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(v1.3.0.9032) support skimr

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dr. M.S. (Matthijs) Berends
2020-09-28 01:08:55 +02:00
parent 22f6ceb3e4
commit 519aada54f
25 changed files with 123 additions and 30 deletions
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17
R/mo.R
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@ -1637,11 +1637,24 @@ freq.mo <- function(x, ...) {
decimal.mark = "."),
" (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
")"),
`No. of genera` = pm_n_distinct(mo_genus(x_noNA, language = NULL)),
`No. of species` = pm_n_distinct(paste(mo_genus(x_noNA, language = NULL),
`Nr. of genera` = pm_n_distinct(mo_genus(x_noNA, language = NULL)),
`Nr. of species` = pm_n_distinct(paste(mo_genus(x_noNA, language = NULL),
mo_species(x_noNA, language = NULL)))))
}
# will be exported using s3_register() in R/zzz.R
get_skimmers.mo <- function(column) {
sfl <- import_fn("sfl", "skimr", error_on_fail = FALSE)
sfl(
skim_type = "mo",
unique_total = n_unique,
gram_negative = ~sum(mo_gramstain(stats::na.omit(.), language = NULL) == "Gram-negative", na.rm = TRUE),
gram_positive = ~sum(mo_gramstain(stats::na.omit(.), language = NULL) == "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]
)
}
#' @method print mo
#' @export
#' @noRd