measurementCohort - allow valueAsNumber without a unit concept id

[edward-burn]

Would want the second case below to work

library(CohortConstructor)
cdm <- mockCohortConstructor(con = NULL, seed = 1)
cdm$concept <- cdm$concept |>
  dplyr::union_all(
    dplyr::tibble(
      concept_id = c(4326744, 4298393, 45770407, 8876, 4124457, 999999, 123456) |> as.integer(),
      concept_name = c("Blood pressure", "Systemic blood pressure",
                       "Baseline blood pressure", "millimeter mercury column",
                       "Normal range", "Normal", "outObs"),
      domain_id = "Measurement",
      vocabulary_id = c("SNOMED", "SNOMED", "SNOMED", "UCUM", "SNOMED", "SNOMED", "hi"),
      standard_concept = "S",
      concept_class_id = c("Observable Entity", "Observable Entity",
                           "Observable Entity", "Unit", "Qualifier Value",
                           "Qualifier Value", "hi"),
      concept_code = NA,
      valid_start_date = NA,
      valid_end_date = NA,
      invalid_reason = NA
    )
  )
cdm$measurement <- dplyr::tibble(
  measurement_id = 1:3L,
  person_id = as.integer(c(1, 2, 3)),
  measurement_concept_id = c(4326744L, 4326744L, 4326744L),
  measurement_date = as.Date(c("2000-07-01", "2000-12-11", "2002-09-08")),
  measurement_type_concept_id = NA_integer_,
  value_as_number = c(100, 105, 110),
  value_as_concept_id = c(0, 0, 0) ,
  unit_concept_id = c(8876, 8876, 0)
)



measurementCohort(
  cdm = cdm,
  name = "cohort",
  conceptSet = list("normal_blood_pressure" = c(4326744, 4298393, 45770407)),
  valueAsConcept = c(4124457),
  valueAsNumber = list("8876" = c(70L, 120L))
)
#> Warning: ! `codelist` contains numeric values, they are casted to integers.
#> ℹ Subsetting measurement table.
#> ℹ Applying measurement requirements.
#> ! cohort columns will be reordered to match the expected order:
#>   cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date.
#> ℹ Getting records in observation.
#> ℹ Creating cohort attributes.
#> ✔ Cohort cohort created.
#> # A tibble: 2 × 4
#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
#> *                <int>      <int> <date>            <date>         
#> 1                    1          1 2000-07-01        2000-07-01     
#> 2                    1          2 2000-12-11        2000-12-11

# removing unit_concept_id 8876 - should mean any value between 70 and 120 would be included
# and we should now get person 3 included
measurementCohort(
  cdm = cdm,
  name = "cohort",
  conceptSet = list("normal_blood_pressure" = c(4326744L, 4298393L, 45770407L)),
  valueAsConcept = c(4124457),
  valueAsNumber = list(c(70L, 120L))
)
#> Error in `validateValueAsNumber()`:
#> ✖ `valueAsNumber` must be named.
#> ! `valueAsNumber` must be a list with objects of class integer and numeric; it
#>   can not contain NA; it has to be named.
#> Backtrace:
#>     ▆
#>  1. └─CohortConstructor::measurementCohort(...)
#>  2.   └─CohortConstructor:::validateValueAsNumber(valueAsNumber)
#>  3.     └─omopgenerics::assertList(...)
#>  4.       └─omopgenerics:::errorMessage(...)
#>  5.         └─cli::cli_abort(message = message, call = call)
#>  6.           └─rlang::abort(...)

^{Created on 2024-11-26 with reprex v2.0.2}

[edward-burn]

We should though require all named or none - otherwise the unnamed would supersede the named (as it would apply to all)