How to specify valueAsConcept in cohort definition (and valid death cohort)

[vojtechhuser]

Great package. Thank you for developing it.

problem 1
how to specify valueAsConcept in measurement cohort?

(current error is)

Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `purrr::map_chr()`:
ℹ In index: 1.
ℹ With name: valueAsConcept.
Caused by error in `.x@name`:
! no applicable method for `@` applied to an object of class "integer"
Run `rlang::last_trace()` to see where the error occurred.

 ch_m2 <- cohort(
  entry = entry(
    measurement(cs_meas, valueAsConcept = 9191L) #9191 is concetp for positive (no using descendants, just one specific value (is not using conceptset an option here)
  ),
  exit = exit(
    endStrategy = observationExit()
  )
)

 cohortsToCreate<- bind_rows(cohortsToCreate, tibble::tibble(cohortId = 6,cohortName = "meas2",sql = CirceR::buildCohortQuery(
   expression = CirceR::cohortExpressionFromJson(ch_m2 |>toCirce()|>jsonlite::toJSON(pretty = TRUE, auto_unbox = TRUE) |>  as.character()),
   options = CirceR::createGenerateOptions(generateStats = FALSE))))

problem 2:
what is valid capr version of simplest cohort ever (death as entry event)

ch_d<-cohort(
  entry = entry(
    death()
  ))

[ablack3]

Hi @vojtechhuser how about this?

remotes::install_github("ohdsi/Capr", "issue125-decompile")
#> Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.
#> Skipping install of 'Capr' from a github remote, the SHA1 (01ff6ce0) has not changed since last install.
#>   Use `force = TRUE` to force installation


library(Capr)

cs_meas <- cs(3000905L, name = "Lab")

ch_m2 <- cohort(
  entry = entry(
    measurement(
      cs_meas,
      valueAsConceptSet(cs(9191L, name = "Positive"))
    )
  ),
  exit = exit(
    endStrategy = observationExit()
  )
)

cohortsToCreate <- list() # previously created cohort set
cohortsToCreate <- dplyr::bind_rows(cohortsToCreate, tibble::tibble(cohortId = 6,cohortName = "meas2",sql = CirceR::buildCohortQuery(
  expression = CirceR::cohortExpressionFromJson(ch_m2 |>toCirce()|>jsonlite::toJSON(pretty = TRUE, auto_unbox = TRUE) |>  as.character()),
  options = CirceR::createGenerateOptions(generateStats = FALSE))))

cohortsToCreate
#> # A tibble: 1 × 3
#>   cohortId cohortName sql                                                       
#>      <dbl> <chr>      <chr>                                                     
#> 1        6 meas2      "CREATE TABLE #Codesets (\r\n  codeset_id int NOT NULL,\r…

^{Created on 2026-02-16 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.5.1 (2025-06-13)
#>  os       macOS Tahoe 26.2
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#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       UTC
#>  date     2026-02-16
#>  pandoc   3.6.3 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#>  quarto   1.8.27 @ /usr/local/bin/quarto
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