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Develop #324

Merged
merged 157 commits into from
Aug 22, 2024
Merged

Develop #324

merged 157 commits into from
Aug 22, 2024

Commits on Feb 5, 2024

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Commits on Feb 12, 2024

  1. Update cohort-method.html

    temp fix for CohortMethod module automatically opening help link - disabling link
    nhall6 committed Feb 12, 2024
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Commits on Feb 16, 2024

  1. protocol generator fix

    - added message when generating
    - added trycatch when target cohort json has issues (subset?)
    - added chunk names for debugging
    jreps committed Feb 16, 2024
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  2. Merge pull request #256 from OHDSI/issue_111

    protocol generator fix
    jreps authored Feb 16, 2024
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Commits on Feb 22, 2024

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Commits on Feb 23, 2024

  1. fixing plot color palette to work for a higher number of dbs in stand…

    …ard plots and to be colorblind-friendly
    nhall6 committed Feb 23, 2024
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  3. home module

    - adding home module
    jreps committed Feb 23, 2024
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  4. Dynamic module load

    azimov committed Feb 23, 2024
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  6. splitting up column definition for evidence synth cohort method and sccs

    splitting up column definition for evidence synth cohort method and sccs
    jreps committed Feb 23, 2024
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  7. Merge pull request #260 from OHDSI/es_sccs_cm_dynamic_load

    Fixes for query and module load
    jreps authored Feb 23, 2024
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  8. Update evidence-synth-main.R

    adding distinct to sccs column name pull
    jreps committed Feb 23, 2024
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  10. Merge pull request #259 from OHDSI/es_sccs_cm_dynamic_load

    Dynamic module load
    azimov authored Feb 23, 2024
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Commits on Feb 26, 2024

  1. Merge pull request #258 from OHDSI/incidence_plot_fixes

    Incidence plot fixes
    jreps authored Feb 26, 2024
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  2. Merge pull request #255 from OHDSI/issue_173

    updating documentation on the html help files for all modules
    jreps authored Feb 26, 2024
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Commits on Mar 1, 2024

  1. Update characterization-main.R

    fixing wrong position of selectVal = F causing tab to not show in characterization if 'Target Viewer' is not run.
    jreps committed Mar 1, 2024
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Commits on Mar 14, 2024

  1. updating about module

    nhall6 committed Mar 14, 2024
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  2. Update about-main.R

    nhall6 committed Mar 14, 2024
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Commits on Mar 15, 2024

  1. Updating new about module

    nhall6 committed Mar 15, 2024
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  2. Update about.html

    nhall6 committed Mar 15, 2024
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Commits on Mar 22, 2024

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Commits on Mar 26, 2024

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Commits on Mar 28, 2024

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  2. style tweaks

    fdefalco committed Mar 28, 2024
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  3. Delete about-dataSources.html

    nhall6 committed Mar 28, 2024
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Commits on Apr 1, 2024

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  3. Delete app.R

    jreps committed Apr 1, 2024
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Commits on Apr 2, 2024

  1. report module

    adding initial code to generate reports
    jreps committed Apr 2, 2024
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  3. Merge pull request #269 from OHDSI/about-updates

    About module updates to content and UI
    jreps authored Apr 2, 2024
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  4. Merge pull request #270 from OHDSI/report-module

    report module
    jreps authored Apr 2, 2024
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  5. Update DESCRIPTION

    jreps committed Apr 2, 2024
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Commits on Apr 3, 2024

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Commits on Apr 4, 2024

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Commits on Apr 5, 2024

  1. Update _pkgdown.yml

    -updating the pkgdown yml
    jreps committed Apr 5, 2024
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  3. updating pkgdown

    nhall6 committed Apr 5, 2024
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Commits on Apr 9, 2024

  1. updating pkgdown yml

    nhall6 committed Apr 9, 2024
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Commits on Apr 10, 2024

  1. Merge pull request #271 from OHDSI/vignette-updates

    Vignette updates
    jreps authored Apr 10, 2024
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Commits on Apr 11, 2024

