Bind two or more cohort tables

Usage

# S3 method for class 'cohort_table'
bind(..., name)

Arguments

...: Generated cohort set objects to bind. At least two must be provided.
name: Name of the new generated cohort set.

Value

The cdm object with a new generated cohort set containing all of the cohorts passed.

Examples

library(omopgenerics)
library(dplyr, warn.conflicts = FALSE)

cohort1 <- tibble(
  cohort_definition_id = 1,
  subject_id = 1:3,
  cohort_start_date = as.Date("2010-01-01"),
  cohort_end_date = as.Date("2010-01-05")
)
cohort2 <- tibble(
  cohort_definition_id = c(2, 2, 3, 3, 3),
  subject_id = c(1, 2, 3, 1, 2),
  cohort_start_date = as.Date("2010-01-01"),
  cohort_end_date = as.Date("2010-01-05")
)
cdm <- cdmFromTables(
  tables = list(
    "person" = tibble(
      person_id = c(1, 2, 3), gender_concept_id = 0, year_of_birth = 1990,
      race_concept_id = 0, ethnicity_concept_id = 0
    ),
    "observation_period" = tibble(
      observation_period_id = 1:3, person_id = 1:3,
      observation_period_start_date = as.Date("2000-01-01"),
      observation_period_end_date = as.Date("2023-12-31"),
      period_type_concept_id = 0
    )
  ),
  cdmName = "mock",
  cohortTables = list("cohort1" = cohort1, "cohort2" = cohort2)
)
#> Warning: ! 5 column in person do not match expected column type:
#> • `person_id` is numeric but expected integer
#> • `gender_concept_id` is numeric but expected integer
#> • `year_of_birth` is numeric but expected integer
#> • `race_concept_id` is numeric but expected integer
#> • `ethnicity_concept_id` is numeric but expected integer
#> Warning: ! 1 column in observation_period do not match expected column type:
#> • `period_type_concept_id` is numeric but expected integer
#> Warning: ! 1 column in cohort1 do not match expected column type:
#> • `cohort_definition_id` is numeric but expected integer
#> Warning: ! 2 column in cohort2 do not match expected column type:
#> • `cohort_definition_id` is numeric but expected integer
#> • `subject_id` is numeric but expected integer

cdm <- bind(cdm$cohort1, cdm$cohort2, name = "cohort3")
#> Warning: ! 1 column in cohort3 do not match expected column type:
#> • `subject_id` is numeric but expected integer
settings(cdm$cohort3)
#> # A tibble: 3 × 2
#>   cohort_definition_id cohort_name
#>                  <int> <chr>      
#> 1                    1 cohort_1   
#> 2                    2 cohort_2   
#> 3                    3 cohort_3   
cdm$cohort3
#> # A tibble: 8 × 4
#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
#> *                <int>      <dbl> <date>            <date>         
#> 1                    1          1 2010-01-01        2010-01-05     
#> 2                    1          2 2010-01-01        2010-01-05     
#> 3                    1          3 2010-01-01        2010-01-05     
#> 4                    2          1 2010-01-01        2010-01-05     
#> 5                    2          2 2010-01-01        2010-01-05     
#> 6                    3          3 2010-01-01        2010-01-05     
#> 7                    3          1 2010-01-01        2010-01-05     
#> 8                    3          2 2010-01-01        2010-01-05