Diagnostics of a codelist of measurement codes within a cohort

Usage

summariseCohortMeasurementUse(
  codes,
  cohort,
  timing = "during",
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL,
  dateRange = as.Date(c(NA, NA)),
  checks = c("measurement_timings", "measurement_value_as_numeric",
    "measurement_value_as_concept")
)

Arguments

codes: A codelist of measurement/observation codes for which to perform diagnostics.
cohort: A cohort in which to perform the diagnostics of the measurement codes provided.
timing: Three options: 1) "any" if the interest is on measurement recorded any time, 2) "during", if interested in measurements while the subject is in the cohort (or in observation if cohort = NULL), and 3) "cohort_start_date" for measurements occurring at cohort start date (or at "observation_period_start_date if cohort = NULL).
byConcept: TRUE or FALSE. If TRUE code use will be summarised by concept.
byYear: TRUE or FALSE. If TRUE code use will be summarised by year.
bySex: TRUE or FALSE. If TRUE code use will be summarised by sex.
ageGroup: If not NULL, a list of ageGroup vectors of length two.
dateRange: Two dates. The first indicating the earliest measurement date and the second indicating the latest possible measurement date.
checks: Diagnostics to run. Options are: "measurement_timing", "measurement_value_as_numeric", and "measurement_value_as_concept".

Value

A summarised result

Examples

# \donttest{
library(MeasurementDiagnostics)
cdm <- mockMeasurementDiagnostics()
result <- summariseCohortMeasurementUse(
  codes = list("test_codelist" = c(3001467L, 45875977L)),
  cohort = cdm$my_cohort, timing = "cohort_start_date"
)
#> → Getting measurement records based on 2 concepts.
#> → Subsetting records to the subjects and timing of interest.
#> → Getting time between records per person.
#> ! 2 duplicated rows eliminated.
#> → Summarising results - value as number.
#> → Summarising results - value as concept.
#> → Binding all diagnostic results.
CDMConnector::cdmDisconnect(cdm = cdm)
# }