plotEventDuration: plotEventDuration

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

plotEventDuration

Description

plotEventDuration

Usage

plotEventDuration(
  eventDurations,
  minCellCount = 0,
  treatmentGroups = "both",
  eventLines = NULL,
  includeOverall = TRUE
)

Arguments

eventDurations	(data.frame) Contents of summaryEventDuration.csv file.
minCellCount	(numeric(1): 0) Min Cell Count per event group.
treatmentGroups	(character(1): "both") "group": Only mono-, and combination-events. "individual": Only individual (combination) events. "both": Both mono-, and combination-events, and individual (combination) events.
eventLines	(numeric(n): NULL) Event lines to include, i.e. c(1, 2, 3) includes first (1), second (2), and third (3) lines of events. NULL will include all eventLines.
includeOverall	(logical(1): TRUE) TRUE: Include an overall column with the eventLines. FALSE: Exclude the overall column.

Value

ggplot

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) {
  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 = eunomiaDir())
  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
  )

  results <- export(outputEnv)

  plotEventDuration(
    eventDurations = results$summary_event_duration,
    minCellCount = 5,
    treatmentGroups = "group",
    eventLines = 1:4,
    includeOverall = FALSE
  )

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

TreatmentPatterns documentation built on April 16, 2025, 5:11 p.m.