagnostic results in more detail

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the summary module

    + + +

    The user interface to the summary module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticHelperFile(), dataDiagnosticServer(), @@ -138,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticHelperFile.html b/docs/reference/dataDiagnosticHelperFile.html index 7147d9d2..db08a85d 100644 --- a/docs/reference/dataDiagnosticHelperFile.html +++ b/docs/reference/dataDiagnosticHelperFile.html @@ -1,9 +1,9 @@ -The location of the data-diagnostic module helper file — dataDiagnosticHelperFile • OhdsiShinyModulesThe location of the data-diagnostic module helper file — dataDiagnosticHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the data-diagnostic module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the data-diagnostic module helper file

    Value

    -

    string location of the data-diagnostic helper file

    + + +

    string location of the data-diagnostic helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticServer(), @@ -130,15 +132,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticServer.html b/docs/reference/dataDiagnosticServer.html index f5c3ddf5..19f00982 100644 --- a/docs/reference/dataDiagnosticServer.html +++ b/docs/reference/dataDiagnosticServer.html @@ -1,9 +1,9 @@ -The module server for exploring data-diagnostic — dataDiagnosticServer • OhdsiShinyModulesThe module server for exploring data-diagnostic — dataDiagnosticServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring data-diagnostic

    - +
    @@ -105,23 +105,23 @@

    The module server for exploring data-diagnostic

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the data-diagnostic result schema

    Value

    -

    The server for the data-diagnostic module

    + + +

    The server for the data-diagnostic module

    Details

    @@ -129,7 +129,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -150,15 +150,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticSummaryServer.html b/docs/reference/dataDiagnosticSummaryServer.html index 5d7344cd..ef719a1c 100644 --- a/docs/reference/dataDiagnosticSummaryServer.html +++ b/docs/reference/dataDiagnosticSummaryServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction summary results — dataDiagnosticSummaryServer • OhdsiShinyModulesThe module server for exploring prediction summary results — dataDiagnosticSummaryServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction summary results

    - +
    @@ -101,23 +101,23 @@

    The module server for exploring prediction summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the summary module

    + + +

    The server to the summary module

    Details

    @@ -125,7 +125,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -146,15 +146,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticSummaryViewer.html b/docs/reference/dataDiagnosticSummaryViewer.html index 1038a1b0..917c3cd8 100644 --- a/docs/reference/dataDiagnosticSummaryViewer.html +++ b/docs/reference/dataDiagnosticSummaryViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring data-diagnostic summary results — dataDiagnosticSummaryViewer • OhdsiShinyModulesThe module viewer for exploring data-diagnostic summary results — dataDiagnosticSummaryViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring data-diagnostic summary results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring data-diagnostic summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the summary module

    + + +

    The user interface to the summary module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -138,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/dataDiagnosticViewer.html b/docs/reference/dataDiagnosticViewer.html index acc3a8da..169aaf73 100644 --- a/docs/reference/dataDiagnosticViewer.html +++ b/docs/reference/dataDiagnosticViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring data-diagnostic — dataDiagnosticViewer • OhdsiShinyModulesThe module viewer for exploring data-diagnostic — dataDiagnosticViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring data-diagnostic

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring data-diagnostic

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the data-diagnostic viewer module

    + + +

    The user interface to the data-diagnostic viewer module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other DataDiagnostics: +

    Other DataDiagnostics: dataDiagnosticDrillServer(), dataDiagnosticDrillViewer(), dataDiagnosticHelperFile(), @@ -138,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/databaseInformationView.html b/docs/reference/databaseInformationView.html index 74fd2105..aba3805d 100644 --- a/docs/reference/databaseInformationView.html +++ b/docs/reference/databaseInformationView.html @@ -1,9 +1,9 @@ -database Information View — databaseInformationView • OhdsiShinyModulesdatabase Information View — databaseInformationView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    database Information View

    - +
    @@ -101,15 +101,13 @@

    database Information View

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("databaseInformation") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/datasourcesHelperFile.html b/docs/reference/datasourcesHelperFile.html index d607c6c5..2214d5bb 100644 --- a/docs/reference/datasourcesHelperFile.html +++ b/docs/reference/datasourcesHelperFile.html @@ -1,9 +1,9 @@ -Define the helper file for the module — datasourcesHelperFile • OhdsiShinyModulesDefine the helper file for the module — datasourcesHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Define the helper file for the module

    - +
    @@ -101,18 +101,20 @@

    Define the helper file for the module

    Value

    -

    The helper html file for the datasources module

    + + +

    The helper html file for the datasources module

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesServer(), datasourcesViewer(), @@ -133,15 +135,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/datasourcesServer.html b/docs/reference/datasourcesServer.html index 53b6802a..284cdf20 100644 --- a/docs/reference/datasourcesServer.html +++ b/docs/reference/datasourcesServer.html @@ -1,9 +1,9 @@ -The server function for the datasources module — datasourcesServer • OhdsiShinyModulesThe server function for the datasources module — datasourcesServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The server function for the datasources module

    - +
    @@ -101,34 +101,34 @@

    The server function for the datasources module

    Arguments

    - - -
    id
    +
    id

    The unique id for the datasources server namespace

    -
    connectionHandler
    +
    connectionHandler

    A connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    A named list containing the cohort generator results database details (schema, table prefix)

    Value

    -

    The server for the datasources module

    + + +

    The server for the datasources module

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesViewer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesViewer(), @@ -149,15 +149,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/datasourcesViewer.html b/docs/reference/datasourcesViewer.html index efa84cb6..7fbbd366 100644 --- a/docs/reference/datasourcesViewer.html +++ b/docs/reference/datasourcesViewer.html @@ -1,9 +1,9 @@ -The viewer function for hte datasources module — datasourcesViewer • OhdsiShinyModulesThe viewer function for hte datasources module — datasourcesViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The viewer function for hte datasources module

    - +
    @@ -101,26 +101,26 @@

    The viewer function for hte datasources module

    Arguments

    - - -
    id
    +
    id

    The unique id for the datasources viewer namespace

    Value

    -

    The UI for the datasources module

    + + +

    The UI for the datasources module

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), makeButtonLabel(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -141,15 +141,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/estimationHelperFile.html b/docs/reference/estimationHelperFile.html index 353c29dd..0db7d286 100644 --- a/docs/reference/estimationHelperFile.html +++ b/docs/reference/estimationHelperFile.html @@ -1,9 +1,9 @@ -The location of the estimation module helper file — estimationHelperFile • OhdsiShinyModulesThe location of the estimation module helper file — estimationHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the estimation module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the estimation module helper file

