-Site built with pkgdown 2.0.5.
+Site built with pkgdown 2.0.7.
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 0e118f7d0..2043de551 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -95,7 +95,7 @@ All vignettes
diff --git a/docs/authors.html b/docs/authors.html
index a3b2413dd..478196a77 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -128,7 +128,7 @@ Citation
diff --git a/docs/index.html b/docs/index.html
index 4380a75e0..c7d82f7d1 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -39,7 +39,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -102,7 +102,7 @@
-
+
CohortDiagnostics is part of HADES.
@@ -255,7 +249,7 @@ Dev status
diff --git a/docs/news/index.html b/docs/news/index.html
index eb69bb02f..1a39727f8 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -72,6 +72,12 @@ Changelog
Source: NEWS.md
+
+
+
Bug Fix:
+
Added support for newer API to OhdsiShinyModules (while maintaining support for old version)
+Resolved issue with incidence rates sometimes exporting as null/infinite by setting to 0 in all error cases
+
- Resolved issue where concept sets were only exported when diagnostics for them were executed. All concept sets are now always exported into results csv and imported into databases
@@ -407,7 +413,7 @@
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 3c6a48ff7..b615b8513 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
-pandoc: 2.19.2
-pkgdown: 2.0.5
+pandoc: 3.1.1
+pkgdown: 2.0.7
pkgdown_sha: ~
articles:
CreatingAStudyPackage: CreatingAStudyPackage.html
@@ -7,5 +7,5 @@ articles:
RunningCohortDiagnostics: RunningCohortDiagnostics.html
ViewingResultsUsingDiagnosticsExplorer: ViewingResultsUsingDiagnosticsExplorer.html
WhatIsCohortDiagnostics: WhatIsCohortDiagnostics.html
-last_built: 2023-07-20T14:57Z
+last_built: 2023-09-19T21:26Z
diff --git a/docs/reference/CohortDiagnostics-package.html b/docs/reference/CohortDiagnostics-package.html
index 99f516b39..790dcf7d4 100644
--- a/docs/reference/CohortDiagnostics-package.html
+++ b/docs/reference/CohortDiagnostics-package.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -107,7 +107,7 @@ Author
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html
index ee14f4df2..853a42554 100644
--- a/docs/reference/checkInputFileEncoding.html
+++ b/docs/reference/checkInputFileEncoding.html
@@ -18,7 +18,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -108,7 +108,7 @@ Value
diff --git a/docs/reference/createDiagnosticsExplorerZip.html b/docs/reference/createDiagnosticsExplorerZip.html
index 517f638dc..ac9d8ea7d 100644
--- a/docs/reference/createDiagnosticsExplorerZip.html
+++ b/docs/reference/createDiagnosticsExplorerZip.html
@@ -20,7 +20,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -125,7 +125,7 @@ Arguments
diff --git a/docs/reference/createMergedResultsFile.html b/docs/reference/createMergedResultsFile.html
index fb18655aa..a7ca7393f 100644
--- a/docs/reference/createMergedResultsFile.html
+++ b/docs/reference/createMergedResultsFile.html
@@ -19,7 +19,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -124,7 +124,7 @@ Arguments
diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html
index 2fda86eda..ad99e2687 100644
--- a/docs/reference/createResultsDataModel.html
+++ b/docs/reference/createResultsDataModel.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -116,7 +116,7 @@ Details
diff --git a/docs/reference/executeDiagnostics.html b/docs/reference/executeDiagnostics.html
index e180d7729..693ab6b4a 100644
--- a/docs/reference/executeDiagnostics.html
