MeasurementDiagnostics (version 0.3.0)

summariseCohortMeasurementUse: Diagnostics of a codelist of measurement codes within a cohort

Description

Diagnostics of a codelist of measurement codes within a cohort

Usage

summariseCohortMeasurementUse(
  cohort,
  codes = NULL,
  timing = "during",
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL,
  dateRange = as.Date(c(NA, NA)),
  estimates = list(measurement_summary = c("min", "q25", "median", "q75", "max",
    "density"), measurement_value_as_number = c("min", "q01", "q05", "q25", "median",
    "q75", "q95", "q99", "max", "count_missing", "percentage_missing", "density"),
    measurement_value_as_concept = c("count", "percentage")),
  histogram = NULL,
  checks = c("measurement_summary", "measurement_value_as_number",
    "measurement_value_as_concept")
)

Value

A summarised result

Arguments

cohort

A cohort in which to perform the diagnostics of the measurement codes provided.

codes

A codelist of measurement/observation codes for which to perform diagnostics. If NULL it uses the codelist used to create each of the cohorts.

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, and 3) "cohort_start_date" for measurements occurring at cohort start date.

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.

estimates

A named list indicating, for each measurement diagnostics check, which estimates to retrieve. The names of the list should correspond to the diagnostics checks, and each list element should be a character vector specifying the estimates to compute.

Allowed estimates are those supported by the `summariseResult()` function in the **PatientProfiles** package. If omitted, all available estimates for each check will be returned.

histogram

Named list where names point to checks for which to get estimates for a histogram, and elements are numeric vectors indicating the bind-width. See function examples. Histogram only available for "measurement_summary" and "measurement_value_as_number".

checks

Diagnostics to run. Options are: "measurement_summary", "measurement_value_as_number", and "measurement_value_as_concept".

Examples

# \donttest{
library(MeasurementDiagnostics)

cdm <- mockMeasurementDiagnostics()

result <- summariseCohortMeasurementUse(
  codes = list("test_codelist" = c(3001467L, 45875977L)),
  cohort = cdm$my_cohort, timing = "cohort_start_date"
)

# Histogram
result <- summariseCohortMeasurementUse(
  codes = list("test_codelist" = c(3001467L, 45875977L)),
  cohort = cdm$my_cohort, timing = "cohort_start_date",
  histogram = list(
    "days_between_measurements" = list(
      '0 to 100' = c(0, 100), '110 to 200' = c(110, 200),
      '210 to 300' = c(210, 300), '310 to Inf' = c(310, Inf)
    ),
    "measurements_per_subject" = list(
      '0 to 10' = c(0, 10), '11 to 20' = c(11, 20), '21 to 30' = c(21, 30),
      '31 to Inf' = c(31, Inf)
    ),
    "value_as_number" =  list(
      '0 to 5' = c(0, 5), '6 to 10' = c(6, 10), '11 to 15' = c(11, 15),
      '>15' = c(16, Inf)
    )
  )
)

# Different age groups
result <- summariseCohortMeasurementUse(
  codes = list("test_codelist" = c(3001467L, 45875977L)),
  cohort = cdm$my_cohort,
  ageGroup = list(
    "age_group_1" = list(c(0, 17), c(18, 64), c(65, 150)),
    "age_group_2" = list(c(0, 19), c(20, 39), c(40, 59), c(60, 79), c(80, 99), c(100, 120))
  )
)

CDMConnector::cdmDisconnect(cdm = cdm)
# }