Merge branch 'rc_v2'

.Rbuildignore

@@ -20,5 +20,5 @@ target/
 docs
 compare_versions
 _pkgdown.yml
-exampleComparativeCohortStudy
+examplePhenotypeLibraryPackage
 examplePackage

.gitignore

@@ -5,6 +5,8 @@
 *.RData
 inst/shiny/DiagnosticsExplorer/data/phenotypeDescription.csv
 inst/shiny/DiagnosticsExplorer/data/cohortDescription.csv
-inst/shiny/DiagnosticsExplorer/data/cohortDescription.csv
-inst/shiny/DiagnosticsExplorer/data/phenotypeDescription.csv
 *.zip
+errorReportSql.txt
+errorReportR.txt
+*.tex
+.DS_Store

.travis.yml

@@ -1,10 +1,12 @@
 language: R
 cache: packages
-sudo: false
 
 branches:
   except:
     - /^*-v[0-9]/
+
+before_install:
+  - sudo $(which R) CMD javareconf
 
 r_packages:
   - covr

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CohortDiagnostics
 Type: Package
-Title: Diagnostics for OHDSI Studies
-Version: 1.2.7
-Date: 2020-09-08
+Title: Diagnostics for OHDSI Cohorts
+Version: 2.0.0
+Date: 2020-10-07
 Authors@R: c(
     person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
     person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),
@@ -11,45 +11,47 @@ Authors@R: c(
     person("Observational Health Data Science and Informatics", role = c("cph"))
   )
 Maintainer: Gowtham Rao <[email protected]>
-Description: Diagnostics for studies that use the OMOP Common Data Model and the OHDSI tools.
+Description: Diagnostics for cohorts that use the OMOP Common Data Model and the OHDSI tools.
 Depends:
 	DatabaseConnector (>= 3.0.0),
+	FeatureExtraction (>= 3.1.0),
 	R (>= 3.5.0)
 Imports:
   Andromeda,
   checkmate,
   digest,
   dplyr (>= 1.0.0),
-  FeatureExtraction (>= 3.0.1),
   ggplot2,
+  ggiraph,
   ParallelLogger (>= 2.0.0),
-  readr,
+  readr (>= 1.4.0),
   rlang,
   RJSONIO,
-  ROhdsiWebApi (>= 1.1.0),
+  ROhdsiWebApi (>= 1.1.2),
   SqlRender (>= 1.6.7),
   stringr,
-  tibble (>= 3.0.0),
-  tidyr (>= 1.0.0)
+  tidyr (>= 1.0.0),
+  methods
 Suggests:
+  shiny,
+  shinydashboard,
+  shinyWidgets,
   DT,
-  Eunomia,
-  RSQLite (> 2.2.0),
-  htmltools,
-  knitr,
   plotly,
+  htmltools,
   RColorBrewer,
-  rmarkdown,
   scales,
-  shiny,
-  shinydashboard,
-  VennDiagram,
-  testthat
+  knitr,
+  rmarkdown,
+  Eunomia,
+  testthat,
+  RSQLite (>= 2.2.1),
+  zip
 Remotes:
   ohdsi/Eunomia,
   ohdsi/FeatureExtraction,
   ohdsi/ROhdsiWebApi,
-  r-dbi/RSQLite
+  ohdsi/DatabaseConnector,
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics

NAMESPACE

@@ -1,35 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
-export(breakDownIndexEvents)
-export(compareCohortCharacteristics)
-export(computeCohortOverlap)
+export(checkInputFileEncoding)
 export(createCohortTable)
-export(createConceptCountsTable)
-export(extractConceptSetsJsonFromCohortJson)
-export(extractConceptSetsSqlFromCohortSql)
-export(findCohortIncludedSourceConcepts)
-export(findCohortOrphanConcepts)
-export(findOrphanConcepts)
-export(getCohortCharacteristics)
+export(createResultsDataModel)
 export(getCohortCounts)
-export(getCohortsJsonAndSql)
-export(getIncidenceRate)
-export(getInclusionStatistics)
-export(getInclusionStatisticsFromFiles)
-export(getTimeDistributions)
-export(getUniqueConceptIds)
+export(getResultsDataModelSpecifications)
 export(instantiateCohort)
 export(instantiateCohortSet)
 export(launchCohortExplorer)
 export(launchDiagnosticsExplorer)
-export(plotincidenceRate)
 export(preMergeDiagnosticsFiles)
 export(runCohortDiagnostics)
-export(runCohortDiagnosticsUsingExternalCounts)
-export(writeOmopvocabularyTables)
+export(uploadResults)
 import(DatabaseConnector)
 import(dplyr)
+importFrom(FeatureExtraction,createDefaultCovariateSettings)
+importFrom(FeatureExtraction,createTemporalCovariateSettings)
 importFrom(grDevices,rgb)
+importFrom(methods,is)
 importFrom(rlang,.data)
 importFrom(stats,aggregate)
 importFrom(utils,install.packages)

