plotEventDuration
Usage
plotEventDuration(
eventDurations,
minCellCount = 0,
treatmentGroups = "both",
eventLines = NULL,
includeOverall = TRUE
)
Arguments
- eventDurations
(
data.frame
) Contents ofsummaryEventDuration.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 alleventLines
.- includeOverall
(
logical(1)
:TRUE
)TRUE
: Include an overall column with theeventLines
.FALSE
: Exclude the overall column.
Examples
# \donttest{
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 = 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
)
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)
}
#>
#> Download completed!
#> Creating CDM database /tmp/RtmpsdqEev/file2507d6f9017/GiBleed_5.3.zip
#> ! cdm name not specified and could not be inferred from the cdm source table
#> ℹ Generating 8 cohorts
#> ℹ Generating cohort (1/8) - acetaminophen
#> ✔ Generating cohort (1/8) - acetaminophen [160ms]
#>
#> ℹ Generating cohort (2/8) - amoxicillin
#> ✔ Generating cohort (2/8) - amoxicillin [150ms]
#>
#> ℹ Generating cohort (3/8) - aspirin
#> ✔ Generating cohort (3/8) - aspirin [148ms]
#>
#> ℹ Generating cohort (4/8) - clavulanate
#> ✔ Generating cohort (4/8) - clavulanate [146ms]
#>
#> ℹ Generating cohort (5/8) - death
#> ✔ Generating cohort (5/8) - death [113ms]
#>
#> ℹ Generating cohort (6/8) - doxylamine
#> ✔ Generating cohort (6/8) - doxylamine [146ms]
#>
#> ℹ Generating cohort (7/8) - penicillinv
#> ✔ Generating cohort (7/8) - penicillinv [137ms]
#>
#> ℹ Generating cohort (8/8) - viralsinusitis
#> ✔ Generating cohort (8/8) - viralsinusitis [209ms]
#>
#> -- Qualifying records for cohort definitions: 1, 2, 3, 4, 5, 6, 7, 8
#> Records: 14041
#> Subjects: 2693
#> -- Removing records < minEraDuration (0)
#> Records: 11386
#> Subjects: 2159
#> >> Starting on target: 8 (viralsinusitis)
#> -- Removing events where index date < target index date + indexDateOffset (0)
#> Records: 8381
#> Subjects: 2159
#> -- splitEventCohorts
#> Records: 8366
#> Subjects: 2144
#> -- Collapsing eras, eraCollapse (30)
#> Records: 8366
#> Subjects: 2144
#> -- Iteration 1: minPostCombinationDuration (30), combinatinoWindow (30)
#> Records: 558
#> Subjects: 512
#> -- Iteration 2: minPostCombinationDuration (30), combinatinoWindow (30)
#> Records: 554
#> Subjects: 512
#> -- After Combination
#> Records: 554
#> Subjects: 512
#> -- filterTreatments (First)
#> Records: 553
#> Subjects: 512
#> -- treatment construction done
#> Records: 553
#> Subjects: 512
# }