diff --git a/NEWS.md b/NEWS.md index ac0902f92..92ea27cad 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,11 +4,7 @@ Bug Fix: 1. Added support for newer API to OhdsiShinyModules (while maintaining support for old version) -CohortDiagnostics 3.2.3 -======================= -Bug Fix: - -1. Resolved issue with incidence rates sometimes exporting as null/infinite by setting to 0 in all error cases +2. Resolved issue with incidence rates sometimes exporting as null/infinite by setting to 0 in all error cases CohortDiagnostics 3.2.3 diff --git a/R/IncidenceRates.R b/R/IncidenceRates.R index aa3d91aef..345421f3e 100644 --- a/R/IncidenceRates.R +++ b/R/IncidenceRates.R @@ -166,8 +166,8 @@ getIncidenceRate <- function(connectionDetails = NULL, result$incidenceRate <- 1000 * result$cohortCount / result$personYears result$incidenceRate[is.nan(result$incidenceRate) | - is.infinite(result$incidenceRate) | - is.null(result$incidenceRate)] <- 0 + is.infinite(result$incidenceRate) | + is.null(result$incidenceRate)] <- 0 delta <- Sys.time() - start ParallelLogger::logInfo(paste( "Computing incidence rates took", diff --git a/docs/404.html b/docs/404.html index f6686940d..5e7a49d8d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ CohortDiagnostics - 3.2.3 + 3.2.4 @@ -115,7 +115,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html index ed3ad29f6..01773dc89 100644 --- a/docs/articles/CreatingAStudyPackage.html +++ b/docs/articles/CreatingAStudyPackage.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.3 + 3.2.4 @@ -97,7 +97,7 @@

Creating a study package

Gowtham A. Rao

-

2023-07-20

+

2023-09-19

Source: vignettes/CreatingAStudyPackage.Rmd @@ -341,7 +341,7 @@

option A: Using Hydra and ROhdsiW

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html index 304db91eb..23cfe96cc 100644 --- a/docs/articles/DatabaseModeInDiagnosticsExplorer.html +++ b/docs/articles/DatabaseModeInDiagnosticsExplorer.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.3 + 3.2.4 @@ -97,7 +97,7 @@

Database mode in Diagnostics Explorer

Gowtham Rao

-

2023-07-20

+

2023-09-19

Source: vignettes/DatabaseModeInDiagnosticsExplorer.Rmd @@ -135,34 +135,34 @@

Database mode
# Alter these configuration settings for usage with remote databases
-connectionDetails:
-  dbms: "postgresql"
-  server: "my-database-server.com/myDatabaseName"
-  user: "postrgres"
-  password: "secret_password"
-  port: 5432
-
-# Store connection details as a json string in keyring
-# Store with keyring::key_set_with_value("KEYNAME", jsonlite::toJSON(myConnectionDetails))
-connectionDetailsSecureKey: ~
-
-# If you used a table prefix to store the results (e.g. cd_)
-tablePrefix: ""
-
-# Results schema being used
-resultsDatabaseSchema: "cohort_diagnostics"
-
-# Vocabulary schemas. Should include the reuslts schema and optional custom vocabularies
-vocabularyDatabaseSchemas: ["cohort_diagnostics"]
-
-# Custom table name for cohorts and cdm databases (probably not needed, ignores table prefix)
-cohortTableName: "cohort"
-databaseTableName: "database"
-
-# If you wish to enable annotation - not currently reccomended in multi-user environments
-enableAnnotation: FALSE
-enableAuthorization: FALSE
+
# Alter these configuration settings for usage with remote databases
+connectionDetails:
+  dbms: "postgresql"
+  server: "my-database-server.com/myDatabaseName"
+  user: "postrgres"
+  password: "secret_password"
+  port: 5432
+
+# Store connection details as a json string in keyring
+# Store with keyring::key_set_with_value("KEYNAME", jsonlite::toJSON(myConnectionDetails))
+connectionDetailsSecureKey: ~
+
+# If you used a table prefix to store the results (e.g. cd_)
+tablePrefix: ""
+
+# Results schema being used
+resultsDatabaseSchema: "cohort_diagnostics"
+
+# Vocabulary schemas. Should include the reuslts schema and optional custom vocabularies
+vocabularyDatabaseSchemas: ["cohort_diagnostics"]
+
+# Custom table name for cohorts and cdm databases (probably not needed, ignores table prefix)
+cohortTableName: "cohort"
+databaseTableName: "database"
+
+# If you wish to enable annotation - not currently reccomended in multi-user environments
+enableAnnotation: FALSE
+enableAuthorization: FALSE

Publishing @@ -198,7 +198,7 @@

Publishing

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html index 8dabd7b81..2d1af9433 100644 --- a/docs/articles/RunningCohortDiagnostics.html +++ b/docs/articles/RunningCohortDiagnostics.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.3 + 3.2.4 @@ -97,7 +97,7 @@

Running Cohort Diagnostics

Gowtham Rao and James P. Gilbert

-

2023-07-20

+

2023-09-19

Source: vignettes/RunningCohortDiagnostics.Rmd @@ -148,7 +148,7 @@

Configuring the connection to

For the purposes of this example, we will use the Eunomia test CDM package that is in an Sqlite database stored locally.

-connectionDetails <- Eunomia::getEunomiaConnectionDetails()
+connectionDetails <- Eunomia::getEunomiaConnectionDetails()
 
 cdmDatabaseSchema <- "main"
 tempEmulationSchema <- NULL
@@ -336,7 +336,7 @@ 

Creating an sqlite db file

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html index 3a8a6831a..515d223a2 100644 --- a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html +++ b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.3 + 3.2.4 @@ -97,7 +97,7 @@

Viewing results using Diagnostics Explorer

Gowtham Rao

-

2023-07-20

+

2023-09-19

Source: vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd @@ -118,8 +118,8 @@

Viewing the diagnostics - @@ -97,7 +97,7 @@

What is Cohort Diagnostics?

Gowtham Rao

-

2023-07-20

+

2023-09-19

Source: vignettes/WhatIsCohortDiagnostics.Rmd @@ -163,7 +163,7 @@

Features

-

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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 @@
- +

Build Status codecov.io

CohortDiagnostics is part of HADES.

@@ -127,8 +127,8 @@

Features

Screenshot

-
-

The Diagnostics Explorer Shiny app

+
+The Diagnostics Explorer Shiny app
The Diagnostics Explorer Shiny app
@@ -236,13 +236,7 @@

Developers

-
-

Dev status

-
    -
  • Build Status
  • -
  • codecov.io
  • -
-
+

@@ -255,7 +249,7 @@

Dev status

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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:

+
  1. Added support for newer API to OhdsiShinyModules (while maintaining support for old version)

  2. +
  3. Resolved issue with incidence rates sometimes exporting as null/infinite by setting to 0 in all error cases

  4. +
  1. 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
  2. @@ -407,7 +413,7 @@
-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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
-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.7.

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 +