Reads columns clean_human_spec() already produced to flag duplicate
specimens, blank collection dates, unreconciled GUIDs and inadequate
specimens. See checks_afp() for the return shape.
Usage
checks_hum_spec(hum_spec, reference_date = Sys.Date())Arguments
- hum_spec
A cleaned human-specimen tibble (from
clean_human_spec()).- reference_date
Date treated as "today" for future-date checks (default
Sys.Date()).
Value
A named list (summary + one tibble per flagged check); see
checks_afp().
Examples
hs <- data.frame(id = 1, specimen_id = c("S1"), collection_date = NA)
checks_hum_spec(hs)$summary
#> # A tibble: 4 × 7
#> check domain severity n_flagged status missing_columns description
#> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 hum_spec_missing… HumSp… error NA not_r… "adm1_guid, ad… Specimens …
#> 2 hum_spec_no_coll… HumSp… warning 1 check… "" Specimens …
#> 3 hum_spec_duplica… HumSp… warning 0 check… "" Duplicate …
#> 4 hum_spec_inadequ… HumSp… info NA not_r… "adequate" Specimens …