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  2. update pkgdown_yml

    nhall6 committed Apr 11, 2024
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  3. changing doctype in OhdsiShinyModules.R

    #'
    @doctype _PACKAGE
    to be:
    #' @doctype
    package
    nhall6 committed Apr 11, 2024
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  4. oxygenizing

    nhall6 committed Apr 11, 2024
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  5. Merge pull request #273 from OHDSI/website-updates

    Website updates
    jreps authored Apr 11, 2024
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Commits on Apr 12, 2024

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  3. Merge pull request #274 from OHDSI/website-updates

    Website updates
    jreps authored Apr 12, 2024
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Commits on Apr 19, 2024

  1. Fixes and optimisations for cd load up on postgres servers causing ha…

    …ngs when using DBI functions
    azimov committed Apr 19, 2024
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  2. Fixed missing reports error

    azimov committed Apr 19, 2024
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  3. Fix for sqlite

    azimov committed Apr 19, 2024
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  4. Actual fix for sqlite...

    azimov committed Apr 19, 2024
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Commits on Apr 23, 2024

  1. Merge pull request #276 from OHDSI/postgres-dbi-issues

    DBI issues fix
    jreps authored Apr 23, 2024
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  3. Merge branch 'hotfix-3.1.3' into develop

    # Conflicts:
    #	DESCRIPTION
    #	NEWS.md
    #	docs/404.html
    #	docs/authors.html
    #	docs/index.html
    #	docs/pkgdown.yml
    #	man/OhdsiShinyModules.Rd
    azimov committed Apr 23, 2024
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Commits on Apr 25, 2024

  1. Fixed missing library call

    azimov committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. Merge branch 'hotfix-2.1.14' into develop

    # Conflicts:
    #	DESCRIPTION
    #	NEWS.md
    azimov committed Apr 26, 2024
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Commits on May 2, 2024

  1. example app added

    adding example app in extra folder and example Eunomia result data
    jreps committed May 2, 2024
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  2. Update report-main.R

    bug fixes to report-main.R
    jreps committed May 2, 2024
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Commits on May 3, 2024

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Commits on May 6, 2024

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  2. Merge pull request #281 from OHDSI/issue-265

    Adding database filter to results selection to address issue #265
    jreps authored May 6, 2024
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  3. Merge pull request #280 from OHDSI/cm-covariate-balance-table

    CM covariate balance table addition after primary key generation
    jreps authored May 6, 2024
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Commits on May 8, 2024

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Commits on May 9, 2024

  1. estimation module

    - adding estimation module that includes CM/SCCS/Evidence synthesis
    jreps committed May 9, 2024
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  2. estimation module updates

    - adding evidence synth into SCCS
    - adding plots for SCCS and CM
    jreps committed May 9, 2024
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  3. estimation edits

    - optimizing sccs negative control plot
    - removing prints
    jreps committed May 9, 2024
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Commits on May 17, 2024

  1. - updating characterization

    - updating characterization
    jreps committed May 17, 2024
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Commits on May 20, 2024

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  2. Merge pull request #283 from OHDSI/removing-help-sections

    remove help & information sections in most modules due to About modul...
    nhall6 authored May 20, 2024
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Commits on May 21, 2024

  1. improving characterization

    jreps committed May 21, 2024
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  2. Update characterization-incidence.R

    - adding code to use CI TAR lookup if available
    jreps committed May 21, 2024
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Commits on May 22, 2024

  1. minor exclude fixes

    minor exclude fixes
    jreps committed May 22, 2024
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  3. fixes

    fixes
    jreps committed May 22, 2024
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  4. Update characterization-caseSeries.R

    adding two extra columns
    jreps committed May 22, 2024
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  5. Update characterization-caseSeries.R

    restricting case series to during covariates
    jreps committed May 22, 2024
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  6. Update characterization-main.R

    adding CI outcomes to char options
    jreps committed May 22, 2024
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Commits on May 23, 2024

