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custom mo update
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Package: AMR
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Version: 1.8.2.9071
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Date: 2022-12-27
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Version: 1.8.2.9072
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Date: 2022-12-28
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9071
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# AMR 1.8.2.9072
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -30,7 +30,7 @@
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#' Add Custom Microorganisms to This Package
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#'
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#' With [add_custom_microorganisms()] you can add your own custom antimicrobial drug codes to the `AMR` package.
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#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "mo", "genus" and "species"
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#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "genus" and "species"
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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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@ -39,7 +39,7 @@
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#'
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#' **Method 1:** Save the microorganisms to a local or remote file (can even be the internet). To use this method:
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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 columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
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#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least columns "genus" and "species") 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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#' 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 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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@ -60,8 +60,7 @@
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#' # Add custom antibiotic drug codes:
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#' library(AMR)
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#' add_custom_microorganisms(
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#' data.frame(mo = "ENT_ASB_CLO",
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#' genus = "Enterobacter",
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#' data.frame(genus = "Enterobacter",
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#' species = "asburiae/cloacae")
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#' )
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#' ```
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@ -80,36 +79,32 @@
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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(mo = "ENT_ASB_CLO",
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#' genus = "Enterobacter",
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#' data.frame(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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#' # "ENT_ASB_CLO" is now a new microorganism:
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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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#' as.mo("ent_asb_clo")
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#' mo_name("ent_asb_clo")
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#' # its code:
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#' as.mo("Enterobacter asburiae/cloacae")
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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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#' # and even the taxonomy was added based on the genus!
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#' mo_family("ent_asb_clo")
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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("ent_asb_clo")
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#' mo_info("Enterobacter asburiae/cloacae")
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#' }
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add_custom_microorganisms <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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required_cols <- c("mo", "genus", "species")
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stop_ifnot(
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all(required_cols %in% colnames(x)),
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paste0("`x` must contain columns ", vector_and(required_cols, sort = FALSE), ".")
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)
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stop_if(
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any(x$mo %in% AMR_env$MO_lookup$mo),
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"Microorganism code(s) ", vector_and(x$mo[x$mo %in% AMR_env$MO_lookup$mo]), " already exist in the internal `microorganisms` data set."
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all(c("genus", "species") %in% colnames(x)),
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paste0("`x` must contain columns ", vector_and(c("genus", "species"), sort = FALSE), ".")
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)
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# remove any extra class/type, such as grouped tbl, or data.table:
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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# rename 'name' to 'fullname' if it's in the data set
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@ -126,14 +121,14 @@ add_custom_microorganisms <- function(x) {
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x$genus <- trimws2(x$genus)
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x$species <- trimws2(x$species)
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x$subspecies <- trimws2(x$subspecies)
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x$genus[x$genus == ""] <- NA_character_
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x$species[x$species == ""] <- NA_character_
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x$subspecies[x$subspecies == ""] <- NA_character_
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stop_if(any(x$genus[!is.na(x$genus)] %like% " "),
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x$genus[is.na(x$genus)] <- ""
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x$species[is.na(x$species)] <- ""
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x$subspecies[is.na(x$subspecies)] <- ""
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stop_if(any(x$genus %like% " "),
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"the 'genus' column must not contain spaces")
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stop_if(any(x$species[!is.na(x$species)] %like% " "),
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stop_if(any(x$species %like% " "),
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"the 'species' column must not contain spaces")
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stop_if(any(x$subspecies[!is.na(x$subspecies)] %like% " "),
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stop_if(any(x$subspecies %like% " "),
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"the 'subspecies' column must not contain spaces")
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if ("rank" %in% colnames(x)) {
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@ -147,14 +142,13 @@ add_custom_microorganisms <- function(x) {
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call. = FALSE))))
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}
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if (!"fullname" %in% colnames(x)) {
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x$fullname <- paste(x$genus, x$species, x$subspecies)
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x$fullname <- gsub(" NA", "", x$fullname)
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x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies))
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}
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if (!"kingdom" %in% colnames(x)) x$kingdom <- NA_character_
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if (!"phylum" %in% colnames(x)) x$phylum <- NA_character_
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if (!"class" %in% colnames(x)) x$class <- NA_character_
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if (!"order" %in% colnames(x)) x$order <- NA_character_
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if (!"family" %in% colnames(x)) x$family <- NA_character_