+++ b/docs/reference/executeDiagnostics.html
@@ -22,7 +22,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -342,7 +342,7 @@ Examples
diff --git a/docs/reference/getCdmDataSourceInformation.html b/docs/reference/getCdmDataSourceInformation.html
index 92d84898c..e39eecb97 100644
--- a/docs/reference/getCdmDataSourceInformation.html
+++ b/docs/reference/getCdmDataSourceInformation.html
@@ -18,7 +18,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -129,7 +129,7 @@ Value
diff --git a/docs/reference/getCohortCounts.html b/docs/reference/getCohortCounts.html
index 80462ee55..96357a4b8 100644
--- a/docs/reference/getCohortCounts.html
+++ b/docs/reference/getCohortCounts.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -138,7 +138,7 @@ Value
diff --git a/docs/reference/getDataMigrator.html b/docs/reference/getDataMigrator.html
index 95285fc78..61c802b3f 100644
--- a/docs/reference/getDataMigrator.html
+++ b/docs/reference/getDataMigrator.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -114,7 +114,7 @@ Value
diff --git a/docs/reference/getDefaultCovariateSettings.html b/docs/reference/getDefaultCovariateSettings.html
index 9b6b65e83..7853cc908 100644
--- a/docs/reference/getDefaultCovariateSettings.html
+++ b/docs/reference/getDefaultCovariateSettings.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -94,7 +94,7 @@ Get default covariate settings
diff --git a/docs/reference/getDefaultVocabularyTableNames.html b/docs/reference/getDefaultVocabularyTableNames.html
index 0bddbef0b..1f40bfd3a 100644
--- a/docs/reference/getDefaultVocabularyTableNames.html
+++ b/docs/reference/getDefaultVocabularyTableNames.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html
index a57f85df5..7f8eef6cf 100644
--- a/docs/reference/getResultsDataModelSpecifications.html
+++ b/docs/reference/getResultsDataModelSpecifications.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -100,7 +100,7 @@ Value
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 72c5309bd..1bbee13f5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -91,6 +91,10 @@ All functions createResultsDataModel()
Create the results data model tables on a database server. |
+
+ deployShinyApp()
+ |
+ Deploy shiny app to rsconnect platform |
executeDiagnostics()
|
@@ -156,7 +160,7 @@ All functions
diff --git a/docs/reference/launchDiagnosticsExplorer.html b/docs/reference/launchDiagnosticsExplorer.html
index 19e961251..57b08053a 100644
--- a/docs/reference/launchDiagnosticsExplorer.html
+++ b/docs/reference/launchDiagnosticsExplorer.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -196,7 +196,7 @@ Details
diff --git a/docs/reference/migrateDataModel.html b/docs/reference/migrateDataModel.html
index 56c9d7bf8..a72bf29d2 100644
--- a/docs/reference/migrateDataModel.html
+++ b/docs/reference/migrateDataModel.html
@@ -19,7 +19,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/runCohortRelationshipDiagnostics.html b/docs/reference/runCohortRelationshipDiagnostics.html
index c2ffd3a16..c0f9c2f9e 100644
--- a/docs/reference/runCohortRelationshipDiagnostics.html
+++ b/docs/reference/runCohortRelationshipDiagnostics.html
@@ -18,7 +18,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -149,7 +149,7 @@ Arguments
diff --git a/docs/reference/runCohortTimeSeriesDiagnostics.html b/docs/reference/runCohortTimeSeriesDiagnostics.html
index 548fea1f0..1bd102b8c 100644
--- a/docs/reference/runCohortTimeSeriesDiagnostics.html
+++ b/docs/reference/runCohortTimeSeriesDiagnostics.html