  1. Update characterization-riskFactors.R

    fixing multiple washout and min obs bug in risk factors
    jreps committed May 23, 2024
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Commits on May 28, 2024

  1. Update cohort-diagnostics-main.R

    Get table names faile when schema specified
    azimov authored May 28, 2024
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  2. Update cohort-diagnostics-main.R

    Get table names faile when schema specified
    azimov committed May 28, 2024
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Commits on Jun 1, 2024

  1. updating for new char tables

    updating for new char tables
    jreps committed Jun 1, 2024
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Commits on Jun 3, 2024

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Commits on Jun 4, 2024

  1. Update characterization-timeToEvent.R

    changing selection for tte
    jreps committed Jun 4, 2024
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Commits on Jun 6, 2024

  1. cleaning characterization tables

    cleaning characterization tables
    jreps committed Jun 6, 2024
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  2. minor update

    adding box to show selected tar/database for RF and case series.
    jreps committed Jun 6, 2024
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  3. Update characterization-dechallengeRechallenge.R

    updating warning for dechal-rechal
    jreps committed Jun 6, 2024
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  4. Update characterization-dechallengeRechallenge.R

    - only display warning when there are warnings
    jreps committed Jun 6, 2024
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Commits on Jun 7, 2024

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  2. fixing scrolls

    fixing scrolls
    jreps committed Jun 7, 2024
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Commits on Jun 11, 2024

  1. Update characterization-cohorts.R

    fixing SMD calculation in cohorts
    jreps committed Jun 11, 2024
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  2. minor bug fixes

    - fixing tar changing before generate in case series
    - fixing columns showing in selection that should be hidden
    jreps committed Jun 11, 2024
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  3. updating table download

    - updating csv export to excel export with a details sheet
    jreps committed Jun 11, 2024
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  4. Update components-data-viewer.R

    changing saving file type
    jreps committed Jun 11, 2024
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  5. adding details to exported results

    adding details to exported results for characterization cohorts and databases
    jreps committed Jun 11, 2024
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Commits on Jun 12, 2024

  1. Update components-data-viewer.R

    fixing actions not being includes as it is an extra column that is added outside the coldDef
    jreps committed Jun 12, 2024
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  2. Update characterization-caseSeries.R

    - adding details to case-series download
    jreps committed Jun 12, 2024
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  3. Merge pull request #287 from OHDSI/pooled_connection_tablenames

    Fix issue with pooled connection
    azimov authored Jun 12, 2024
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Commits on Jun 13, 2024

  1. fixing issue with SCCS not showing

    fixing issue with SCCS not showing
    jreps committed Jun 13, 2024
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  2. fixing characterization

    updating data downloads for char tables, fixing cohort names in CI, adding caption to custom CI plot
    nhall6 committed Jun 13, 2024
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  3. Update characterization-main.R

    sorting outcomes in char
    jreps committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. fixing estimation

    - adding missing shiny::
    - updating code to get T and Os for SCCS so it removed negative controls
    jreps committed Jun 14, 2024
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  2. adding fix for ci_lookup

    adding fix for ci_lookup
    jreps committed Jun 14, 2024
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Commits on Jun 20, 2024

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  2. Update DESCRIPTION

    adding Nathan Hall and Jamie Gilbert as co-authors
    nhall6 authored Jun 20, 2024
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Commits on Jun 28, 2024

  1. minor updates

    - fixed bug with control estimates plot not showing all results
    - added ease value to control estimate plot
    - added validation checks to print informative reason for missing plots
    jreps committed Jun 28, 2024
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  2. error handling for estimation plots

    replacing estimation plot error message with useful notification
    jreps committed Jun 28, 2024
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  3. minor updates to estimation

    - removing old sccs and cohort method files
    - making estimation options be ordered by cohort name
    - adding indication column into sccs diagnostics
    - updating estimation outcome input to have the search options
    jreps committed Jun 28, 2024
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Commits on Jul 2, 2024

