aou_concept_set {allofus}

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

Description

Retrieves occurrences of a concept set from the All of Us database for a given cohort.

Usage

aou_concept_set(
  cohort = NULL,
  concepts,
  start_date = NULL,
  end_date = NULL,
  domains = c("condition", "measurement", "observation", "procedure", "drug", "device",
    "visit"),
  output = "indicator",
  concept_set_name = "concept_set",
  min_n = 1,
  collect = FALSE,
  ...,
  con = getOption("aou.default.con")
)

Arguments

cohort

Reference to a remote table or local dataframe with a column called "person_id", and (possibly) columns for start_date and end_date. If not provided, defaults to entire All of Us cohort.

concepts

a vector of concept ids

start_date

chr; the name of the start_date column in the cohort table; defaults to NULL to pull data across all dates

end_date

chr; the name of the end_date column in the cohort table; defaults to NULL to pull data across all dates

domains

chr; a vector of domains to search for the concepts in ("condition", "measurement", "observation", "procedure", "drug", "device", "visit"); defaults to all

output

one of "indicator", "count", "all"; do you want to return a 1 if a person has any matching concepts and 0 if not ("indicator"), the number of matching concepts per person ("count"), or all info about the matching concepts ("all"). Defaults to "indicator"

concept_set_name

chr; If output = "indicator" or output = "n", name for that column. Defaults to "concept_set".

min_n

dbl; If output = "indicator", the minimum number of occurrences per person to consider the indicator true. Defaults to 1.

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 created automatically with aou_connect().

Value

A dataframe if collect = TRUE; a reference to a remote database table if not.

Examples

# indicator for any aspirin at any time
aspirin_users <- aou_concept_set(dplyr::tbl(con, "person"),
  concepts = 1191, concept_set_name = "aspirin", domains = "drug"
)

# starting with person table to create a cohort
people <- dplyr::tbl(con, "person") %>%
  dplyr::filter(person_id < 2000000) %>%
  dplyr::mutate(
    start = as.Date("2021-01-01"),
    end = as.Date("2023-12-31")
  )

dat <- aou_concept_set(
  cohort = people,
  concepts = c(725115, 1612146, 1613031),
  start_date = "start",
  end_date = "end",
  concept_set_name = "CGM",
  output = "all"
)