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fix for antibiogram(), transform WHONET data set to sir

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dr. M.S. (Matthijs) Berends
2023-02-22 15:40:05 +01:00
parent dad25302f2
commit c2cfc5ef84
10 changed files with 20 additions and 30 deletions
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30
R/antibiogram.R
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@ -31,7 +31,7 @@
#'
#' Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker *et al.* and Barbieri *et al.* (see *Source*), and allow reporting in e.g. R Markdown and Quarto as well.
#' @param x a [data.frame] containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see [as.sir()])
#' @param antibiotics vector of column names, or (any combinations of) [antibiotic selectors][antibiotic_class_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be column names separated with `"+"`, such as "TZP+TOB" given that the data set contains columns "TZP" and "TOB". See *Examples*.
#' @param antibiotics vector of any antibiotic name or code (will be evaluated with [as.ab()], column name of `x`, or (any combinations of) [antibiotic selectors][antibiotic_class_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be set to values separated with `"+"`, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in `x`. See *Examples*.
#' @param mo_transform a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
#' @param ab_transform a character to transform antibiotic input - must be one of the column names of the [antibiotics] data set: `r vector_or(colnames(antibiotics), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
#' @param syndromic_group a column name of `x`, or values calculated to split rows of `x`, e.g. by using [ifelse()] or [`case_when()`][dplyr::case_when()]. See *Examples*.
@ -165,8 +165,9 @@
#' mo_transform = "gramstain"
#' )
#'
#' # names of antibiotics do not need to resemble columns exactly:
#' antibiogram(example_isolates,
#' antibiotics = c("TZP", "TZP+TOB"),
#' antibiotics = c("Cipro", "cipro + genta"),
#' mo_transform = "gramstain",
#' ab_transform = "name",
#' sep = " & "
@ -313,25 +314,16 @@ antibiogram <- function(x,
# get antibiotics from user
user_ab <- suppressMessages(suppressWarnings(lapply(antibiotics, as.ab, flag_multiple_results = FALSE, info = FALSE)))
user_ab <- lapply(user_ab, function(x) unname(df_ab[match(x, names(df_ab))]))
#
# names(user_ab) <- antibiotics.bak
# user_ab <- user_ab
return(1)
# cols <-
# convert antibiotics to valid AB codes
abx_ab <- suppressMessages(suppressWarnings(lapply(antibiotics, as.ab, flag_multiple_results = FALSE, info = FALSE)))
# match them to existing column names
abx_user <- lapply(abx_ab, function(a) unname(names(cols)[match(a, names(cols))]))
# remove non-existing columns
non_existing <- unlist(antibiotics)[is.na(unlist(abx_ab))]
if (length(non_existing) > 0) {
warning_("The following antibiotics were not available and ignored: ", vector_and(non_existing, sort = FALSE))
abx_user <- Map(antibiotics, abx_user, f = function(input, ab) input[!is.na(ab)])
}
# non_existing <- unlist(antibiotics)[is.na(unlist(abx_ab))]
# if (length(non_existing) > 0) {
# warning_("The following antibiotics were not available and ignored: ", vector_and(non_existing, sort = FALSE))
# abx_user <- Map(antibiotics, abx_user, f = function(input, ab) input[!is.na(ab)])
# }
# make list unique
antibiotics <- unique(abx_user)
print(antibiotics)
antibiotics <- unique(user_ab)
# go through list to set AMR in combinations
for (i in seq_len(length(antibiotics))) {
abx <- antibiotics[[i]]