Merge pull request #323 from OHDSI/fix_sampleCohorts_issue

Fix sample cohorts issue

R/sampleCohorts.R

@@ -5,7 +5,7 @@
 #' people. All records of these individuals are preserved.
 #'
 #' @inheritParams cohortDoc
-#' @inheritParams cohortIdSubsetDoc
+#' @inheritParams cohortIdModifyDoc
 #' @inheritParams nameDoc
 #' @param n Number of people to be sampled for each included cohort.
 #'

vignettes/a07_filter_cohorts.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "a06_filter_cohorts"
+title: "Filter Cohorts"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{a06_filter_cohorts}
+  %\VignetteIndexEntry{a07_filter_cohorts}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -16,4 +16,47 @@ knitr::opts_chunk$set(
 
 ```{r setup}
 library(CohortConstructor)
+library(CohortCharacteristics)
+library(ggplot2)
+```
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  eval = TRUE, message = FALSE, warning = FALSE,
+  comment = "#>"
+)
+
+library(CDMConnector)
+library(dplyr, warn.conflicts = FALSE)
+
+if (Sys.getenv("EUNOMIA_DATA_FOLDER") == ""){
+  Sys.setenv("EUNOMIA_DATA_FOLDER" = file.path(tempdir(), "eunomia"))}
+if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))){ dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
+  downloadEunomiaData()  
+}
+```
+
+For this example we'll use the Eunomia synthetic data from the CDMConnector package.
+
+```{r}
+con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
+cdm <- cdm_from_con(con, cdm_schema = "main", 
+                    write_schema = c(prefix = "my_study_", schema = "main"))
+```
+
+Let's start by creating two drug cohorts, one for users of diclofenac and another for users of acetaminophen.
+
+```{r}
+cdm$medications <- conceptCohort(cdm = cdm, 
+                                 conceptSet = list("diclofenac" = 1124300,
+                                                   "acetaminophen" = 1127433), 
+                                 name = "medications")
+cohortCount(cdm$medications)
+```
+
+```{r}
+cdm$medications_sample <- sampleCohorts(cdm$medications,cohortId = 1, n = 100, name = "medications_sample")
+
+cohortCount(cdm$medications_sample)
 ```