    Value

    -

    string location of the characterization helper file

    + + +

    string location of the characterization helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -142,15 +144,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/estimationServer.html b/docs/reference/estimationServer.html index 8f1c79cc..7e16ba7e 100644 --- a/docs/reference/estimationServer.html +++ b/docs/reference/estimationServer.html @@ -1,9 +1,9 @@ -The module server for exploring estimation studies — estimationServer • OhdsiShinyModulesThe module server for exploring estimation studies — estimationServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring estimation studies

    - +
    @@ -105,23 +105,23 @@

    The module server for exploring estimation studies

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    Value

    -

    The server for the estimation module

    + + +

    The server for the estimation module

    Details

    @@ -129,7 +129,7 @@

    Details

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -162,15 +162,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/estimationViewer.html b/docs/reference/estimationViewer.html index b893545d..ef6c65e5 100644 --- a/docs/reference/estimationViewer.html +++ b/docs/reference/estimationViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring characterization studies — estimationViewer • OhdsiShinyModulesThe module viewer for exploring characterization studies — estimationViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring characterization studies

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring characterization studies

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the characterization viewer module

    + + +

    The user interface to the characterization viewer module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other Estimation: +

    Other Estimation: cohortMethodAttritionServer(), cohortMethodAttritionViewer(), cohortMethodCovariateBalanceServer(), @@ -150,15 +150,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/getCirceRenderedExpression.html b/docs/reference/getCirceRenderedExpression.html index b9c3a34a..e0fc6855 100644 --- a/docs/reference/getCirceRenderedExpression.html +++ b/docs/reference/getCirceRenderedExpression.html @@ -1,9 +1,9 @@ -Returns list with circe generated documentation — getCirceRenderedExpression • OhdsiShinyModulesReturns list with circe generated documentation — getCirceRenderedExpression • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Returns list with circe generated documentation

    - +
    @@ -105,29 +105,29 @@

    Returns list with circe generated documentation

    Arguments

    - - -
    cohortDefinition
    +
    cohortDefinition

    An R object (list) with a list representation of the cohort definition expression, that may be converted to a cohort expression JSON using RJSONIO::toJSON(x = cohortDefinition, digits = 23, pretty = TRUE)

    -
    cohortName
    +
    cohortName

    Name for the cohort definition

    -
    includeConceptSets
    +
    includeConceptSets

    Do you want to inclued concept set in the documentation

    Value

    -

    list object

    + + +

    list object

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -162,15 +162,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/getEnabledCdReports.html b/docs/reference/getEnabledCdReports.html index bfe2c539..18c718c5 100644 --- a/docs/reference/getEnabledCdReports.html +++ b/docs/reference/getEnabledCdReports.html @@ -1,9 +1,9 @@ -Get enable cd reports from available data — getEnabledCdReports • OhdsiShinyModulesGet enable cd reports from available data — getEnabledCdReports • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Get enable cd reports from available data

    - +
    @@ -101,15 +101,13 @@

    Get enable cd reports from available data

    Arguments

    - - -
    dataSource
    +
    dataSource

    Cohort diagnostics data source

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/getExampleConnectionDetails.html b/docs/reference/getExampleConnectionDetails.html index b3527854..257062bc 100644 --- a/docs/reference/getExampleConnectionDetails.html +++ b/docs/reference/getExampleConnectionDetails.html @@ -1,9 +1,9 @@ -A connection details to an example result database — getExampleConnectionDetails • OhdsiShinyModulesA connection details to an example result database — getExampleConnectionDetails • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    A connection details to an example result database

    - +
    @@ -101,11 +101,13 @@

    A connection details to an example result database

    Value

    -

    The connection details to an example result database

    + + +

    The connection details to an example result database

    Details

    -

    Finds the location within the package of an sqlite database with example results for 1) CohortGenerator, +

    Finds the location within the package of an sqlite database with example results for 1) CohortGenerator, 2) Characterization, 3) PatientLevelPrediction, 4) CohortMethod, 5) SelfControlledCaseSeries and 6) CohortIncidence

    @@ -121,15 +123,15 @@

    Details

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/getLogoImage.html b/docs/reference/getLogoImage.html index 79059378..675c39e8 100644 --- a/docs/reference/getLogoImage.html +++ b/docs/reference/getLogoImage.html @@ -1,9 +1,9 @@ -The location of the OHDSI logo — getLogoImage • OhdsiShinyModulesThe location of the OHDSI logo — getLogoImage • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the OHDSI logo

    - +
    @@ -101,7 +101,9 @@

    The location of the OHDSI logo

    Value

    -

    string location of the OHDSI logo

    + + +

    string location of the OHDSI logo

    Details

    @@ -120,15 +122,15 @@

    Details

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/homeHelperFile.html b/docs/reference/homeHelperFile.html index 2ead48f1..3b7bf9d1 100644 --- a/docs/reference/homeHelperFile.html +++ b/docs/reference/homeHelperFile.html @@ -1,9 +1,9 @@ -The location of the home module helper file — homeHelperFile • OhdsiShinyModulesThe location of the home module helper file — homeHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the home module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the home module helper file

    Value

    -

    string location of the home helper file

    + + +

    string location of the home helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other Home: +

    Other Home: homeServer(), homeViewer()

    @@ -126,15 +128,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/homeServer.html b/docs/reference/homeServer.html index 15125146..6afe104f 100644 --- a/docs/reference/homeServer.html +++ b/docs/reference/homeServer.html @@ -1,9 +1,9 @@ -The module server for exploring home — homeServer • OhdsiShinyModulesThe module server for exploring home — homeServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring home

    - +
    @@ -101,23 +101,23 @@

    The module server for exploring home

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the prediction result schema and connection details

    Value

    -

    The server for the home module

    + + +

    The server for the home module

    Details

    @@ -125,7 +125,7 @@

    Details

    See also

    -

    Other Home: +

    Other Home: homeHelperFile(), homeViewer()

    @@ -142,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/homeViewer.html b/docs/reference/homeViewer.html index 36cd980d..9f278b61 100644 --- a/docs/reference/homeViewer.html +++ b/docs/reference/homeViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring home — homeViewer • OhdsiShinyModulesThe module viewer for exploring home — homeViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring home

