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@ -32,26 +32,26 @@
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#' With [add_custom_microorganisms()] you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.
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#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing column "genus" (case-insensitive)
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#' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
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#'
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#' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
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#'
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#'
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#' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
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#'
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#' There are two ways to automate this process:
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#'
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#'
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#' **Method 1:** Using the option [`AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
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#'
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#'
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#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
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#'
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#'
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#' 2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
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#'
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#' ```r
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#' # Add custom microorganism codes:
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#' options(AMR_custom_mo = "~/my_custom_mo.rds")
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#' ```
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#'
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#'
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#' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function.
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#'
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#'
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#' **Method 2:** Loading the microorganism directly from your `.Rprofile` file. An important downside is that this requires the `AMR` package to be installed or else this method will fail. To use this method:
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#'
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#'
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#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
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#'
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#' 2. Add a text like below and save the file:
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@ -77,44 +77,49 @@
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#' # now add a custom entry - it will be considered by as.mo() and
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#' # all mo_*() functions
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#' add_custom_microorganisms(
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#' data.frame(genus = "Enterobacter",
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#' species = "asburiae/cloacae"
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#' data.frame(
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#' genus = "Enterobacter",
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#' species = "asburiae/cloacae"
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#' )
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#' )
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#'
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#' # E. asburiae/cloacae is now a new microorganism:
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#' mo_name("Enterobacter asburiae/cloacae")
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#'
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#'
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#' # its code:
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#' as.mo("Enterobacter asburiae/cloacae")
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#'
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#'
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#' # all internal algorithms will work as well:
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#' mo_name("Ent asburia cloacae")
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#'
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#'
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#' # and even the taxonomy was added based on the genus!
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#' mo_family("E. asburiae/cloacae")
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#' mo_gramstain("Enterobacter asburiae/cloacae")
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#'
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#' mo_info("Enterobacter asburiae/cloacae")
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#'
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#'
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#'
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#'
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#' # the function tries to be forgiving:
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#' add_custom_microorganisms(
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#' data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
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#' SPECIES = "SPECIES")
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#' data.frame(
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#' GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
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#' SPECIES = "SPECIES"
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#' )
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#' )
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#' mo_name("BACTEROIDES / PARABACTEROIDES")
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#' mo_rank("BACTEROIDES / PARABACTEROIDES")
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#'
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#'
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#' # taxonomy still works, although a slashline genus was given as input:
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#' mo_family("Bacteroides/Parabacteroides")
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#'
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#'
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#'
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#'
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#' # for groups and complexes, set them as species or subspecies:
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#' add_custom_microorganisms(
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#' data.frame(genus = "Citrobacter",
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#' species = c("freundii", "braakii complex"),
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#' subspecies = c("complex", ""))
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#' data.frame(
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#' genus = "Citrobacter",
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#' species = c("freundii", "braakii complex"),
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#' subspecies = c("complex", "")
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#' )
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#' )
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#' mo_name(c("C. freundii complex", "C. braakii complex"))
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#' mo_species(c("C. freundii complex", "C. braakii complex"))
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@ -123,9 +128,9 @@
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add_custom_microorganisms <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'."))
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add_MO_lookup_to_AMR_env()
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# remove any extra class/type, such as grouped tbl, or data.table:
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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colnames(x) <- tolower(colnames(x))
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@ -135,7 +140,7 @@ add_custom_microorganisms <- function(x) {
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}
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# keep only columns available in the microorganisms data set
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x <- x[, colnames(AMR_env$MO_lookup)[colnames(AMR_env$MO_lookup) %in% colnames(x)], drop = FALSE]
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# clean the input ----
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for (col in c("genus", "species", "subspecies")) {
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if (!col %in% colnames(x)) {
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@ -152,7 +157,7 @@ add_custom_microorganisms <- function(x) {
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col_ <- gsub(" *([/-]) *", "\\1", col_, perl = TRUE)
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# groups are in our taxonomic table with a capital G
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col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE)
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col_[is.na(col_)] <- ""
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if (col == "genus") {
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substr(col_, 1, 1) <- toupper(substr(col_, 1, 1))
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@ -163,19 +168,27 @@ add_custom_microorganisms <- function(x) {
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x[, col] <- col_
