Merge pull request #3 from mi-erasmusmc/develop

Adding renv files
mi-erasmusmc · Nov 9, 2022 · 446c0f8 · 446c0f8
2 parents fa8f01e + 2dd3fcb
commit 446c0f8
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Showing 6 changed files with 2,303 additions and 7 deletions.
diff --git a/extras/CodeToRunEunomia4.R b/extras/CodeToRunEunomia4.R
@@ -57,7 +57,8 @@ Eunomia::createCohorts(connectionDetails = connectionDetails)
 # Database details ---------
 databaseDetails <- PatientLevelPrediction::createDatabaseDetails(connectionDetails = connectionDetails, 
                                                                  cdmDatabaseSchema = cdmDatabaseSchema, 
-                                                                 cdmDatabaseName = cdmDatabaseName, 
+                                                                 cdmDatabaseName = cdmDatabaseName,
+                                                                 cdmDatabaseId = cdmDatabaseName,
                                                                  cohortDatabaseSchema = cohortDatabaseSchema, 
                                                                  cohortTable = cohortTable, 
                                                                  outcomeDatabaseSchema = outcomeDatabaseSchema, 
@@ -173,11 +174,12 @@ analysisSettings <- list(
 )
 
 # Execute study -----
-PredictiveValueFPs::execute(runExtractAtemporalData = FALSE, 
-                            runExtractTemporalData = FALSE, 
+PredictiveValueFPs::execute(runExtractAtemporalData = TRUE, 
+                            runExtractTemporalData = TRUE, 
                             runPrepareData = TRUE,
                             runExtractFPs = TRUE, 
-                            runGenerateFPObjects = TRUE, 
+                            runGenerateFPObjects = TRUE,
+                            runBaseline = FALSE,
                             runPrediction = FALSE,
                             runPlpSettings = runPlpSettings, 
                             runFrequentPatternsSettings = runFrequentPatternsSettings,

diff --git a/extras/execute_CodeToRunEunomia4.R b/extras/execute_CodeToRunEunomia4.R
@@ -2,12 +2,12 @@ outcomeId = 3
 outcomeName = "gi"
 databaseName = "Eunomia"
 rscriptLoc =file.path(getwd(), "extras/CodeToRunEunomia4.R")
-inputDir = file.path(getwd(), "data", "Eunomia6")
-outputDir = file.path(getwd(), "Eunomia8")
+inputDir = file.path(getwd(), "data", "Eunomia8")
+outputDir = file.path(getwd(), "Eunomia11")
 
 # rscriptLoc = file.path(getwd(), "experimentation/testing_optparse.R")
 
 # system(paste("Rscript", rscriptLoc, "-o", outcomeId, "-c", outcomeName,"-d", databaseName ,"-i", inputDir ))
-system(paste("Rscript", rscriptLoc, outcomeId,outcomeName, databaseName ,inputDir, outputDir))
+system(paste("Rscript", rscriptLoc, outcomeId, outcomeName, databaseName ,inputDir, outputDir))