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring home

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the home viewer module

    + + +

    The user interface to the home viewer module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other Home: +

    Other Home: homeHelperFile(), homeServer()

    @@ -134,15 +134,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/incidenceRatesView.html b/docs/reference/incidenceRatesView.html index 61a73b14..9434af2f 100644 --- a/docs/reference/incidenceRatesView.html +++ b/docs/reference/incidenceRatesView.html @@ -1,9 +1,9 @@ -incidence Rates View — incidenceRatesView • OhdsiShinyModulesincidence Rates View — incidenceRatesView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    incidence Rates View

    - +
    @@ -101,15 +101,13 @@

    incidence Rates View

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("incidenceRates") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/inclusionRulesView.html b/docs/reference/inclusionRulesView.html index b58fe654..65a9e43f 100644 --- a/docs/reference/inclusionRulesView.html +++ b/docs/reference/inclusionRulesView.html @@ -1,9 +1,9 @@ -inclusion Rules View — inclusionRulesView • OhdsiShinyModulesinclusion Rules View — inclusionRulesView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    inclusion Rules View

    - +
    @@ -101,15 +101,13 @@

    inclusion Rules View

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("inclusionRules") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/index.html b/docs/reference/index.html index 8dbcd0b3..f951a6bb 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Package index • OhdsiShinyModulesFunction reference • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +
    @@ -578,13 +578,13 @@

    Large Table

    Utilities for tables that contain large amounts of rows

    -

    createLargeSqlQueryDt()

    - -

    Create Large Sql Query Data Table

    -

    LargeDataTable

    Large Data Table

    + +

    createLargeSqlQueryDt()

    + +

    Create Large Sql Query Data Table

    largeTableServer()

    @@ -662,15 +662,15 @@

    Home

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/indexEventBreakdownView.html b/docs/reference/indexEventBreakdownView.html index e91dfb88..5a40032c 100644 --- a/docs/reference/indexEventBreakdownView.html +++ b/docs/reference/indexEventBreakdownView.html @@ -1,9 +1,9 @@ -Index event breakdown view — indexEventBreakdownView • OhdsiShinyModulesIndex event breakdown view — indexEventBreakdownView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Index event breakdown view

    - +
    @@ -101,15 +101,13 @@

    Index event breakdown view

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("indexEvents") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/largeTableServer.html b/docs/reference/largeTableServer.html index 8c2fc2bc..74cf261b 100644 --- a/docs/reference/largeTableServer.html +++ b/docs/reference/largeTableServer.html @@ -1,9 +1,9 @@ -Large Table Component Server — largeTableServer • OhdsiShinyModulesLarge Table Component Server — largeTableServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Large Table Component Server

    - +
    @@ -108,36 +108,34 @@

    Large Table Component Server

    Arguments

    - - -
    id
    +
    id

    Shiny module id. Must match Large Table Viewer

    -
    ldt
    +
    ldt

    LargeDataTable instance

    -
    inputParams
    +
    inputParams

    reactive that returns list of parameters to be passed to ldt

    -
    modifyData
    +
    modifyData

    optional callback function that takes the data page, page number, page size as parameters must return data.frame compatable instance

    -
    columns
    +
    columns

    List or reactable returning list of reactable::columnDef objects

    -
    ...
    +
    ...

    Additional reactable options (searchable, sortable

    See also

    -

    Other LargeTables: +

    Other LargeTables: createLargeSqlQueryDt(), largeTableView()

    @@ -154,15 +152,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/largeTableView.html b/docs/reference/largeTableView.html index 8397a6c2..a2a4772b 100644 --- a/docs/reference/largeTableView.html +++ b/docs/reference/largeTableView.html @@ -1,11 +1,11 @@ -Large Table Component Viewer — largeTableView • OhdsiShinyModulesLarge Table Component Viewer — largeTableView • OhdsiShinyModules - +
    @@ -27,7 +27,7 @@
    - +

    Large Table Component Viewer

    - +
    @@ -110,27 +110,25 @@

    Large Table Component Viewer

    Arguments

    - - -
    id
    +
    id

    Shiny module id. Must match largeTableServer

    -
    pageSizeChoices
    +
    pageSizeChoices

    numeric selection options for pages

    -
    selectedPageSize
    +
    selectedPageSize

    numeric selection options for pages

    -
    fullDownloads
    +
    fullDownloads

    allow download button of full dataset from query

    See also

    -

    Other LargeTables: +

    Other LargeTables: createLargeSqlQueryDt(), largeTableServer()

    @@ -147,15 +145,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/makeButtonLabel.html b/docs/reference/makeButtonLabel.html index eff24662..e275ca29 100644 --- a/docs/reference/makeButtonLabel.html +++ b/docs/reference/makeButtonLabel.html @@ -1,9 +1,9 @@ -Make a label for an html button — makeButtonLabel • OhdsiShinyModulesMake a label for an html button — makeButtonLabel • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Make a label for an html button

    - +
    @@ -101,26 +101,26 @@

    Make a label for an html button

    Arguments

    - - -
    label
    +
    label

    The desired label for hte button

    Value

    -

    html code to make a button label

    + + +

    html code to make a button label

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), resultTableServer(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -141,15 +141,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/orpahanConceptsView.html b/docs/reference/orpahanConceptsView.html index 433eed90..49d5cd59 100644 --- a/docs/reference/orpahanConceptsView.html +++ b/docs/reference/orpahanConceptsView.html @@ -1,9 +1,9 @@ -Orphan Concepts View — orpahanConceptsView • OhdsiShinyModulesOrphan Concepts View — orpahanConceptsView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Orphan Concepts View

    - +
    @@ -101,15 +101,13 @@

    Orphan Concepts View

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("orphanConcepts") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -130,7 +128,7 @@

    See also

    indexEventBreakdownView(), timeDistributionsView(), visitContextView()

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -165,15 +163,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionCalibrationServer.html b/docs/reference/patientLevelPredictionCalibrationServer.html index a065bd10..6a6852ae 100644 --- a/docs/reference/patientLevelPredictionCalibrationServer.html +++ b/docs/reference/patientLevelPredictionCalibrationServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction validation results — patientLevelPredictionCalibrationServer • OhdsiShinyModulesThe module server for exploring prediction validation results — patientLevelPredictionCalibrationServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction validation results

    - +
    @@ -107,31 +107,31 @@

    The module server for exploring prediction validation results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the prediction calibration module