  1. characterization test updates

    - updating characterization tests and fixing issues identified by tests
    jreps committed Jul 2, 2024
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Commits on Jul 9, 2024

  1. Update characterization-main.R

    removing odd code
    jreps committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. passing R check

    - passing tests 78% coverage
    - cleaning checks but still some notes
    jreps committed Jul 10, 2024
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Commits on Jul 15, 2024

  1. Merge pull request #286 from OHDSI/shiny-pool-issue

    Update cohort-diagnostics-main.R
    azimov authored Jul 15, 2024
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  2. Merge branch 'develop' into hotfix-2.1.5-develop-merge

    # Conflicts:
    #	DESCRIPTION
    #	NEWS.md
    #	R/OhdsiShinyModules.R
    #	_pkgdown.yml
    #	docs/articles/AddingShinyModules.html
    #	docs/articles/index.html
    #	docs/news/index.html
    #	docs/reference/LargeDataTable.html
    #	docs/reference/OhdsiShinyModules.html
    #	docs/reference/aboutHelperFile.html
    #	docs/reference/aboutServer.html
    #	docs/reference/aboutViewer.html
    #	docs/reference/characterizationAggregateFeaturesServer.html
    #	docs/reference/characterizationAggregateFeaturesViewer.html
    #	docs/reference/characterizationDechallengeRechallengeServer.html
    #	docs/reference/characterizationDechallengeRechallengeViewer.html
    #	docs/reference/characterizationHelperFile.html
    #	docs/reference/characterizationIncidenceServer.html
    #	docs/reference/characterizationIncidenceViewer.html
    #	docs/reference/characterizationServer.html
    #	docs/reference/characterizationTableServer.html
    #	docs/reference/characterizationTableViewer.html
    #	docs/reference/characterizationTimeToEventServer.html
    #	docs/reference/characterizationTimeToEventViewer.html
    #	docs/reference/characterizationViewer.html
    #	docs/reference/cohortCountsModule.html
    #	docs/reference/cohortCountsView.html
    #	docs/reference/cohortDefinitionsModule.html
    #	docs/reference/cohortDefinitionsView.html
    #	docs/reference/cohortDiagCharacterizationView.html
    #	docs/reference/cohortDiagnosticsHelperFile.html
    #	docs/reference/cohortDiagnosticsServer.html
    #	docs/reference/cohortDiagnosticsView.html
    #	docs/reference/cohortGeneratorHelperFile.html
    #	docs/reference/cohortGeneratorServer.html
    #	docs/reference/cohortGeneratorViewer.html
    #	docs/reference/cohortMethodAttritionServer.html
    #	docs/reference/cohortMethodAttritionViewer.html
    #	docs/reference/cohortMethodCovariateBalanceServer.html
    #	docs/reference/cohortMethodCovariateBalanceViewer.html
    #	docs/reference/cohortMethodDiagnosticsSummaryServer.html
    #	docs/reference/cohortMethodDiagnosticsSummaryViewer.html
    #	docs/reference/cohortMethodHelperFile.html
    #	docs/reference/cohortMethodKaplanMeierServer.html
    #	docs/reference/cohortMethodKaplanMeierViewer.html
    #	docs/reference/cohortMethodPopulationCharacteristicsServer.html
    #	docs/reference/cohortMethodPopulationCharacteristicsViewer.html
    #	docs/reference/cohortMethodPowerServer.html
    #	docs/reference/cohortMethodPowerViewer.html
    #	docs/reference/cohortMethodPropensityModelServer.html
    #	docs/reference/cohortMethodPropensityModelViewer.html
    #	docs/reference/cohortMethodPropensityScoreDistServer.html
    #	docs/reference/cohortMethodPropensityScoreDistViewer.html
    #	docs/reference/cohortMethodResultSummaryServer.html
    #	docs/reference/cohortMethodResultSummaryViewer.html
    #	docs/reference/cohortMethodServer.html
