Get occurrences of of a concept set from ATLAS for a given cohort

Usage

pull_concept_set(
  cohort,
  concept_set_id,
  start_date,
  end_date,
  concept_set_name = NULL,
  min_n = NULL,
  n = FALSE,
  keep_all = FALSE,
  con = getOption("con.default.value"),
  atlas_url = getOption("atlas_url.default.value"),
  write_schema = getOption("write_schema.default.value"),
  ...
)

Arguments

cohort: tbl; reference to a table created in a user schema with a column called "person_id", and columns for start_date and end_date
concept_set_id: num; the number associated with the concept_set_id in ATLAS
start_date: the name of the start_date column in the cohort table (unquoted)
end_date: the name of the end_date column in the cohort table (unquoted)
concept_set_name: chr; Name to describe the concept set, used to create an indicator variable
min_n: dbl; the minimum number of occurrences per person to consider the indicator true
n: dbl; count the number of occurrences per person (will not include zeros)
keep_all: lgl; keep columns with information about the concept (e.g., concept name, id, etc.)
con: the connection object to ohdsilab
atlas_url: chr; the base url for ATLAS (not ohdsilab)
write_schema: chr; schema for the user

Value

a dataframe

Examples

if (FALSE) { # \dontrun{
tobacco <- pull_concepts(cohort, concept_set_id = 1157, start_date = covariate_start_date,
 end_date = cohort_start_date, name = "tobacco"
 )} # }