    + + +

    The server to the prediction calibration module

    Details

    @@ -139,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), patientLevelPredictionCovariateSummaryViewer(), @@ -176,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionCalibrationViewer.html b/docs/reference/patientLevelPredictionCalibrationViewer.html index 88285cd3..85067ef5 100644 --- a/docs/reference/patientLevelPredictionCalibrationViewer.html +++ b/docs/reference/patientLevelPredictionCalibrationViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction model calibration results — patientLevelPredictionCalibrationViewer • OhdsiShinyModulesThe module viewer for exploring prediction model calibration results — patientLevelPredictionCalibrationViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction model calibration results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction model calibration results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the prediction model calibration module

    + + +

    The user interface to the prediction model calibration module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCovariateSummaryServer(), patientLevelPredictionCovariateSummaryViewer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionCovariateSummaryServer.html b/docs/reference/patientLevelPredictionCovariateSummaryServer.html index acba2c1f..b95ecb1a 100644 --- a/docs/reference/patientLevelPredictionCovariateSummaryServer.html +++ b/docs/reference/patientLevelPredictionCovariateSummaryServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction covariate summary results — patientLevelPredictionCovariateSummaryServer • OhdsiShinyModulesThe module server for exploring prediction covariate summary results — patientLevelPredictionCovariateSummaryServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction covariate summary results

    - +
    @@ -109,39 +109,39 @@

    The module server for exploring prediction covariate summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    unique id for the model design

    -
    developmentDatabaseId
    +
    developmentDatabaseId

    unique id for the development database

    -
    performanceId
    +
    performanceId

    unique id for the performance results

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the covariate summary module

    + + +

    The server to the covariate summary module

    Details

    @@ -149,7 +149,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryViewer(), @@ -186,15 +186,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionCovariateSummaryViewer.html b/docs/reference/patientLevelPredictionCovariateSummaryViewer.html index 7547d5fa..53cd8363 100644 --- a/docs/reference/patientLevelPredictionCovariateSummaryViewer.html +++ b/docs/reference/patientLevelPredictionCovariateSummaryViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction covariate summary results — patientLevelPredictionCovariateSummaryViewer • OhdsiShinyModulesThe module viewer for exploring prediction covariate summary results — patientLevelPredictionCovariateSummaryViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction covariate summary results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction covariate summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the covariate summary module

    + + +

    The user interface to the covariate summary module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionCutoffServer.html b/docs/reference/patientLevelPredictionCutoffServer.html index 6da203d4..0ea84d54 100644 --- a/docs/reference/patientLevelPredictionCutoffServer.html +++ b/docs/reference/patientLevelPredictionCutoffServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction cut-off results — patientLevelPredictionCutoffServer • OhdsiShinyModulesThe module server for exploring prediction cut-off results — patientLevelPredictionCutoffServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction cut-off results

    - +
    @@ -107,31 +107,31 @@

    The module server for exploring prediction cut-off results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the prediction cut-off module

    + + +

    The server to the prediction cut-off module

    Details

    @@ -139,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -176,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionCutoffViewer.html b/docs/reference/patientLevelPredictionCutoffViewer.html index 1c2c5b58..8992a5d9 100644 --- a/docs/reference/patientLevelPredictionCutoffViewer.html +++ b/docs/reference/patientLevelPredictionCutoffViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction cut-off results — patientLevelPredictionCutoffViewer • OhdsiShinyModulesThe module viewer for exploring prediction cut-off results — patientLevelPredictionCutoffViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction cut-off results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction cut-off results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the prediction cut-off module

    + + +

    The user interface to the prediction cut-off module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionDesignSummaryServer.html b/docs/reference/patientLevelPredictionDesignSummaryServer.html index 9b3b41d8..ed3e0fad 100644 --- a/docs/reference/patientLevelPredictionDesignSummaryServer.html +++ b/docs/reference/patientLevelPredictionDesignSummaryServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction designs in the results — patientLevelPredictionDesignSummaryServer • OhdsiShinyModulesThe module server for exploring prediction designs in the results — patientLevelPredictionDesignSummaryServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction designs in the results

    - +
    @@ -105,23 +105,23 @@

    The module server for exploring prediction designs in the results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the prediction design module

    + + +

    The server to the prediction design module

    Details

    @@ -129,7 +129,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -166,15 +166,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionDesignSummaryViewer.html b/docs/reference/patientLevelPredictionDesignSummaryViewer.html index 0ad4b4e7..6510b21b 100644 --- a/docs/reference/patientLevelPredictionDesignSummaryViewer.html +++ b/docs/reference/patientLevelPredictionDesignSummaryViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction designs that have been run — patientLevelPredictionDesignSummaryViewer • OhdsiShinyModulesThe module viewer for exploring prediction designs that have been run — patientLevelPredictionDesignSummaryViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction designs that have been run

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction designs that have been run

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the prediction design module

    + + +

    The user interface to the prediction design module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionDiagnosticsServer.html b/docs/reference/patientLevelPredictionDiagnosticsServer.html index 4314ffc9..6ce22da7 100644 --- a/docs/reference/patientLevelPredictionDiagnosticsServer.html +++ b/docs/reference/patientLevelPredictionDiagnosticsServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction diagnostic results — patientLevelPredictionDiagnosticsServer • OhdsiShinyModulesThe module server for exploring prediction diagnostic results — patientLevelPredictionDiagnosticsServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction diagnostic results

    - +
    @@ -106,27 +106,27 @@

    The module server for exploring prediction diagnostic results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    the unique id for the model design

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the prediction diagnostic module

    + + +

    The server to the prediction diagnostic module

    Details

    @@ -134,7 +134,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -171,15 +171,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionDiagnosticsViewer.html b/docs/reference/patientLevelPredictionDiagnosticsViewer.html index eb343b94..aeb78a89 100644 --- a/docs/reference/patientLevelPredictionDiagnosticsViewer.html +++ b/docs/reference/patientLevelPredictionDiagnosticsViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction diagnostic results — patientLevelPredictionDiagnosticsViewer • OhdsiShinyModulesThe module viewer for exploring prediction diagnostic results — patientLevelPredictionDiagnosticsViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction diagnostic results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction diagnostic results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the prediction diagnostic module

