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(v1.4.0.9020) mo_is_intrinsic_resistant

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dr. M.S. (Matthijs) Berends
2020-11-16 11:03:24 +01:00
parent 9666b78ea7
commit 05fb213a7c
24 changed files with 228 additions and 144 deletions
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9
R/mo.R
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@ -148,8 +148,9 @@
#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRPA
#'
#' # All mo_* functions use as.mo() internally too (see ?mo_property):
#' mo_genus("E. coli") # returns "Escherichia"
#' mo_gramstain("E. coli") # returns "Gram negative"
#' mo_genus("E. coli") # returns "Escherichia"
#' mo_gramstain("E. coli") # returns "Gram negative"
#' mo_is_intrinsic_resistant("E. coli", "vanco") # returns TRUE
#' }
as.mo <- function(x,
Becker = FALSE,
@ -1620,8 +1621,8 @@ get_skimmers.mo <- function(column) {
sfl(
skim_type = "mo",
unique_total = ~pm_n_distinct(., na.rm = TRUE),
gram_negative = ~sum(is_gram_negative(stats::na.omit(.))),
gram_positive = ~sum(is_gram_positive(stats::na.omit(.))),
gram_negative = ~sum(mo_is_gram_negative(stats::na.omit(.))),
gram_positive = ~sum(mo_is_gram_positive(stats::na.omit(.))),
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]
)