@@ -25,7 +25,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -191,7 +191,7 @@ Arguments
diff --git a/docs/reference/timeExecution.html b/docs/reference/timeExecution.html
index d97c95661..44250f40e 100644
--- a/docs/reference/timeExecution.html
+++ b/docs/reference/timeExecution.html
@@ -17,7 +17,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -102,7 +102,7 @@ Internal utility function for logging execution of variables
diff --git a/docs/reference/uploadResults.html b/docs/reference/uploadResults.html
index 86fec260b..5eb3a6514 100644
--- a/docs/reference/uploadResults.html
+++ b/docs/reference/uploadResults.html
@@ -19,7 +19,7 @@
CohortDiagnostics
- 3.2.3
+ 3.2.4
@@ -149,7 +149,7 @@ Arguments
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index c353684ce..f9a99ba7b 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -87,6 +87,9 @@
/reference/createResultsDataModel.html
+
+ /reference/deployShinyApp.html
+
/reference/dropDdl.html
diff --git a/inst/doc/RunningCohortDiagnostics.pdf b/inst/doc/RunningCohortDiagnostics.pdf
index 4c9145da3..ac855cd4a 100644
Binary files a/inst/doc/RunningCohortDiagnostics.pdf and b/inst/doc/RunningCohortDiagnostics.pdf differ
diff --git a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf
index 2fa37e58a..46ab0568e 100644
Binary files a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf and b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf differ
diff --git a/inst/doc/WhatIsCohortDiagnostics.pdf b/inst/doc/WhatIsCohortDiagnostics.pdf
index c43cf304f..23ea367e6 100644
Binary files a/inst/doc/WhatIsCohortDiagnostics.pdf and b/inst/doc/WhatIsCohortDiagnostics.pdf differ
diff --git a/inst/shiny/DiagnosticsExplorer/global.R b/inst/shiny/DiagnosticsExplorer/global.R
index a9ea4eaf7..c3895f518 100644
--- a/inst/shiny/DiagnosticsExplorer/global.R
+++ b/inst/shiny/DiagnosticsExplorer/global.R
@@ -104,3 +104,4 @@ if (packageVersion("OhdsiShinyModules") >= as.numeric_version("1.2.0")) {
}
+
diff --git a/inst/shiny/DiagnosticsExplorer/renv.lock b/inst/shiny/DiagnosticsExplorer/renv.lock
index c02a39e00..46f050bb5 100644
--- a/inst/shiny/DiagnosticsExplorer/renv.lock
+++ b/inst/shiny/DiagnosticsExplorer/renv.lock
@@ -70,7 +70,7 @@
"RemoteRepo": "DatabaseConnector",
"RemoteUsername": "OHDSI",
"RemoteRef": "HEAD",
- "RemoteSha": "c2ae089af5e0be8eb9de4b9e2c39e539b9ed695e",
+ "RemoteSha": "5867bc151cda2dcf30a682b23eb0afa1997f9abd",
"Requirements": [
"DBI",
"R",
@@ -87,7 +87,7 @@
"urltools",
"utils"
],
- "Hash": "bb708ff95f9db30dffb1f61dbcc291b8"
+ "Hash": "7b09eb5986ea9b0f7e9ea79949b6236d"
},
"MASS": {
"Package": "MASS",
@@ -218,9 +218,9 @@
},
"RSQLite": {
"Package": "RSQLite",
- "Version": "2.3.0",
+ "Version": "2.3.1",
"Source": "Repository",
- "Repository": "CRAN",
+ "Repository": "RSPM",
"Requirements": [
"DBI",
"R",
@@ -232,7 +232,7 @@
"pkgconfig",
"plogr"
],
- "Hash": "264c1861d7ac1dc71ecb5ac5c4c1318a"
+ "Hash": "207c90cd5438a1f596da2cd54c606fee"
},
"Rcpp": {
"Package": "Rcpp",
diff --git a/inst/sql/sql_server/UpdateVersionNumber.sql b/inst/sql/sql_server/UpdateVersionNumber.sql
index 7cada8199..b9b3bcdbf 100644
--- a/inst/sql/sql_server/UpdateVersionNumber.sql
+++ b/inst/sql/sql_server/UpdateVersionNumber.sql
@@ -1,5 +1,5 @@
{DEFAULT @package_version = package_version}
-{DEFAULT @version_number = '3.2.3'}
+{DEFAULT @version_number = '3.2.4'}
DELETE FROM @database_schema.@table_prefix@package_version;
INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALUES ('@version_number');
@@ -9,3 +9,4 @@ INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALU
+