Update cohort attrition.
Examples
library(omopgenerics)
library(dplyr, warn.conflicts = FALSE)
person <- tibble(
person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
race_concept_id = 0, ethnicity_concept_id = 0
)
observation_period <- tibble(
observation_period_id = 1, person_id = 1,
observation_period_start_date = as.Date("2000-01-01"),
observation_period_end_date = as.Date("2023-12-31"),
period_type_concept_id = 0
)
cohort <- tibble(
cohort_definition_id = c(1, 1, 1, 2),
subject_id = 1,
cohort_start_date = as.Date(c("2020-01-01", "2021-01-01", "2022-01-01", "2022-01-01")),
cohort_end_date = as.Date(c("2020-01-01", "2021-01-01", "2022-01-01", "2022-01-01")),
)
cdm <- cdmFromTables(
tables = list("person" = person, "observation_period" = observation_period),
cdmName = "my_example_cdm",
cohortTables = list("cohort1" = cohort)
)
#> Warning: ! 5 casted column in person as do not match expected column type:
#> • `person_id` from numeric to integer
#> • `gender_concept_id` from numeric to integer
#> • `year_of_birth` from numeric to integer
#> • `race_concept_id` from numeric to integer
#> • `ethnicity_concept_id` from numeric to integer
#> Warning: ! 3 casted column in observation_period as do not match expected column type:
#> • `observation_period_id` from numeric to integer
#> • `person_id` from numeric to integer
#> • `period_type_concept_id` from numeric to integer
#> Warning: ! 2 casted column in cohort1 as do not match expected column type:
#> • `cohort_definition_id` from numeric to integer
#> • `subject_id` from numeric to integer
cdm$cohort1
#> # A tibble: 4 × 4
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
#> 1 1 1 2020-01-01 2020-01-01
#> 2 1 1 2021-01-01 2021-01-01
#> 3 1 1 2022-01-01 2022-01-01
#> 4 2 1 2022-01-01 2022-01-01
attrition(cdm$cohort1)
#> # A tibble: 2 × 7
#> cohort_definition_id number_records number_subjects reason_id reason
#> <int> <int> <int> <int> <chr>
#> 1 1 3 1 1 Initial qualify…
#> 2 2 1 1 1 Initial qualify…
#> # ℹ 2 more variables: excluded_records <int>, excluded_subjects <int>
cdm$cohort1 <- cdm$cohort1 |>
group_by(cohort_definition_id, subject_id) |>
filter(cohort_start_date == min(cohort_start_date)) |>
ungroup() |>
compute(name = "cohort1", temporary = FALSE) |>
recordCohortAttrition("Restrict to first observation")
cdm$cohort1
#> # A tibble: 2 × 4
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> * <int> <int> <date> <date>
#> 1 1 1 2020-01-01 2020-01-01
#> 2 2 1 2022-01-01 2022-01-01
attrition(cdm$cohort1)
#> # A tibble: 4 × 7
#> cohort_definition_id number_records number_subjects reason_id reason
#> <int> <int> <int> <int> <chr>
#> 1 1 3 1 1 Initial qualify…
#> 2 1 1 1 2 Restrict to fir…
#> 3 2 1 1 1 Initial qualify…
#> 4 2 1 1 2 Restrict to fir…
#> # ℹ 2 more variables: excluded_records <int>, excluded_subjects <int>