computePathways: computePathways

In TreatmentPatterns: Analyzes Real-World Treatment Patterns of a Study Population of Interest

computePathways

Description

Compute treatment patterns according to the specified parameters within specified cohorts.

Usage

computePathways(
  cohorts,
  cohortTableName,
  cdm = NULL,
  connectionDetails = NULL,
  cdmSchema = NULL,
  resultSchema = NULL,
  tempEmulationSchema = NULL,
  includeTreatments = "startDate",
  periodPriorToIndex = 0,
  minEraDuration = 0,
  splitEventCohorts = NULL,
  splitTime = NULL,
  eraCollapseSize = 30,
  combinationWindow = 30,
  minPostCombinationDuration = 30,
  filterTreatments = "First",
  maxPathLength = 5
)

Arguments

cohorts	(data.frame()) Data frame containing the following columns and data types: cohortId numeric(1) Cohort ID's of the cohorts to be used in the cohort table. cohortName character(1) Cohort names of the cohorts to be used in the cohort table. type character(1) ["target", "event', "exit"] Cohort type, describing if the cohort is a target, event, or exit cohort
cohortTableName	(character(1)) Cohort table name.
cdm	(CDMConnector::cdm_from_con(): NULL) Optional; Ignores connectionDetails, cdmSchema, and resultSchema.
connectionDetails	(DatabaseConnector::createConnectionDetails(): NULL) Optional; In congruence with cdmSchema and resultSchema. Ignores cdm.
cdmSchema	(character(1): NULL) Optional; In congruence with connectionDetails and resultSchema. Ignores cdm.
resultSchema	(character(1): NULL) Optional; In congruence with connectionDetails and cdmSchema. Ignores cdm.
tempEmulationSchema	Schema used to emulate temp tables
includeTreatments	(character(1): "startDate") "startDate" Include treatments after the target cohort start date and onwards. "endDate" Include treatments before target cohort end date and before.
periodPriorToIndex	(integer(1): 0) Number of days prior to the index date of the target cohort | that event cohorts are allowed to start
minEraDuration	(integer(1): 0) Minimum time an event era should last to be included in analysis
splitEventCohorts	(character(n): "") Specify event cohort to split in acute (< X days) and therapy (>= X days)
splitTime	(integer(1): 30) Specify number of days (X) at which each of the split event cohorts should be split in acute and therapy
eraCollapseSize	(integer(1): 30) Window of time between which two eras of the same event cohort are collapsed into one era
combinationWindow	(integer(1): 30) Window of time two event cohorts need to overlap to be considered a combination treatment
minPostCombinationDuration	(integer(1): 30) Minimum time an event era before or after a generated combination treatment should last to be included in analysis
filterTreatments	(character(1): "First" ["first", "Changes", "all"]) Select first occurrence of (‘First’); changes between (‘Changes’); or all event cohorts (‘All’).
maxPathLength	(integer(1): 5) Maximum number of steps included in treatment pathway

Value

(Andromeda::andromeda()) andromeda object containing non-sharable patient level data outcomes.

Examples

ableToRun <- all(
  require("CirceR", character.only = TRUE, quietly = TRUE),
  require("CDMConnector", character.only = TRUE, quietly = TRUE),
  require("TreatmentPatterns", character.only = TRUE, quietly = TRUE),
  require("dplyr", character.only = TRUE, quietly = TRUE)
)

if (ableToRun) {
  library(TreatmentPatterns)
  library(CDMConnector)
  library(dplyr)

  withr::local_envvar(
    R_USER_CACHE_DIR = tempfile(),
    EUNOMIA_DATA_FOLDER = Sys.getenv("EUNOMIA_DATA_FOLDER", unset = tempfile())
  )

  tryCatch({
    if (Sys.getenv("skip_eunomia_download_test") != "TRUE") {
      CDMConnector::downloadEunomiaData(overwrite = TRUE)
    }
  }, error = function(e) NA)

  con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
  cdm <- cdmFromCon(con, cdmSchema = "main", writeSchema = "main")

  cohortSet <- readCohortSet(
    path = system.file(package = "TreatmentPatterns", "exampleCohorts")
  )

  cdm <- generateCohortSet(
    cdm = cdm,
    cohortSet = cohortSet,
    name = "cohort_table"
  )

  cohorts <- cohortSet %>%
    # Remove 'cohort' and 'json' columns
    select(-"cohort", -"json") %>%
    mutate(type = c("event", "event", "event", "event", "exit", "event", "event", "target")) %>%
    rename(
      cohortId = "cohort_definition_id",
      cohortName = "cohort_name",
    ) %>%
    select("cohortId", "cohortName", "type")

  outputEnv <- computePathways(
    cohorts = cohorts,
    cohortTableName = "cohort_table",
    cdm = cdm
  )

  Andromeda::close(outputEnv)
  DBI::dbDisconnect(con, shutdown = TRUE)
}

TreatmentPatterns documentation built on Sept. 11, 2024, 8:59 p.m.