    #	docs/reference/cohortMethodSystematicErrorServer.html
    #	docs/reference/cohortMethodSystematicErrorViewer.html
    #	docs/reference/cohortMethodViewer.html
    #	docs/reference/cohortOverlapView.html
    #	docs/reference/compareCohortCharacterizationView.html
    #	docs/reference/conceptsInDataSourceView.html
    #	docs/reference/createCdDatabaseDataSource.html
    #	docs/reference/createCustomColDefList.html
    #	docs/reference/createLargeSqlQueryDt.html
    #	docs/reference/dataDiagnosticDrillServer.html
    #	docs/reference/dataDiagnosticDrillViewer.html
    #	docs/reference/dataDiagnosticHelperFile.html
    #	docs/reference/dataDiagnosticServer.html
    #	docs/reference/dataDiagnosticSummaryServer.html
    #	docs/reference/dataDiagnosticSummaryViewer.html
    #	docs/reference/dataDiagnosticViewer.html
    #	docs/reference/databaseInformationView.html
    #	docs/reference/datasourcesHelperFile.html
    #	docs/reference/datasourcesServer.html
    #	docs/reference/datasourcesViewer.html
    #	docs/reference/evidenceSynthesisHelperFile.html
    #	docs/reference/evidenceSynthesisServer.html
    #	docs/reference/evidenceSynthesisViewer.html
    #	docs/reference/getCirceRenderedExpression.html
    #	docs/reference/getEnabledCdReports.html
    #	docs/reference/getLogoImage.html
    #	docs/reference/incidenceRatesView.html
    #	docs/reference/inclusionRulesView.html
    #	docs/reference/index.html
    #	docs/reference/indexEventBreakdownView.html
    #	docs/reference/largeTableServer.html
    #	docs/reference/largeTableView.html
    #	docs/reference/makeButtonLabel.html
    #	docs/reference/orpahanConceptsView.html
    #	docs/reference/patientLevelPredictionCalibrationServer.html
    #	docs/reference/patientLevelPredictionCalibrationViewer.html
    #	docs/reference/patientLevelPredictionCovariateSummaryServer.html
    #	docs/reference/patientLevelPredictionCovariateSummaryViewer.html
    #	docs/reference/patientLevelPredictionCutoffServer.html
    #	docs/reference/patientLevelPredictionCutoffViewer.html
    #	docs/reference/patientLevelPredictionDesignSummaryServer.html
    #	docs/reference/patientLevelPredictionDesignSummaryViewer.html
    #	docs/reference/patientLevelPredictionDiagnosticsServer.html
    #	docs/reference/patientLevelPredictionDiagnosticsViewer.html
    #	docs/reference/patientLevelPredictionDiscriminationServer.html
    #	docs/reference/patientLevelPredictionDiscriminationViewer.html
    #	docs/reference/patientLevelPredictionHelperFile.html
    #	docs/reference/patientLevelPredictionModelSummaryServer.html
    #	docs/reference/patientLevelPredictionModelSummaryViewer.html
    #	docs/reference/patientLevelPredictionNbServer.html
    #	docs/reference/patientLevelPredictionNbViewer.html
    #	docs/reference/patientLevelPredictionServer.html
    #	docs/reference/patientLevelPredictionSettingsServer.html
    #	docs/reference/patientLevelPredictionSettingsViewer.html
    #	docs/reference/patientLevelPredictionValidationServer.html
    #	docs/reference/patientLevelPredictionValidationViewer.html
    #	docs/reference/patientLevelPredictionViewer.html
    #	docs/reference/phevaluatorHelperFile.html
    #	docs/reference/phevaluatorServer.html
    #	docs/reference/phevaluatorViewer.html
    #	docs/reference/resultTableServer.html
    #	docs/reference/resultTableViewer.html
    #	docs/reference/sccsHelperFile.html
    #	docs/reference/sccsServer.html
    #	docs/reference/sccsView.html
    #	docs/reference/timeDistributionsView.html
    #	docs/reference/visitContextView.html
    #	docs/sitemap.xml
    azimov committed Jul 15, 2024
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  3. Merge pull request #305 from OHDSI/hotfix-2.1.5-develop-merge