NEWS.md

@@ -1,24 +1,29 @@
-CohortDiagnostics 1.2.7
+CohortDiagnostics 2.0.0
 =======================
-Note: 
 
-1.2.x is last release of v 1.x.x series. Future releases with new functionality are expected to have breaking changes with no backward compatability and will be 2.x.x series.
+Changes:
 
-Bug fixes:
+1. Many improvements in performance when computing diagnostics. Now allows computation of diagnostics for many (>100) cohorts at once. 
 
-1. Temporal choice error message during mismatch with temporal characterization output not having timeId
+2. The Diagnostics Explorer Shiny app can now also run against results data in a database. Added functions for uploading the diagnostics data to a database. This becomes necessary when dealing with very large data (e.g. more than 100 cohort definitions).
 
+3. Added ability to group cohort definitions by phenotypes, and add descriptions of phenotypes. Currently the only consequence of grouping by phenotype is that cohort overlap is only computed within a phenotype. Grouping by phenotypes is done by adding a `phenotypeId` field to the `cohortsToCreate` file, and by adding a `phenotypeDescription` file. See the `examplePhenotypeLibraryPackage` in the repo for an example.
 
-CohortDiagnostics 1.2.6
-=======================
+4. The cohort overlap plot now uses stacked bar charts instead of a Venn diagram to allow showing multiple comparisons across multiple databases at once.
+
+5. The cohort characteristics comparison plot now colors by domain, and allows filtering by domain.
+
+6. Switching from 'plotly' to 'ggiraph' for interactive plotting.
+
+7. Added a Visit Context diagnostic.
 
 
 Bug fixes:
 
-1. Additional bug fixes for characterization/temporal characterization.
+1. Fixing numerous bugs introduced in v1.2.x.
 
 
-CohortDiagnostics 1.2.5
+CohortDiagnostics 1.2.6
 =======================
 
 Bug fixes:
@@ -51,32 +56,6 @@ Bug fixes:
 2. Removed ohdsi/SqlRender from Remotes https://github.com/OHDSI/CohortDiagnostics/issues/189
 3. Fixed Digit precision for RJSONIO::toJson and fromJSON https://github.com/OHDSI/CohortDiagnostics/issues/161 This is an important fix. If digit precision is not explicitly specified in RJSONIO, then scientific notation is used. This issue seems to only happen when an integer id (conceptId, conceptSetId, cohortId etc) >= 10,000,000 (which is rare). Please use this update if you have id's > 10,000,000.
 
-CohortDiagnostics 1.2.2
-=======================
-Changes:
-1. Minor UI changes to Diagnostics explorer. Added missing sort.
-2. Added better labels for plots.
-3. Download plots.
-
-Bug fixes:
-1. Changes dependency to ROhdsiWebApi (>= 1.1.0)
-2. DiagnosticsExplorer display bug fixes
-
-CohortDiagnostics 1.2.1
-=======================
-Changes:
-1. All objects in DiagnosticsExplorer are sorted by default #173
-2. Multi select for concepts #199
-
-Bug fixes:
-1. Ensure concept sets across cohort definitions are unique #174 (changes dependency to ROhdsiWebApi (>= 1.1.0))
-
-Note: 1.2.x are the last planned release in v1.x.x series. No new functionalities will 
-be added to 1.2.x moving forward. All future releases in 1.2.x series will be bug fixes.
-
-Version 2.x is planned for release by October 2020, and will be a breaking change. Output of 
-Versions 2.x will use a different data model and will not be backward compatible with 1.x.
-
 CohortDiagnostics 1.2.2
 =======================
 New features:
@@ -97,15 +76,6 @@ New features:
 Bug fixes:
 1. Ensure concept sets across cohort definitions are unique #174 (changes dependency to ROhdsiWebApi (>= 1.1.0))
 
-CohortDiagnostics 1.2.0
-=======================
-Changes:
-1. All objects in DiagnosticsExplorer are sorted by default #173
-2. Multi select for concepts #199
-
-Bug fixes:
-1. Ensure concept sets across cohort definitions are unique #174
-
 CohortDiagnostics 1.2.0
 =======================
 Changes:
@@ -151,7 +121,7 @@ get the JSON and parameterized OHDSI SQL for the cohorts for which diagnostics h
 
 Note: The code has been partially refactored to depend on tidyverse. 
 
-CohortDiagnostics 1.0.0
+CohortDiagnostics 1.0.2
 =======================
 
 Changes: