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Summarise characteristics of cohorts in a cohort table
Source:R/summariseCharacteristics.R
summariseCharacteristics.Rd
Summarise characteristics of cohorts in a cohort table
Usage
summariseCharacteristics(
cohort,
cohortId = NULL,
strata = list(),
counts = TRUE,
demographics = TRUE,
ageGroup = NULL,
tableIntersectFlag = list(),
tableIntersectCount = list(),
tableIntersectDate = list(),
tableIntersectDays = list(),
cohortIntersectFlag = list(),
cohortIntersectCount = list(),
cohortIntersectDate = list(),
cohortIntersectDays = list(),
conceptIntersectFlag = list(),
conceptIntersectCount = list(),
conceptIntersectDate = list(),
conceptIntersectDays = list(),
otherVariables = character(),
otherVariablesEstimates = c("min", "q25", "median", "q75", "max", "count",
"percentage")
)
Arguments
- cohort
A cohort table in the cdm.
- cohortId
Vector of cohort definition ids to include. If NULL all cohort will be selected.
- strata
A list of variables to stratify results. These variables must have been added as additional columns in the cohort table.
- counts
TRUE or FALSE. If TRUE, record and person counts will be produced.
- demographics
TRUE or FALSE. If TRUE, patient demographics (cohort start date, cohort end date, age, sex, prior observation, and future observation will be summarised).
- ageGroup
A list of age groups to stratify results by.
- tableIntersectFlag
A list of arguments that uses PatientProfiles::addTableIntersectFlag() to add variables to summarise.
- tableIntersectCount
A list of arguments that uses PatientProfiles::addTableIntersectCount() to add variables to summarise.
- tableIntersectDate
A list of arguments that uses PatientProfiles::addTableIntersectDate() to add variables to summarise.
- tableIntersectDays
A list of arguments that uses PatientProfiles::addTableIntersectDays() to add variables to summarise.
- cohortIntersectFlag
A list of arguments that uses PatientProfiles::addCohortIntersectFlag() to add variables to summarise.
- cohortIntersectCount
A list of arguments that uses PatientProfiles::addCohortIntersectCount() to add variables to summarise.
- cohortIntersectDate
A list of arguments that uses PatientProfiles::addCohortIntersectDate() to add variables to summarise.
- cohortIntersectDays
A list of arguments that uses PatientProfiles::addCohortIntersectDays() to add variables to summarise.
- conceptIntersectFlag
A list of arguments that uses PatientProfiles::addConceptIntersectFlag() to add variables to summarise.
- conceptIntersectCount
A list of arguments that uses PatientProfiles::addConceptIntersectCount() to add variables to summarise.
- conceptIntersectDate
A list of arguments that uses PatientProfiles::addConceptIntersectDate() to add variables to summarise.
- conceptIntersectDays
A list of arguments that uses PatientProfiles::addConceptIntersectDays() to add variables to summarise.
- otherVariables
Other variables contained in cohort that you want to be summarised.
- otherVariablesEstimates
Name of the estimates for the otherVariables columns.
Examples
# \donttest{
library(dplyr)
library(CohortCharacteristics)
library(PatientProfiles)
cdm <- mockCohortCharacteristics()
#> ! cohort columns will be reordered to match the expected order:
#> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date.
#> ! cohort columns will be reordered to match the expected order:
#> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date.
cdm$cohort1 |>
addSex() |>
addAge(
ageGroup = list(c(0, 40), c(41, 150))
) |>
summariseCharacteristics(
strata = list("sex", "age_group"),
cohortIntersectFlag = list (
"Cohort 2 Flag" = list(
targetCohortTable = "cohort2",
window = c(-365, 0)
)
),
cohortIntersectCount = list (
"Cohort 2 Count" = list(
targetCohortTable = "cohort2",
window = c(-365, 0)
)
)
) |>
glimpse()
#> ℹ adding demographics columns
#> ℹ adding cohortIntersectFlag 1/1
#> ℹ adding cohortIntersectCount 1/1
#> ℹ summarising data
#> ✔ summariseCharacteristics finished!
#> Rows: 750
#> Columns: 13
#> $ result_id <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name <chr> "PP_MOCK", "PP_MOCK", "PP_MOCK", "PP_MOCK", "PP_MOCK"…
#> $ group_name <chr> "cohort_name", "cohort_name", "cohort_name", "cohort_…
#> $ group_level <chr> "cohort_2", "cohort_3", "cohort_1", "cohort_2", "coho…
#> $ strata_name <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name <chr> "Number records", "Number records", "Number records",…
#> $ variable_level <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "7", "2", "1", "7", "2", "1", "1942-03-21", "2021-10-…
#> $ additional_name <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…
mockDisconnect(cdm = cdm)
# }