Merge branch 'develop' of github.com:OHDSI/Capr into develop

OHDSI · Sep 6, 2023 · d75253d · d75253d
2 parents ec9f312 + bc63c2f
commit d75253d
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Showing 2 changed files with 21 additions and 15 deletions.
diff --git a/R/cohort.R b/R/cohort.R
@@ -425,15 +425,15 @@ writeCohort <- function(x, path) {
 # }
 
 
-capr_to_circe <- function(cd) {
-
-  circeJson <- toCirce(cd) %>%
-    jsonlite::toJSON(auto_unbox = TRUE, pretty = TRUE) %>%
-    as.character()
-
-  return(circeJson)
-
-}
+# capr_to_circe <- function(cd) {
+#
+#   circeJson <- toCirce(cd) %>%
+#     jsonlite::toJSON(auto_unbox = TRUE, pretty = TRUE) %>%
+#     as.character()
+#
+#   return(circeJson)
+#
+# }
 
 #' Make a cohort dataframe for cohort generator
 #' @param ... multiple capr cohorts to bind into a dataframe
@@ -456,7 +456,7 @@ makeCohortSet <- function(...) {
   cohortName <- names(cohortList)
 
   # get cohort json
-  cohortJson <- purrr::map_chr(cohortList, ~capr_to_circe(.x))
+  cohortJson <- purrr::map_chr(cohortList, ~compile(.x))
 
   # get ohdsi sql
   ohdsiSql <- purrr::map_chr(

diff --git a/vignettes/Examples.Rmd b/vignettes/Examples.Rmd
@@ -53,10 +53,12 @@ cs1 <- cs(descendants(443238, 201820, 442793),
 ch <- cohort(
   entry = conditionOccurrence(cs1),
   attrition = attrition(
-    atLeast(1, 
-            observationPeriod(), 
+    withAll(
+          atLeast(1, 
+            observationPeriod(), #function not currently in Capr
             duringInterval(eventStarts(-Inf, -365, "startDate"))
     )
+    )
   ),
   exit = exit(
     endStrategy = observationExit()
@@ -112,8 +114,12 @@ ch <- cohort(
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition(
-    exactly(0, conditionOccurrence(cs1), duringInterval(eventStarts(-Inf, 0))),
+    't1d' = withAll(
+    exactly(0, conditionOccurrence(cs1), duringInterval(eventStarts(-Inf, 0)))
+    ),
+    'secondaryDiabetes' = withAll(
     exactly(0, conditionOccurrence(cs2), duringInterval(eventStarts(-Inf, 0)))
+    )
   ),
   exit = exit(
     endStrategy = observationExit()
@@ -224,8 +230,8 @@ ch <- cohort(
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition(
-    "no prior T2DM" = exactly(0, conditionOccurrence(cs0), duringInterval(eventStarts(-Inf, 0))),
-    "no prior secondary T1DM" = exactly(0, conditionOccurrence(cs2), duringInterval(eventStarts(-Inf, 0)))
+    "no prior T2DM" = withAll(exactly(0, conditionOccurrence(cs0), duringInterval(eventStarts(-Inf, 0)))),
+    "no prior secondary T1DM" = withAll(exactly(0, conditionOccurrence(cs2), duringInterval(eventStarts(-Inf, 0))))
   )
 )