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adding mo fixes

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dr. M.S. (Matthijs) Berends
2023-01-14 19:50:25 +01:00
parent ca79068604
commit b94bc6c67b
12 changed files with 69 additions and 44 deletions
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35
R/custom_microorganisms.R
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@ -27,9 +27,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Add Custom Microorganisms to This Package
#' Add Custom Microorganisms
#'
#' With [add_custom_microorganisms()] you can add your own custom microorganisms to the `AMR` package, such the non-taxonomic outcome of laboratory analysis.
#' With [add_custom_microorganisms()] you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing column "genus" (case-insensitive)
#' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
#'
@ -66,7 +66,7 @@
#' ```
#'
#' Use [clear_custom_microorganisms()] to clear the previously added antimicrobials.
#' @seealso [add_custom_antimicrobials()] to add custom antimicrobials to this package.
#' @seealso [add_custom_antimicrobials()] to add custom antimicrobials.
#' @rdname add_custom_microorganisms
#' @export
#' @examples
@ -102,15 +102,23 @@
#'
#' # the function tries to be forgiving:
#' add_custom_microorganisms(
#' data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
#' SPECIES = "SPECIES"))
#' data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
#' SPECIES = "SPECIES")
#' )
#' mo_name("ESCHERICHIA / KLEBSIELLA")
#' mo_rank("ESCHERICHIA / KLEBSIELLA")
#' # taxonomy still works, although a slashline genus was given as input:
#' mo_family("Escherichia/Klebsiella")
#'
#' # for groups and complexes, set them as species or subspecies:
#' add_custom_microorganisms(
#' data.frame(genus = "Citrobacter", species = "freundii complex"))
#' mo_name("C. freundii complex")
#' mo_gramstain("C. freundii complex")
#' data.frame(genus = "Citrobacter",
#' species = c("freundii", "braakii complex"),
#' subspecies = c("complex", ""))
#' )
#' mo_name(c("C. freundii complex", "C. braakii complex"))
#' mo_species(c("C. freundii complex", "C. braakii complex"))
#' mo_gramstain(c("C. freundii complex", "C. braakii complex"))
#' }
add_custom_microorganisms <- function(x) {
meet_criteria(x, allow_class = "data.frame")
@ -135,12 +143,13 @@ add_custom_microorganisms <- function(x) {
x[, col] <- as.character(x[, col, drop = TRUE])
}
col_ <- x[, col, drop = TRUE]
col_ <- tolower(trimws2(col_))
col_ <- tolower(col_)
col_ <- gsub("slashline", "", col_, fixed = TRUE)
col_ <- trimws2(col_)
col_[col_ %like% "(sub)?species"] <- ""
col_ <- gsub(" *([/-]) *", "\\1", col_, perl = TRUE)
# groups are in our taxonomic table with a capital G, and complexes might be added by the user
# groups are in our taxonomic table with a capital G
col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE)
col_ <- gsub(" complex( |$)", " Complex\\1", col_, perl = TRUE)
col_[is.na(col_)] <- ""
if (col == "genus") {
@ -151,6 +160,10 @@ add_custom_microorganisms <- function(x) {
}
x[, col] <- col_
}
# if subspecies is a group or complex, add it to the species and empty the subspecies
x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))])
x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))] <- ""
if ("rank" %in% colnames(x)) {
stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),