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}
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# if subspecies is a group or complex, add it to the species and empty the subspecies
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x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
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x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))])
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x$species[which(x$subspecies %in% c("group", "Group", "complex"))] <- paste(
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x$species[which(x$subspecies %in% c("group", "Group", "complex"))],
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x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))]
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)
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x$subspecies[which(x$subspecies %in% c("group", "Group", "complex"))] <- ""
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if ("rank" %in% colnames(x)) {
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stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),
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"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank))
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stop_ifnot(
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all(x$rank %in% AMR_env$MO_lookup$rank),
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"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank)
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)
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} else {
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x$rank <- ifelse(x$subspecies != "", "subspecies",
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ifelse(x$species != "", "species",
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ifelse(x$genus != "", "genus",
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stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added",
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call. = FALSE))))
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ifelse(x$species != "", "species",
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ifelse(x$genus != "", "genus",
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stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added",
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call. = FALSE
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)
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)
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)
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)
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}
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x$source <- "Added by user"
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if (!"fullname" %in% colnames(x)) {
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@ -191,7 +204,7 @@ add_custom_microorganisms <- function(x) {
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x$class[is.na(x$class)] <- ""
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x$order[is.na(x$order)] <- ""
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x$family[is.na(x$family)] <- ""
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for (col in colnames(x)) {
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if (is.factor(x[, col, drop = TRUE])) {
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x[, col] <- as.character(x[, col, drop = TRUE])
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@ -200,7 +213,7 @@ add_custom_microorganisms <- function(x) {
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x[, col] <- as.list(x[, col, drop = TRUE])
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}
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}
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# fill in taxonomy based on genus
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genus_to_check <- gsub("^(.*)[^a-zA-Z].*", "\\1", x$genus, perl = TRUE)
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x$kingdom[which(x$kingdom == "" & genus_to_check != "")] <- AMR_env$MO_lookup$kingdom[match(genus_to_check[which(x$kingdom == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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@ -208,7 +221,7 @@ add_custom_microorganisms <- function(x) {
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x$class[which(x$class == "" & genus_to_check != "")] <- AMR_env$MO_lookup$class[match(genus_to_check[which(x$class == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$order[which(x$order == "" & genus_to_check != "")] <- AMR_env$MO_lookup$order[match(genus_to_check[which(x$order == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
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# fill in other columns that are used in internal algorithms
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x$prevalence <- NA_real_
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x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)]
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@ -222,7 +235,7 @@ add_custom_microorganisms <- function(x) {
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x$full_first <- substr(x$fullname_lower, 1, 1)
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x$species_first <- tolower(substr(x$species, 1, 1))
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x$subspecies_first <- tolower(substr(x$subspecies, 1, 1))
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if (!"mo" %in% colnames(x)) {
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# create the mo code
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x$mo <- NA_character_
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@ -230,19 +243,27 @@ add_custom_microorganisms <- function(x) {
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x$mo <- trimws2(as.character(x$mo))
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x$mo[x$mo == ""] <- NA_character_
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current <- sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE)
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x$mo[is.na(x$mo)] <- paste0("CUSTOM",
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seq.int(from = current + 1, to = current + nrow(x), by = 1),
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"_",
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toupper(unname(abbreviate(gsub(" +", " _ ",
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gsub("[^A-Za-z0-9-]", " ",
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trimws2(paste(x$genus, x$species, x$subspecies)))),
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minlength = 10))))
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x$mo[is.na(x$mo)] <- paste0(
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"CUSTOM",
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seq.int(from = current + 1, to = current + nrow(x), by = 1),
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"_",
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toupper(unname(abbreviate(
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gsub(
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" +", " _ ",
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gsub(
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"[^A-Za-z0-9-]", " ",
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trimws2(paste(x$genus, x$species, x$subspecies))
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)
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),
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minlength = 10
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)))
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)
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stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package")
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# add to package ----
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AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
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class(AMR_env$MO_lookup$mo) <- "character"
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new_df <- AMR_env$MO_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
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rownames(new_df) <- NULL
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list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
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@ -254,10 +275,10 @@ add_custom_microorganisms <- function(x) {
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# assign new values
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new_df[, col] <- x[, col, drop = TRUE]
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}
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# clear previous coercions
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suppressMessages(mo_reset_session())
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AMR_env$MO_lookup <- unique(rbind(AMR_env$MO_lookup, new_df))
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class(AMR_env$MO_lookup$mo) <- c("mo", "character")
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if (nrow(x) <= 3) {
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@ -271,11 +292,11 @@ add_custom_microorganisms <- function(x) {
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#' @export
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clear_custom_microorganisms <- function() {
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n <- nrow(AMR_env$MO_lookup)
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# reset
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AMR_env$MO_lookup <- NULL
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add_MO_lookup_to_AMR_env()
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n2 <- nrow(AMR_env$MO_lookup)
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AMR_env$custom_mo_codes <- character(0)
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AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(AMR_env$mo_previously_coerced$mo %in% AMR_env$MO_lookup$mo), , drop = FALSE]
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