Reads columns clean_es() already produced to flag duplicate sample IDs,
blank/future collection dates, unreconciled GUIDs and missing/zero
coordinates. See checks_afp() for the return shape.
Usage
checks_es(es, reference_date = Sys.Date())Arguments
- es
A cleaned ES tibble (from
clean_es()).- 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
es <- data.frame(
id = 1, sample_id = "E1", adm0 = "CHAD",
collection_date = "2024-02-01"
)
checks_es(es)$summary
#> # A tibble: 3 × 5
#> check domain severity n_flagged description
#> <chr> <chr> <chr> <int> <chr>
#> 1 es_duplicates ES warning 0 Duplicate sample ID + admin0
#> 2 es_no_collection_date ES warning 0 ES samples with no collection…
#> 3 es_future_collection ES warning 0 Collection date later than th…