Minor fixes

OHDSI · Oct 8, 2020 · 770847a · 770847a
1 parent dccc2f4
commit 770847a
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/R/CohortConstruction.R b/R/CohortConstruction.R
@@ -128,10 +128,12 @@ getCohortsJsonAndSqlFromWebApi <- function(baseUrl = baseUrl,
     cohortSetReference <- dplyr::rename(cohortSetReference, cohortName = "name")
   }
   cohortSetReference <- makeBackwardsCompatible(cohortSetReference)
+  cohortSetReference$json <- ""
+  cohortSetReference$sql <- ""
 
   ParallelLogger::logInfo("Retrieving cohort definitions from WebAPI")
   for (i in 1:nrow(cohortSetReference)) {
-    ParallelLogger::logInfo("- Retrieving definitions for cohort ", cohortSetReference$cohortFullName[i])
+    ParallelLogger::logInfo("- Retrieving definitions for cohort ", cohortSetReference$cohortName[i])
     cohortDefinition <-  ROhdsiWebApi::getCohortDefinition(cohortId = cohortSetReference$webApiCohortId[i],
                                                            baseUrl = baseUrl)
     cohortSetReference$json[i] <- RJSONIO::toJSON(x = cohortDefinition$expression, digits = 23)

diff --git a/R/IncidenceRates.R b/R/IncidenceRates.R
@@ -110,6 +110,7 @@ getIncidenceRate <- function(connectionDetails = NULL,
                              irYearGender,
                              irYearAgeGender)
   result$incidenceRate <- 1000 * result$cohortCount/result$personYears
+  result$incidenceRate[is.nan(result$incidenceRate)] <- 0
   delta <- Sys.time() - start
   ParallelLogger::logInfo(paste("Computing incidence rates took",
                                 signif(delta, 3),