Add the maximum number of ingredients to which an individual is simultaneously exposed within a specified window

Usage

addPolypharmacy(
  x,
  indexDate = "cohort_start_date",
  window = c(0, 0),
  overlap = TRUE,
  categories = NULL,
  nameStyle = "polypharmacy",
  name = tableName(x)
)

Arguments

x: A cdm_table containing a person identifier column named person_id or subject_id.
indexDate: A character string naming the Date column in x that defines the index date.
window: A numeric vector of length two, c(min, max), defining the window for polypharmacy in days relative to indexDate. Use -Inf or Inf for an unbounded lower or upper limit.
overlap: Logical; if TRUE, count drug eras that overlap in time. If FALSE, count drug eras that occur within the window without requiring them to overlap one another.
categories: A named list of numeric vectors, each containing the lower and upper bounds of a score interval. An additional column with the suffix _categories is added. Intervals are evaluated in the order supplied, and missing scores are labelled missing.
nameStyle: A character string specifying the name of the new column.
name: A character string specifying the name of the output table. If NULL, a temporary table is created.

Value

The table x with a new column containing the maximum number of simultaneous ingredients in the window of interest.

Examples

# \donttest{
library(omock)
library(duckdb)
library(OmopIndices)
library(dplyr)
library(CohortConstructor)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
#> ℹ Loading bundled GiBleed tables from package data.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpNEUAUi/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
cdm$cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = list(sinusitis = c(257012L, 4283893L, 4294548L, 40481087L)),
  name = "cohort"
)
#> ℹ Subsetting table condition_occurrence using 4 concepts with domain:
#>   condition.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort cohort created.

cdm$cohort |>
  addPolypharmacy(window = c(-30, 0)) |>
  select(subject_id, cohort_start_date, polypharmacy) |>
  glimpse()
#> Rows: ??
#> Columns: 3
#> $ subject_id        <int> 411, 950, 1046, 1280, 1358, 1384, 1459, 1493, 1588, …
#> $ cohort_start_date <date> 2002-07-13, 2013-09-19, 1989-09-29, 1993-04-26, 196…
#> $ polypharmacy      <int> 2, 2, 2, 2, 1, 2, 2, 2, 2, 3, 2, 1, 5, 2, 2, 2, 2, 2…
# }