    + + +

    The user interface to the prediction diagnostic module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionDiscriminationServer.html b/docs/reference/patientLevelPredictionDiscriminationServer.html index 773d977d..199901f5 100644 --- a/docs/reference/patientLevelPredictionDiscriminationServer.html +++ b/docs/reference/patientLevelPredictionDiscriminationServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction model discrimination results — patientLevelPredictionDiscriminationServer • OhdsiShinyModulesThe module server for exploring prediction model discrimination results — patientLevelPredictionDiscriminationServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction model discrimination results

    - +
    @@ -107,31 +107,31 @@

    The module server for exploring prediction model discrimination results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the model discrimination module

    + + +

    The server to the model discrimination module

    Details

    @@ -139,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -176,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionDiscriminationViewer.html b/docs/reference/patientLevelPredictionDiscriminationViewer.html index fa6a8e5e..5e887fb2 100644 --- a/docs/reference/patientLevelPredictionDiscriminationViewer.html +++ b/docs/reference/patientLevelPredictionDiscriminationViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction model discrimination results — patientLevelPredictionDiscriminationViewer • OhdsiShinyModulesThe module viewer for exploring prediction model discrimination results — patientLevelPredictionDiscriminationViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction model discrimination results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction model discrimination results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the model discrimination results module

    + + +

    The user interface to the model discrimination results module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionHelperFile.html b/docs/reference/patientLevelPredictionHelperFile.html index 0843ce69..ffc8e4ba 100644 --- a/docs/reference/patientLevelPredictionHelperFile.html +++ b/docs/reference/patientLevelPredictionHelperFile.html @@ -1,9 +1,9 @@ -The location of the prediction module helper file — patientLevelPredictionHelperFile • OhdsiShinyModulesThe location of the prediction module helper file — patientLevelPredictionHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the prediction module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the prediction module helper file

    Value

    -

    string location of the prediction helper file

    + + +

    string location of the prediction helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -146,15 +148,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionModelSummaryServer.html b/docs/reference/patientLevelPredictionModelSummaryServer.html index 4170d5ce..de09743e 100644 --- a/docs/reference/patientLevelPredictionModelSummaryServer.html +++ b/docs/reference/patientLevelPredictionModelSummaryServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction summary results — patientLevelPredictionModelSummaryServer • OhdsiShinyModulesThe module server for exploring prediction summary results — patientLevelPredictionModelSummaryServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction summary results

    - +
    @@ -106,27 +106,27 @@

    The module server for exploring prediction summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    -
    modelDesignId
    +
    modelDesignId

    a reactable id specifying the prediction model design identifier

    Value

    -

    The server to the summary module

    + + +

    The server to the summary module

    Details

    @@ -134,7 +134,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -171,15 +171,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionModelSummaryViewer.html b/docs/reference/patientLevelPredictionModelSummaryViewer.html index a3468208..14e150d4 100644 --- a/docs/reference/patientLevelPredictionModelSummaryViewer.html +++ b/docs/reference/patientLevelPredictionModelSummaryViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction summary results — patientLevelPredictionModelSummaryViewer • OhdsiShinyModulesThe module viewer for exploring prediction summary results — patientLevelPredictionModelSummaryViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction summary results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction summary results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the summary module

    + + +

    The user interface to the summary module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionNbServer.html b/docs/reference/patientLevelPredictionNbServer.html index 82e74f16..820dc1ec 100644 --- a/docs/reference/patientLevelPredictionNbServer.html +++ b/docs/reference/patientLevelPredictionNbServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction net-benefit results — patientLevelPredictionNbServer • OhdsiShinyModulesThe module server for exploring prediction net-benefit results — patientLevelPredictionNbServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction net-benefit results

    - +
    @@ -107,31 +107,31 @@

    The module server for exploring prediction net-benefit results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    performanceId
    +
    performanceId

    the performance id in the database

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the net-benefit module

    + + +

    The server to the net-benefit module

    Details

    @@ -139,7 +139,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -176,15 +176,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionNbViewer.html b/docs/reference/patientLevelPredictionNbViewer.html index 812439e5..4825b634 100644 --- a/docs/reference/patientLevelPredictionNbViewer.html +++ b/docs/reference/patientLevelPredictionNbViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction net-benefit results — patientLevelPredictionNbViewer • OhdsiShinyModulesThe module viewer for exploring prediction net-benefit results — patientLevelPredictionNbViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction net-benefit results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction net-benefit results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the net-benefit module

    + + +

    The user interface to the net-benefit module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionServer.html b/docs/reference/patientLevelPredictionServer.html index e22f6862..0b15008d 100644 --- a/docs/reference/patientLevelPredictionServer.html +++ b/docs/reference/patientLevelPredictionServer.html @@ -1,9 +1,9 @@ -The module server for exploring PatientLevelPrediction — patientLevelPredictionServer • OhdsiShinyModulesThe module server for exploring PatientLevelPrediction — patientLevelPredictionServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring PatientLevelPrediction

    - +
    @@ -105,23 +105,23 @@

    The module server for exploring PatientLevelPrediction

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the prediction result schema and connection details

    Value

    -

    The server for the PatientLevelPrediction module

    + + +

    The server for the PatientLevelPrediction module

    Details

    @@ -129,7 +129,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -166,15 +166,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionSettingsServer.html b/docs/reference/patientLevelPredictionSettingsServer.html index 1a67b538..d7bb129e 100644 --- a/docs/reference/patientLevelPredictionSettingsServer.html +++ b/docs/reference/patientLevelPredictionSettingsServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction settings — patientLevelPredictionSettingsServer • OhdsiShinyModulesThe module server for exploring prediction settings — patientLevelPredictionSettingsServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction settings

    - +
    @@ -109,39 +109,39 @@

    The module server for exploring prediction settings

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    unique id for the model design

    -
    developmentDatabaseId
    +
    developmentDatabaseId

    unique id for the development database

    -
    performanceId
    +
    performanceId

    unique id for the performance results

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the settings module

    + + +

    The server to the settings module

    Details

    @@ -149,7 +149,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -186,15 +186,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionSettingsViewer.html b/docs/reference/patientLevelPredictionSettingsViewer.html index 1e4de580..2ef0c0ae 100644 --- a/docs/reference/patientLevelPredictionSettingsViewer.html +++ b/docs/reference/patientLevelPredictionSettingsViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction settings — patientLevelPredictionSettingsViewer • OhdsiShinyModulesThe module viewer for exploring prediction settings — patientLevelPredictionSettingsViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction settings

