executeTreatmentPatterns {TreatmentPatterns} | R Documentation |
Compute treatment patterns according to the specified parameters within specified cohorts. For more customization, or investigation of patient level outcomes, you can run computePathways and export separately.
executeTreatmentPatterns(
cohorts,
cohortTableName,
outputPath,
cdm = NULL,
connectionDetails = NULL,
cdmSchema = NULL,
resultSchema = NULL,
tempEmulationSchema = NULL,
minEraDuration = 0,
eraCollapseSize = 30,
combinationWindow = 30,
minCellCount = 5
)
cohorts |
(
|
cohortTableName |
( |
outputPath |
( |
cdm |
( |
connectionDetails |
( |
cdmSchema |
( |
resultSchema |
( |
tempEmulationSchema |
( |
minEraDuration |
( |
eraCollapseSize |
( |
combinationWindow |
( |
minCellCount |
( |
(invisible(NULL)
)
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 (require("CirceR", character.only = TRUE, quietly = TRUE)) {
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")
executeTreatmentPatterns(
cohorts = cohorts,
cohortTableName = "cohort_table",
cdm = cdm,
outputPath = tempdir()
)
DBI::dbDisconnect(con, shutdown = TRUE)
}