Reads columns clean_virus() already produced to flag duplicate records,
vaccine viruses with large nucleotide changes, and VDPV positives with no
emergence group. See checks_afp() for the return shape.
Usage
checks_virus(virus, reference_date = Sys.Date())Arguments
- virus
A cleaned virus tibble (from
clean_virus()).- 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
virus <- data.frame(id = c(1, 1), nt_changes = c(7, 7))
checks_virus(virus)$summary
#> # A tibble: 4 × 7
#> check domain severity n_flagged status missing_columns description
#> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 virus_missing_gu… Virus error NA not_r… "adm1_guid, ad… Positives …
#> 2 virus_large_nt Virus warning 2 check… "" Vaccine vi…
#> 3 virus_duplicates Virus warning NA not_r… "epid, classif… Duplicate …
#> 4 virus_missing_em… Virus info NA not_r… "emergence_gro… VDPV posit…