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction settings

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the settings module

    + + +

    The user interface to the settings module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionValidationServer.html b/docs/reference/patientLevelPredictionValidationServer.html index 9860d1f9..06e2c7c0 100644 --- a/docs/reference/patientLevelPredictionValidationServer.html +++ b/docs/reference/patientLevelPredictionValidationServer.html @@ -1,9 +1,9 @@ -The module server for exploring prediction validation results — patientLevelPredictionValidationServer • OhdsiShinyModulesThe module server for exploring prediction validation results — patientLevelPredictionValidationServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for exploring prediction validation results

    - +
    @@ -109,39 +109,39 @@

    The module server for exploring prediction validation results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    modelDesignId
    +
    modelDesignId

    identifier for the model design

    -
    developmentDatabaseId
    +
    developmentDatabaseId

    identifier for the development database

    -
    performanceId
    +
    performanceId

    identifier for the performance

    -
    connectionHandler
    +
    connectionHandler

    the connection to the prediction result database

    -
    inputSingleView
    +
    inputSingleView

    the current tab

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the result schema and prefixes

    Value

    -

    The server to the validation module

    + + +

    The server to the validation module

    Details

    @@ -149,7 +149,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -186,15 +186,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionValidationViewer.html b/docs/reference/patientLevelPredictionValidationViewer.html index b4010978..dcbd2c70 100644 --- a/docs/reference/patientLevelPredictionValidationViewer.html +++ b/docs/reference/patientLevelPredictionValidationViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring prediction validation results — patientLevelPredictionValidationViewer • OhdsiShinyModulesThe module viewer for exploring prediction validation results — patientLevelPredictionValidationViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring prediction validation results

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring prediction validation results

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the validation module

    + + +

    The user interface to the validation module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/patientLevelPredictionViewer.html b/docs/reference/patientLevelPredictionViewer.html index e46404af..56b31ee6 100644 --- a/docs/reference/patientLevelPredictionViewer.html +++ b/docs/reference/patientLevelPredictionViewer.html @@ -1,9 +1,9 @@ -The module viewer for exploring PatientLevelPrediction — patientLevelPredictionViewer • OhdsiShinyModulesThe module viewer for exploring PatientLevelPrediction — patientLevelPredictionViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for exploring PatientLevelPrediction

    - +
    @@ -101,15 +101,15 @@

    The module viewer for exploring PatientLevelPrediction

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the PatientLevelPrediction viewer module

    + + +

    The user interface to the PatientLevelPrediction viewer module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other PatientLevelPrediction: +

    Other PatientLevelPrediction: patientLevelPredictionCalibrationServer(), patientLevelPredictionCalibrationViewer(), patientLevelPredictionCovariateSummaryServer(), @@ -154,15 +154,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/phevaluatorHelperFile.html b/docs/reference/phevaluatorHelperFile.html index 509aad3c..9f4a0d2e 100644 --- a/docs/reference/phevaluatorHelperFile.html +++ b/docs/reference/phevaluatorHelperFile.html @@ -1,9 +1,9 @@ -The location of the phevaluator module helper file — phevaluatorHelperFile • OhdsiShinyModulesThe location of the phevaluator module helper file — phevaluatorHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the phevaluator module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the phevaluator module helper file

    Value

    -

    String location of the phevaluator helper file

    + + +

    String location of the phevaluator helper file

    Details

    @@ -109,10 +111,10 @@

    Details

    See also

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorServer(), phevaluatorViewer()

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorServer(), phevaluatorViewer()

    @@ -129,15 +131,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/phevaluatorServer.html b/docs/reference/phevaluatorServer.html index ef567cb8..43a7f377 100644 --- a/docs/reference/phevaluatorServer.html +++ b/docs/reference/phevaluatorServer.html @@ -1,9 +1,9 @@ -The module server for the main phevaluator module — phevaluatorServer • OhdsiShinyModulesThe module server for the main phevaluator module — phevaluatorServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the main phevaluator module

    - +
    @@ -101,30 +101,30 @@

    The module server for the main phevaluator module

    Arguments

    - - -
    id
    +
    id

    The unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    A connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    A named list containing the cohort generator results database details (schema, table prefix)

    Value

    -

    The phevaluator main module server

    + + +

    The phevaluator main module server

    See also

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorViewer()

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorViewer()

    @@ -141,15 +141,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/phevaluatorViewer.html b/docs/reference/phevaluatorViewer.html index a661b9e0..6fb65e37 100644 --- a/docs/reference/phevaluatorViewer.html +++ b/docs/reference/phevaluatorViewer.html @@ -1,9 +1,9 @@ -The viewer of the phevaluator module — phevaluatorViewer • OhdsiShinyModulesThe viewer of the phevaluator module — phevaluatorViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The viewer of the phevaluator module

    - +
    @@ -101,22 +101,22 @@

    The viewer of the phevaluator module

    Arguments

    - - -
    id
    +
    id

    The unique reference id for the module

    Value

    -

    The user interface to the phevaluator results viewer

    + + +

    The user interface to the phevaluator results viewer

    See also

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorServer()

    -

    Other PheValuator: +

    Other PheValuator: phevaluatorHelperFile(), phevaluatorServer()

    @@ -133,15 +133,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/reportHelperFile.html b/docs/reference/reportHelperFile.html index e14196a1..c7d65733 100644 --- a/docs/reference/reportHelperFile.html +++ b/docs/reference/reportHelperFile.html @@ -1,9 +1,9 @@ -The location of the report module helper file — reportHelperFile • OhdsiShinyModulesThe location of the report module helper file — reportHelperFile • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The location of the report module helper file

    - +
    @@ -101,7 +101,9 @@

    The location of the report module helper file

    Value

    -

    string location of the report helper file

    + + +

    string location of the report helper file

    Details

    @@ -109,7 +111,7 @@

    Details

    See also

    -

    Other Report: +

    Other Report: reportServer(), reportViewer()

    @@ -126,15 +128,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/reportServer.html b/docs/reference/reportServer.html index 502ee584..faa0664b 100644 --- a/docs/reference/reportServer.html +++ b/docs/reference/reportServer.html @@ -1,9 +1,9 @@ -The module server for the shiny app report module — reportServer • OhdsiShinyModulesThe module server for the shiny app report module — reportServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module server for the shiny app report module

