library("allofus")
# generate a simple stroke cohort
# see https://atlas-demo.ohdsi.org/#/cohortdefinition/1788061
# If this cohort is not available, you can create one, or choose one already made.
# aou_cohort_example contains the results of
# cd <- ROhdsiWebApi::getCohortDefinition(1788061, "https://atlas-demo.ohdsi.org/WebAPI")
# for some cohorts, you must use the argument generateStats = FALSE or the cohort (its stats)
# can't be generated on All of Us
# cd_sql <- ROhdsiWebApi::getCohortSql(cd, "https://atlas-demo.ohdsi.org/WebAPI",
# generateStats = FALSE)
cohort <- aou_atlas_cohort(
cohort_definition = aou_cohort_example$cd,
cohort_sql = aou_cohort_example$cd_sql
)
# print query that was executed
cat(attr(cohort, "query"))Retrieve a cohort from ATLAS for use in All of Us
Description
Retrieves a cohort definition from ATLAS and generates the cohort in All of Us. Observation periods are first generated for each subject using the aou_observation_period() function.The resulting cohort is a table with the cohort start and end dates for each person_id.
Usage
aou_atlas_cohort(
cohort_definition,
cohort_sql,
debug = FALSE,
collect = FALSE,
...,
con = getOption("aou.default.con")
)
Arguments
cohort_definition
|
A cohort definition generated using getCohortDefinition() from ROhdsiWebApi
|
cohort_sql
|
The cohort_sql generated using getCohortSql() from ROhdsiWebApi
|
debug
|
Print the query to the console; useful for debugging. |
collect
|
Whether to bring the resulting table into local memory (collect = TRUE) as a dataframe or leave as a reference to a database table (for continued analysis using, e.g., dbplyr). Defaults to FALSE.
|
…
|
Further arguments passed along to collect() if collect = TRUE
|
con
|
Connection to the allofus SQL database. Defaults to getOption("aou.default.con"), which is set automatically if you use aou_connect()
|
Details
The function is based on a similar function in https://github.com/cmayer2/r4aou with some tweaks to generate the appropriate observation periods and incorporate other package functions. Please see the online vignette for additional details.
Value
A dataframe if collect = TRUE; a reference to a remote database table if not. The SQL query used to generate the cohort is stored as an attribute.