    Hotfix 2.1.5 develop merge
    azimov authored Jul 15, 2024
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Commits on Jul 23, 2024

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Commits on Jul 30, 2024

  1. Switch coldef json to CSV.

    chrisknoll committed Jul 30, 2024
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  2. Removed dead code.

    chrisknoll committed Jul 30, 2024
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  3. Configuration menu
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Commits on Jul 31, 2024

  1. fixing tests

    - fixing tests
    - updates for Characterization v1.1.0
    - updating example app
    jreps committed Jul 31, 2024
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  2. fixing example sqlite database_ids

    fixing example sqlite database_ids
    jreps committed Jul 31, 2024
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Commits on Aug 1, 2024

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  2. Merge pull request #310 from OHDSI/estimation-updated-cohortIncidence

    Estimation updated cohort incidence
    jreps authored Aug 1, 2024
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  3. CohortIncidence updates

    - updating test database for new CohortIncidence
    - fixing tests for new CohortIncidence
    jreps committed Aug 1, 2024
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  4. fixing check issues due to cohort incidence

    fixing check issues due to cohort incidence
    jreps committed Aug 1, 2024
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  5. adding hot fixes from main

    - adding hot fixes from main
    - adding incidence results into example app
    jreps committed Aug 1, 2024
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  6. updating example app for CI

    updating example app for CI
    jreps committed Aug 1, 2024
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  7. updating docs

    - website update
    - manual update
    jreps committed Aug 1, 2024
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Commits on Aug 6, 2024

  1. Update characterization-riskFactors.R

    fixing minor bug in risk factor that happens when there is multiple outcomeWashoutdays
    jreps committed Aug 6, 2024
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Commits on Aug 9, 2024

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  2. Fixing issue #314 - adding T, C, and O IDs to the table to allow bett…

    …er filtering to users
    nhall6 committed Aug 9, 2024
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Commits on Aug 15, 2024

  1. addressing issue #307

    adding global fuzzy string matching to table search
    nhall6 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Characterization updates

    - updating Characterization for new censoring
    - adding counts to risk factor view
    jreps committed Aug 16, 2024
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  2. Merge pull request #316 from OHDSI/prerelease-issue#315

    Fixing issue #315 , diagonal line along x = y
    jreps authored Aug 16, 2024
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  3. Merge pull request #317 from OHDSI/prerelease-issue#314

    Fixing issue #314 - adding T, C, and O IDs to the table to allow better filtering capabilities for users in large studies
    jreps authored Aug 16, 2024
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Commits on Aug 19, 2024

  1. Update components-data-viewer.R

    removing new dep on htmlwidgets
    jreps committed Aug 19, 2024
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  2. document updates

    - updating version ready for release
    - updating docs
    - updating readme
    jreps committed Aug 19, 2024
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  3. Merge pull request #321 from OHDSI/prerelease-issue#307

    addressing issue #307
    jreps authored Aug 19, 2024
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Commits on Aug 20, 2024

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  2. Configuration menu
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  3. merging in develop

    - merging in develop
    - recreating docs after merge
    jreps committed Aug 20, 2024
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  4. fixing formatting of authors

    fixing formatting of authors
    jreps committed Aug 20, 2024
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  5. Merge pull request #297 from OHDSI/nhall6-author-updates

    Update DESCRIPTION
    jreps authored Aug 20, 2024
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  6. Merge pull request #312 from OHDSI/prerelease

    Prerelease
    jreps authored Aug 20, 2024
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Commits on Aug 21, 2024

  1. Update characterization-main.R

    fixing missing schema
    jreps committed Aug 21, 2024
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  2. Update characterization-riskFactors.R

    updating as setting id is now a character
    jreps committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. updating website

    jreps committed Aug 22, 2024
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