    - +
    @@ -109,39 +109,39 @@

    The module server for the shiny app report module

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    -
    connectionHandler
    +
    connectionHandler

    a connection to the database with the results

    -
    resultDatabaseSettings
    +
    resultDatabaseSettings

    a list containing the characterization result schema, dbms, tablePrefix, databaseTable and cgTablePrefix

    -
    server
    +
    server

    server for the connection to the results for quarto

    -
    username
    +
    username

    username for the connection to the results for quarto

    -
    password
    +
    password

    password for the connection to the results for quarto

    -
    dbms
    +
    dbms

    dbms for the connection to the results for quarto

    Value

    -

    The server for the shiny app home

    + + +

    The server for the shiny app home

    Details

    @@ -149,7 +149,7 @@

    Details

    See also

    -

    Other Report: +

    Other Report: reportHelperFile(), reportViewer()

    @@ -166,15 +166,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/reportViewer.html b/docs/reference/reportViewer.html index 233ee0c7..e49b23d2 100644 --- a/docs/reference/reportViewer.html +++ b/docs/reference/reportViewer.html @@ -1,9 +1,9 @@ -The module viewer for the shiny app report module — reportViewer • OhdsiShinyModulesThe module viewer for the shiny app report module — reportViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    The module viewer for the shiny app report module

    - +
    @@ -101,15 +101,15 @@

    The module viewer for the shiny app report module

    Arguments

    - - -
    id
    +
    id

    the unique reference id for the module

    Value

    -

    The user interface to the home page module

    + + +

    The user interface to the home page module

    Details

    @@ -117,7 +117,7 @@

    Details

    See also

    -

    Other Report: +

    Other Report: reportHelperFile(), reportServer()

    @@ -134,15 +134,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/resultTableServer.html b/docs/reference/resultTableServer.html index d3a33a80..0db1400f 100644 --- a/docs/reference/resultTableServer.html +++ b/docs/reference/resultTableServer.html @@ -1,9 +1,9 @@ -Result Table Server — resultTableServer • OhdsiShinyModulesResult Table Server — resultTableServer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Result Table Server

    - +
    @@ -112,63 +112,63 @@

    Result Table Server

    Arguments

    - - -
    id
    +
    id

    string, table id must match resultsTableViewer function

    -
    df
    +
    df

    reactive that returns a data frame

    -
    colDefsInput
    +
    colDefsInput

    named list of reactable::colDefs

    -
    details
    +
    details

    The details of the results such as cohort names and database names

    -
    selectedCols
    +
    selectedCols

    string vector of columns the reactable should display to start by default. Defaults to ALL if not specified.

    -
    sortedCols
    +
    sortedCols

    string vector of columns the reactable should sort by by default. Defaults to no sort if not specified.

    -
    elementId
    +
    elementId

    optional string vector of element Id name for custom dropdown filtering if present in the customColDef list. Defaults to NULL.

    -
    addActions
    +
    addActions

    add a button row selector column to the table to a column called 'actions'. actions must be a column in df

    -
    downloadedFileName
    +
    downloadedFileName

    string, desired name of downloaded data file. can use the name from the module that is being used

    -
    groupBy
    +
    groupBy

    The columns to group by

    Value

    -

    shiny module server

    + + +

    shiny module server

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableViewer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -189,15 +189,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/resultTableViewer.html b/docs/reference/resultTableViewer.html index d36b0371..12b47a21 100644 --- a/docs/reference/resultTableViewer.html +++ b/docs/reference/resultTableViewer.html @@ -1,9 +1,9 @@ -Result Table Viewer — resultTableViewer • OhdsiShinyModulesResult Table Viewer — resultTableViewer • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Result Table Viewer

    - +
    @@ -105,34 +105,34 @@

    Result Table Viewer

    Arguments

    - - -
    id
    +
    id

    string

    -
    downloadedFileName
    +
    downloadedFileName

    string, desired name of downloaded data file. can use the name from the module that is being used

    -
    boxTitle
    +
    boxTitle

    the title added to the box

    Value

    -

    shiny module UI

    + + +

    shiny module UI

    See also

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), datasourcesViewer(), makeButtonLabel(), resultTableServer()

    -

    Other Utils: +

    Other Utils: createCustomColDefList(), datasourcesHelperFile(), datasourcesServer(), @@ -153,15 +153,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/timeDistributionsView.html b/docs/reference/timeDistributionsView.html index cd23118e..7516fed4 100644 --- a/docs/reference/timeDistributionsView.html +++ b/docs/reference/timeDistributionsView.html @@ -1,9 +1,9 @@ -timeDistributions view — timeDistributionsView • OhdsiShinyModulestimeDistributions view — timeDistributionsView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    timeDistributions view

    - +
    @@ -101,15 +101,13 @@

    timeDistributions view

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("imeDistributions") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

    + - - + diff --git a/docs/reference/visitContextView.html b/docs/reference/visitContextView.html index 78bfcf43..d530d53c 100644 --- a/docs/reference/visitContextView.html +++ b/docs/reference/visitContextView.html @@ -1,9 +1,9 @@ -Visit context module view — visitContextView • OhdsiShinyModulesVisit context module view — visitContextView • OhdsiShinyModules - +
    @@ -25,7 +25,7 @@
    - +

    Visit context module view

    - +
    @@ -101,15 +101,13 @@

    Visit context module view

    Arguments

    - - -
    id
    +
    id

    Namespace Id - use namespaced id ns("vistConext") inside diagnosticsExplorer module

    See also

    -

    Other CohortDiagnostics: +

    Other CohortDiagnostics: cohortCountsModule(), cohortCountsView(), cohortDefinitionsModule(), @@ -144,15 +142,15 @@

    See also

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.0.7.

