Fix export when there are multiple exposure-outcomes per SCCS data file.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SelfControlledCaseSeries
 Type: Package
 Title: Self-Controlled Case Series
-Version: 5.2.1
-Date: 2024-06-06
+Version: 5.2.2
+Date: 2024-06-10
 Authors@R: c(
   person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
 	person("Patrick", "Ryan", role = c("aut")),

NEWS.md

@@ -1,3 +1,10 @@
+SelfControlledCaseSeries 5.2.2
+==============================
+
+Bugfixes
+
+1. Fix export when there are multiple exposure-outcomes per SCCS data file.
+
 SelfControlledCaseSeries 5.2.1
 ==============================
 

R/Export.R

@@ -762,23 +762,23 @@ exportGroup <- function(group, sccsDiagnosticThresholds, outputFolder, databaseI
                                                     .data$preExposureDiagnostic != "FAIL", 1, 0)) %>%
       select(-"eraId")
     sccsDiagnosticsSummary[[length(sccsDiagnosticsSummary) + 1]] <- table
-    return(list(
-      sccsAgeSpanning = sccsAgeSpanning,
-      sccsAttrition = sccsAttrition,
-      sccsCalendarTimeSpanning = sccsCalendarTimeSpanning,
-      sccsCensorModel = sccsCensorModel,
-      sccsCovariate = sccsCovariate,
-      sccsCovariateResult = sccsCovariateResult,
-      sccsEra = sccsEra,
-      sccsEventDepObservation = sccsEventDepObservation,
-      sccsLikelihoodProfile = sccsLikelihoodProfile,
-      sccsSpline = sccsSpline,
-      sccsTimeToEvent = sccsTimeToEvent,
-      sccsTimeTrend = sccsTimeTrend,
-      sccsTimePeriod = sccsTimePeriod,
-      sccsDiagnosticsSummary = sccsDiagnosticsSummary
-    ))
   }
+  return(list(
+    sccsAgeSpanning = sccsAgeSpanning,
+    sccsAttrition = sccsAttrition,
+    sccsCalendarTimeSpanning = sccsCalendarTimeSpanning,
+    sccsCensorModel = sccsCensorModel,
+    sccsCovariate = sccsCovariate,
+    sccsCovariateResult = sccsCovariateResult,
+    sccsEra = sccsEra,
+    sccsEventDepObservation = sccsEventDepObservation,
+    sccsLikelihoodProfile = sccsLikelihoodProfile,
+    sccsSpline = sccsSpline,
+    sccsTimeToEvent = sccsTimeToEvent,
+    sccsTimeTrend = sccsTimeTrend,
+    sccsTimePeriod = sccsTimePeriod,
+    sccsDiagnosticsSummary = sccsDiagnosticsSummary
+  ))
 }
 
 computeSpans <- function(studyPopulation, variable = "age") {

extras/MultiAnalysesVignetteDataFetch.R

@@ -24,7 +24,7 @@ connectionDetails <- DatabaseConnector::createConnectionDetails(
   user = keyring::key_get("redShiftUserName"),
   password = keyring::key_get("redShiftPassword")
 )
-cdmDatabaseSchema <- "cdm_truven_mdcd_v2565"
+cdmDatabaseSchema <- "cdm_truven_mdcd_v2888"
 cohortDatabaseSchema <- "scratch_mschuemi"
 cohortTable <- "sccs_vignette"
 options(sqlRenderTempEmulationSchema = NULL)
@@ -273,7 +273,8 @@ exportToCsv(
   outputFolder = outputFolder,
   exportFolder = file.path(outputFolder, "export"),
   databaseId = "MDCD",
-  minCellCount = 5
+  minCellCount = 5,
+  maxCores = 1
 )
 
 # Upload results to SQLite -----------------------------------------------------

extras/UploadResultsToSqlite.R

@@ -3,6 +3,7 @@
 # Currently requires installing OhdsiSharing from https://github.com/anthonysena/OhdsiSharing/tree/issue-6-upload-results
 library(OhdsiSharing)
 library(DatabaseConnector)
+library(SelfControlledCaseSeries)
 
 outputFolder <- "d:/temp/sccsVignette2"
 
@@ -19,16 +20,16 @@ file.copy(
   to = file.path(outputFolder, "export")
 )
 
-createResultsDataModelTables(
+createResultsDataModel(
   connectionDetails = connectionDetails,
-  schema = "main",
-  resultsFolder = file.path(outputFolder, "export")
+  databaseSchema = "main"
 )
 
-uploadResults(
+SelfControlledCaseSeries::uploadResults(
   connectionDetails = connectionDetails,
   schema = "main",
-  resultsFolder = file.path(outputFolder, "export")
+  zipFileName = file.path(outputFolder, "export", "Results_MDCD.zip"),
+  purgeSiteDataBeforeUploading = FALSE
 )
 
 # Add cg_cohort_definition table:

vignettes/SingleStudies.Rmd

@@ -688,10 +688,8 @@ if (folderExists) {
 We see that, after removing the COVID blip, the observed-to-expected ratio seems stable. We can perform a formal test for stability:
 
 ```{r eval=FALSE}
-stability <- computeTimeStability(studyPopulation = studyPop,
-                                  sccsModel = model)
-stability %>%
-  filter(!stable)
+computeTimeStability(studyPopulation = studyPop,
+                     sccsModel = model)
 ```
 ```{r echo=FALSE,message=FALSE}
 if (folderExists) {