Summarise concept counts in patient-level data. Only concepts recorded during observation period are counted.

Usage

summariseConceptSetCounts(
  cdm,
  conceptSet,
  countBy = c("record", "person"),
  concept = TRUE,
  interval = "overall",
  sex = FALSE,
  ageGroup = NULL,
  sample = NULL,
  dateRange = NULL
)

Arguments

cdm: A cdm object
conceptSet: List of concept IDs to summarise.
countBy: Either "record" for record-level counts or "person" for person-level counts
concept: TRUE or FALSE. If TRUE code use will be summarised by concept.
interval: Time interval to stratify by. It can either be "years", "quarters", "months" or "overall".
sex: TRUE or FALSE. If TRUE code use will be summarised by sex.
ageGroup: A list of ageGroup vectors of length two. Code use will be thus summarised by age groups.
sample: An integer to sample the tables in the cdm object to only that number of records. If NULL no sample is done.
dateRange: A list containing the minimum and the maximum dates defining the time range within which the analysis is performed.

Value

A summarised_result object with results overall and, if specified, by strata.

Examples

# \donttest{
library(OmopSketch)

cdm <- mockOmopSketch()

cs <- list(sumatriptan = c(35604883, 35604879, 35604880, 35604884))

results <- summariseConceptSetCounts(cdm, conceptSet = cs)
#> Warning: ! `codelist` contains numeric values, they are casted to integers.
#> ℹ Searching concepts from domain drug in drug_exposure.
#> ℹ Counting concepts

results
#> # A tibble: 10 × 13
#>    result_id cdm_name       group_name    group_level strata_name strata_level
#>        <int> <chr>          <chr>         <chr>       <chr>       <chr>       
#>  1         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  2         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  3         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  4         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  5         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  6         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  7         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  8         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#>  9         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#> 10         1 mockOmopSketch codelist_name sumatriptan overall     overall     
#> # ℹ 7 more variables: variable_name <chr>, variable_level <chr>,
#> #   estimate_name <chr>, estimate_type <chr>, estimate_value <chr>,
#> #   additional_name <chr>, additional_level <chr>

PatientProfiles::mockDisconnect(cdm)

# }