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/reference/reportServer.html + + + /reference/reportViewer.html + + + /reference/resultTableServer.html + + + /reference/resultTableViewer.html + + + /reference/sccsHelperFile.html + + + /reference/sccsServer.html + + + /reference/sccsView.html + + + /reference/timeDistributionsView.html + + + /reference/visitContextView.html + - diff --git a/vignettes/Characterization.Rmd b/vignettes/Characterization.Rmd index d83788b5..43888a7b 100644 --- a/vignettes/Characterization.Rmd +++ b/vignettes/Characterization.Rmd @@ -1,6 +1,6 @@ --- title: "Characterization" -author: "Nathan Hall" +author: "Nathan Hall and Jenna Reps" date: '`r Sys.Date()`' header-includes: - \usepackage{fancyhdr} @@ -35,18 +35,39 @@ knitr::opts_chunk$set(echo = TRUE) # Introduction -Characterization, a fundamental aspect of observational health data research, serves as a cornerstone for understanding and analyzing populations based on a myriad of characteristics. The methodologies of characterization play a pivotal role in generating hypotheses about the determinants of health and disease by providing descriptive insights into population demographics, medical history, treatment patterns, and incidence rates of outcomes. There are various methods for characterization, including database-level characterization, cohort characterization, treatment pathways analysis, and incidence measurement. Each of these methods aims to describe populations relative to an event known as the index date, which anchors the analysis of baseline, pre-index, and post-index time periods. Through the lens of use-cases such as disease natural history, treatment utilization, and quality improvement, characterizing cohorts of patients empowers researchers to glean actionable insights from observational healthcare databases. +The OHDSI Characterization package lets users extract descriptive analyses from observational healthcare data sets mapped to the OMOP CDM. There are currently four different types of characterizations analyses (incidence rates, time-to-event, dechallenge-rechallenge and various aggregate covariate cohort comparisons). + +The Characterization package currently lets users answer the following questions: + +* **Incidence Rate**: How often does `````` occur within `````` after first record of ``````? +* **Time-to-event**: When does `````` occur relative to the first recorded of ``````? Is it more common before or after ``````? +* **Dechallenge-rechallenge**: Is there any evidence of `````` causing `````` to be discontinued and then `````` re-occurring once `````` restarts? +* **Cohort Comparison**: What is different at index between patients in `````` and patients in ``````? +* **Database Comparison**: What is different at index between patients in `````` across two or more OMOP CDM databases? +* **Risk factors**: What are the risk factors of `````` occurring within `````` for those exposed to ``````? +* **Case-series**: What happens to cases (those exposure to `````` who have `````` during ``````) before exposure, between exposure and outcome start and after outcome start? How bad are the cases prognosis? + # Features and Functionalities -The Characterization module is dedicated to investigating these factors within and between cohorts, and it contains several useful features that allow for this exploration, including: +Defining a **target cohort** as a set of patients with an exposure or interest and/or with evidence of having an indication of interest and an **outcome cohort** as a set of patients with evidence of the outcome of interest, we run the following analyses: + +1. **Cohort Summary** - computes aggregate covariate summaries for cohorts (targets and/or outcomes), offering a granular view of the cohort's demographics, conditions, drug exposures, and more. This enables a deeper understanding of the cohort's characteristics at various time points at or relative to the index date.: + + **Database Comparison** Lets you compare the same cohort across two or more databases and adds in the standardized mean different calculation when exactly two databases are selected. This is a measure of association between the feature and the cohort, therefore identifying which features differ across databases. + + **Cohort Comparison** Lets you compare two or more cohorts across a database and adds in the standardized mean different calculation when exactly two cohort are selected. This is a measure of association between the feature and the cohort, therefore identifying which features differ across databases. + +2. **Exposed Case Series** - characterizations that look at people in the target cohort who have the outcome during some specified time-at-risk: + + **Risk Factor** Compares aggregate covariate summaries for patients in the target who have the outcome during the time-at-risk period vs patients in the target who do not have the outcome during the time-at-risk period. The standardized mean difference is added to identify covariates that differ between the cohorts. + + **Case Series** Compares aggregate covariate summaries before target start, between target start up to outcome start and after outcome start for people in the target cohort who have the outcome during some specified time-at-risk. This lets you see covariates that are common before exposure and what happens afterwards. + + **Time to Event**: Shows the distribution of when the outcome occurs relative to the target start. This can show you whether the outcome occurs more after or before target exposure. + + **Dechallenge Rechallenge**: Offers the ability to compute dechallenge (withdrawal of a drug or treatment) and rechallenge (reintroduction) results. This analysis is critical for understanding the causality between exposures and outcomes, especially in pharmacovigilance studies and when adverse events following exposure to a drug may occur. -1. **Target Viewer**: Computes detailed results for target cohorts, offering a granular view of the cohort's demographics, conditions, drug exposures, and more. This enables a deeper understanding of the cohort's characteristics at various time points at or relative to the index date. -2. **Outcome Stratified**: For both target and outcome cohorts, the package calculates binary features during the designated time at risk. This analysis helps in identifying specific attributes or exposures that are present or absent in the cohort members, aiding in the differentiation/comparability between cohorts. 3. **Incidence Rate**: Utilizing the [CohortIncidence](https://github.com/OHDSI/CohortIncidence "CohortIncidence") R package, this set of analyses computes incidence rates for both target and outcome cohorts during the time at risk selected. This feature is essential for assessing the frequency of outcomes or conditions within the specified timeframe, providing a quantitative measure of risk or occurrence. Incidence measures are provided in both tabular and graphical form, and can be stratified across calendar year, age, and sex. -4. **Time to Event**: Generates plots for the number of events across different time periods (1, 30, or 365 days) for the selected target and outcome cohorts. These plots visualize the temporal distribution of events, allowing researchers to observe patterns over time and make temporal comparisons between cohorts. -5. **Dechallenge Rechallenge**: Offers the ability to compute dechallenge (withdrawal of a drug or treatment) and rechallenge (reintroduction) results. This analysis is critical for understanding the causality between exposures and outcomes, especially in pharmacovigilance studies and when adverse events following exposure to a drug may occur. # Utility and Application -Characterization serves as a powerful tool for researchers aiming to dissect and understand the nuances of patient cohorts in observational health data. Its capabilities allow for the detailed examination of cohort attributes, the incidence of health outcomes, and the effects of treatment exposures over time. By facilitating a comprehensive analysis of target and comparator cohorts, Characterization enables researchers to draw meaningful conclusions about patient care, treatment efficacy, and health outcomes, thereby contributing to the advancement of evidence-based medicine. For more information on the Characterization R package, please see [here](https://github.com/OHDSI/Characterization "Characterization"). +Characterization serves as a powerful tool for researchers aiming to dissect and understand the nuances of patient cohorts in observational health data. Its capabilities allow for the detailed examination of cohort attributes, the incidence of health outcomes, and the effects of treatment exposures over time. By facilitating a comprehensive analysis of target and comparator cohorts, Characterization enables researchers to draw meaningful conclusions about patient care, treatment efficacy, and health outcomes, thereby contributing to the advancement of evidence-based medicine. + +To find out more about the analyses execution details and see examples, please see [here](https://ohdsi.github.io/OhdsiShinyModules/articles/Characterization.html). + +To see the code behind the Characterization R package, please see [here](https://github.com/OHDSI/Characterization).