Updating vignettes to use latest Capr functions. Fixes #159

OHDSI · Jan 31, 2024 · 79bddeb · 79bddeb
1 parent 22179f4
commit 79bddeb
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Showing 4 changed files with 18 additions and 45 deletions.
diff --git a/extras/MultiAnalysesVignetteDataFetch.R b/extras/MultiAnalysesVignetteDataFetch.R
@@ -37,7 +37,6 @@ cohortTable  <- "cm_vignette"
 
 # Define exposure cohorts ------------------------------------------------------
 library(Capr)
-library(CirceR)
 
 osteoArthritisOfKneeConceptId <- 4079750
 celecoxibConceptId <- 1118084
@@ -46,9 +45,9 @@ osteoArthritisOfKnee <- cs(
   descendants(osteoArthritisOfKneeConceptId),
   name = "Osteoarthritis of knee"
 )
-attrition = attrition(
+attrition <- attrition(
   "prior osteoarthritis of knee" = withAll(
-    atLeast(1, condition(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0)))
+    atLeast(1, conditionOccurrence(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0)))
   )
 )
 celecoxib <- cs(
@@ -61,7 +60,7 @@ diclofenac  <- cs(
 )
 celecoxibCohort <- cohort(
   entry = entry(
-    drug(celecoxib, firstOccurrence()),
+    drugExposure(celecoxib, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
@@ -71,20 +70,15 @@ celecoxibCohort <- cohort(
 )
 diclofenacCohort <- cohort(
   entry = entry(
-    drug(diclofenac, firstOccurrence()),
+    drugExposure(diclofenac, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
   exit = exit(endStrategy = drugExit(diclofenac,
                                      persistenceWindow = 30,
                                      surveillanceWindow = 0))
 )
-exposureCohorts <- tibble(cohortId = c(1,2),
-                          cohortName = c("Celecoxib", "Diclofenac"),
-                          json = c(as.json(celecoxibCohort), as.json(diclofenacCohort)))
-exposureCohorts$sql <- sapply(exposureCohorts$json,
-                              buildCohortQuery,
-                              options = createGenerateOptions())
+exposureCohorts <- makeCohortSet(celecoxibCohort, diclofenacCohort)
 
 # Define outcome cohort --------------------------------------------------------
 library(PhenotypeLibrary)

diff --git a/extras/SingleStudyVignetteDataFetch.R b/extras/SingleStudyVignetteDataFetch.R
@@ -48,7 +48,7 @@ osteoArthritisOfKnee <- cs(
 )
 attrition = attrition(
   "prior osteoarthritis of knee" = withAll(
-    atLeast(1, condition(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0)))
+    atLeast(1, conditionOccurrence(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0)))
   )
 )
 celecoxib <- cs(
@@ -61,7 +61,7 @@ diclofenac  <- cs(
 )
 celecoxibCohort <- cohort(
   entry = entry(
-    drug(celecoxib, firstOccurrence()),
+    drugExposure(celecoxib, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
@@ -71,26 +71,21 @@ celecoxibCohort <- cohort(
 )
 diclofenacCohort <- cohort(
   entry = entry(
-    drug(diclofenac, firstOccurrence()),
+    drugExposure(diclofenac, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
   exit = exit(endStrategy = drugExit(diclofenac,
                                      persistenceWindow = 30,
                                      surveillanceWindow = 0))
 )
+exposureCohorts <- makeCohortSet(celecoxibCohort, diclofenacCohort)
+
 # Define outcome cohort --------------------------------------------------------
 library(PhenotypeLibrary)
 outcomeCohorts <- getPlCohortDefinitionSet(77) # GI bleed
 
