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(v3.0.0.9027) skimr update and as.ab warning - fixes #234, fixes #232

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dr. M.S. (Matthijs) Berends
2025-09-10 13:32:52 +02:00
parent d5a568318b
commit 4d7c4ca52c
13 changed files with 92 additions and 58 deletions
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14
R/mo.R
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@@ -747,13 +747,17 @@ freq.mo <- function(x, ...) {
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
get_skimmers.mo <- function(column) {
mo <- as.mo(column, keep_synonyms = TRUE, language = NULL, info = FALSE)
mo <- mo[!is.na(mo)]
spp <- mo[mo_species(mo, keep_synonyms = TRUE, language = NULL, info = FALSE) != ""]
skimr::sfl(
skim_type = "mo",
unique_total = ~ length(unique(stats::na.omit(.))),
gram_negative = ~ sum(mo_is_gram_negative(.), na.rm = TRUE),
gram_positive = ~ sum(mo_is_gram_positive(.), na.rm = TRUE),
top_genus = ~ names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
top_species = ~ names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
n_unique = ~ length(unique(mo)),
gram_negative = ~ sum(mo_is_gram_negative(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
gram_positive = ~ sum(mo_is_gram_positive(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
yeast = ~ sum(mo_is_yeast(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
top_genus = ~ names(sort(-table(mo_genus(mo, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
top_species = ~ names(sort(-table(mo_name(spp, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
)
}