support tidyselect when passing cohort names to cohortId argument

[edward-burn]

library(omopgenerics)
#> 
#> Attaching package: 'omopgenerics'
#> The following object is masked from 'package:stats':
#> 
#>     filter
library(CDMConnector)
#> 
#> Attaching package: 'CDMConnector'
#> The following objects are masked from 'package:omopgenerics':
#> 
#>     cdmName, recordCohortAttrition, uniqueTableName
library(dplyr)
#> Warning: package 'dplyr' was built under R version 4.2.3
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(CohortConstructor)
#> 
#> Attaching package: 'CohortConstructor'
#> The following objects are masked from 'package:CDMConnector':
#> 
#>     intersectCohorts, unionCohorts

con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
cdm <- cdm_from_con(con, cdm_schema = "main", 
                    write_schema = c(prefix = "my_study_", schema = "main"))
fracture_codes <- newCodelist(list("ankle_fracture" = 4059173L,
                                   "forearm_fracture" = 4278672L,
                                   "hip_fracture" = 4230399L))
cdm$fractures <- cdm |> 
  conceptCohort(conceptSet = fracture_codes,
                name = "fractures")
#> ℹ Subsetting table condition_occurrence using 3 concepts with domain:
#>   condition.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Collapsing records.
#> ✔ Cohort fractures created.


cdm$fractures_2 <- cdm$fractures |> 
  subsetCohorts(cohortId = "forearm_fracture", 
                name = "fractures_2")

cdm$fractures_2 <- cdm$fractures |> 
  subsetCohorts(cohortId = dplyr::starts_with("forearm"), 
                name = "fractures_2")
#> Error:
#> ! `starts_with()` must be used within a *selecting* function.
#> ℹ See <https://tidyselect.r-lib.org/reference/faq-selection-context.html> for
#>   details.
#> Backtrace:
#>     ▆
#>  1. ├─CohortConstructor::subsetCohorts(...)
#>  2. │ └─CohortConstructor:::validateCohortId(cohortId, settings(cohort)) at CohortConstructor/R/subsetCohorts.R:29:3
#>  3. └─dplyr::starts_with("forearm") at CohortConstructor/R/subsetCohorts.R:29:3
#>  4.   ├─vars %||% peek_vars(fn = "starts_with")
#>  5.   └─tidyselect::peek_vars(fn = "starts_with")
#>  6.     └─cli::cli_abort(...)
#>  7.       └─rlang::abort(...)

^{Created on 2024-09-21 with reprex v2.0.2}

[catalamarti]

I would implement this in:

• omopgenerics::validateCohortIdArgument()
• omopgenerics::getCohortId()

So it can be also used by other packages and we ensure consistency.

what do you think @edward-burn ?

[edward-burn]

yes @catalamarti, that would be great!