 # Generate cohorts -------------------------------------------------------------
-library(CirceR)
-exposureCohorts <- tibble(cohortId = c(1,2),
-                          cohortName = c("Celecoxib", "Diclofenac"),
-                          json = c(as.json(celecoxibCohort), as.json(diclofenacCohort)))
-exposureCohorts$sql <- sapply(exposureCohorts$json,
-                              buildCohortQuery,
-                              options = createGenerateOptions())
 allCohorts <- bind_rows(outcomeCohorts,
                         exposureCohorts)
 library(CohortGenerator)

diff --git a/vignettes/MultipleAnalyses.Rmd b/vignettes/MultipleAnalyses.Rmd
@@ -84,7 +84,7 @@ osteoArthritisOfKnee <- cs(
 )
 attrition = attrition(
   "prior osteoarthritis of knee" = withAll(
-    atLeast(1, condition(osteoArthritisOfKnee), 
+    atLeast(1, conditionOccurrence(osteoArthritisOfKnee), 
             duringInterval(eventStarts(-Inf, 0)))
   )
 )
@@ -98,7 +98,7 @@ diclofenac  <- cs(
 )
 celecoxibCohort <- cohort(
   entry = entry(
-    drug(celecoxib, firstOccurrence()),
+    drugExposure(celecoxib, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
@@ -108,14 +108,15 @@ celecoxibCohort <- cohort(
 )
 diclofenacCohort <- cohort(
   entry = entry(
-    drug(diclofenac, firstOccurrence()),
+    drugExposure(diclofenac, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
   exit = exit(endStrategy = drugExit(diclofenac,
                                      persistenceWindow = 30,
                                      surveillanceWindow = 0))
 )
+exposureCohorts <- makeCohortSet(celecoxibCohort, diclofenacCohort)
 ```
 
 We'll pull the outcome definition from the OHDSI `PhenotypeLibrary`:
@@ -146,15 +147,6 @@ negativeControlCohorts <- tibble(
 We combine the exposure and outcome cohort definitions, and use `CohortGenerator` to generate the cohorts:
 
 ```{r eval=FALSE}
-library(CirceR)
-# For exposures, create a cohort definition set table as required by CohortGenerator:
-exposureCohorts <- tibble(cohortId = c(1,2),
-                          cohortName = c("Celecoxib", "Diclofenac"),
-                          json = c(as.json(celecoxibCohort), 
-                                   as.json(diclofenacCohort)))
-exposureCohorts$sql <- sapply(exposureCohorts$json,
-                              buildCohortQuery,
-                              options = createGenerateOptions())
 allCohorts <- bind_rows(outcomeCohorts,
                         exposureCohorts)
 

diff --git a/vignettes/SingleStudies.Rmd b/vignettes/SingleStudies.Rmd
@@ -78,7 +78,7 @@ osteoArthritisOfKnee <- cs(
 )
 attrition = attrition(
   "prior osteoarthritis of knee" = withAll(
-    atLeast(1, condition(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0)))
+    atLeast(1, conditionOccurrence(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0)))
   )
 )
 celecoxib <- cs(
@@ -91,7 +91,7 @@ diclofenac  <- cs(
 )
 celecoxibCohort <- cohort(
   entry = entry(
-    drug(celecoxib, firstOccurrence()),
+    drugExposure(celecoxib, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
@@ -101,14 +101,15 @@ celecoxibCohort <- cohort(
 )
 diclofenacCohort <- cohort(
   entry = entry(
-    drug(diclofenac, firstOccurrence()),
+    drugExposure(diclofenac, firstOccurrence()),
     observationWindow = continuousObservation(priorDays = 365)
   ),
   attrition = attrition,
   exit = exit(endStrategy = drugExit(diclofenac,
                                      persistenceWindow = 30,
                                      surveillanceWindow = 0))
 )
+exposureCohorts <- makeCohortSet(celecoxibCohort, diclofenacCohort)
 ```
 
 We'll pull the outcome definition from the OHDSI `PhenotypeLibrary`:
@@ -121,15 +122,6 @@ outcomeCohorts <- getPlCohortDefinitionSet(77) # GI bleed
 We combine the exposure and outcome cohort definitions, and use `CohortGenerator` to generate the cohorts:
 
 ```{r eval=FALSE}
-library(CirceR)
-# For exposures, create a cohort definition set table as required by CohortGenerator:
-exposureCohorts <- tibble(cohortId = c(1,2),
-                          cohortName = c("Celecoxib", "Diclofenac"),
-                          json = c(as.json(celecoxibCohort), 
-                                   as.json(diclofenacCohort)))
-exposureCohorts$sql <- sapply(exposureCohorts$json,
-                              buildCohortQuery,
-                              options = createGenerateOptions())
 allCohorts <- bind_rows(outcomeCohorts,
                         exposureCohorts)