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if (!"kingdom" %in% colnames(x)) x$kingdom <- ""
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if (!"phylum" %in% colnames(x)) x$phylum <- ""
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if (!"class" %in% colnames(x)) x$class <- ""
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if (!"order" %in% colnames(x)) x$order <- ""
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if (!"family" %in% colnames(x)) x$family <- ""
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for (col in colnames(x)) {
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if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) {
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@ -171,13 +165,32 @@ add_custom_microorganisms <- function(x) {
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x$order <- AMR_env$MO_lookup$order[match(x$genus, AMR_env$MO_lookup$genus)]
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x$family <- AMR_env$MO_lookup$family[match(x$genus, AMR_env$MO_lookup$genus)]
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x$kingdom[is.na(x$kingdom)] <- ""
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x$phylum[is.na(x$phylum)] <- ""
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x$class[is.na(x$class)] <- ""
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x$order[is.na(x$order)] <- ""
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x$family[is.na(x$family)] <- ""
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x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)]
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x$fullname_lower <- tolower(x$fullname)
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x$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$subspecies, 1, 1))
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# add to pacakge ----
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if (!"mo" %in% colnames(x)) {
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# create the mo code
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x$mo <- NA_character_
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}
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x$mo <- trimws2(x$mo)
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x$mo[x$mo == ""] <- NA_character_
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x$mo[is.na(x$mo)] <- paste0("CUSTOM_",
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toupper(abbreviate(gsub(" +", " _ ",
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gsub("[^A-Za-z0-9-]", " ",
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trimws2(paste(x$genus, x$species, x$subspecies)))),
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minlength = 10,
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named = FALSE)))
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# add to package ----
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AMR_env$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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@ -193,8 +206,11 @@ 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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AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(!AMR_env$mo_previously_coerced$mo %in% new_df$mo), , drop = FALSE]
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class(AMR_env$MO_lookup$mo) <- c("mo", "character")
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message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `microorganisms` data set.")
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}
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10
R/mo.R
10
R/mo.R
@ -182,11 +182,11 @@ as.mo <- function(x,
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x_lower <- tolower(x)
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complexes <- x[trimws2(x_lower) %like_case% "complex$"]
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if (length(complexes) > 0) {
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warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored in ", length(complexes), " cases.", call = FALSE)
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complexes <- x[trimws2(x_lower) %like_case% " (complex|group)$"]
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if (length(complexes) > 0 && identical(remove_from_input, mo_cleaning_regex())) {
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warning_("in `as.mo()`: 'complex' and 'group' were ignored from the input in ", length(complexes), " case", ifelse(length(complexes) > 1, "s", ""), ", as they are currently not supported.\nYou can add your own microorganism with `add_custom_microorganisms()`.", call = FALSE)
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}
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# WHONET: xxx = no growth
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x[x_lower %in% c("", "xxx", "na", "nan")] <- NA_character_
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@ -536,7 +536,7 @@ mo_cleaning_regex <- function() {
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"|",
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"([({]|\\[).+([})]|\\])",
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"|",
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"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|complex)[.]*( |$))"
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"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|group|complex)[.]*( |$))"
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)
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}
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@ -10,7 +10,7 @@ add_custom_microorganisms(x)
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clear_custom_microorganisms()
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}
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\arguments{
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\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "mo", "genus" and "species"}
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\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
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}
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\description{
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With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
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@ -24,7 +24,7 @@ There are two ways to automate this process:
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\strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method:
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\enumerate{
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\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "ab" and "name") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
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\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "genus" and "species") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
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\item Set the file location to the \code{AMR_custom_mo} \R option: \code{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 \code{.Rprofile} file so that it will loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
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@ -42,8 +42,7 @@ Upon package load, this file will be loaded and run through the \code{\link[=add
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
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library(AMR)
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add_custom_microorganisms(
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data.frame(mo = "ENT_ASB_CLO",
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genus = "Enterobacter",
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data.frame(genus = "Enterobacter",
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species = "asburiae/cloacae")
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)
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}\if{html}{\out{</div>}}
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@ -61,24 +60,23 @@ mo_name("Enterobacter asburiae/cloacae")
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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(mo = "ENT_ASB_CLO",
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genus = "Enterobacter",
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data.frame(genus = "Enterobacter",
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species = "asburiae/cloacae"
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)
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)
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# "ENT_ASB_CLO" is now a new microorganism:
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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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as.mo("ent_asb_clo")
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mo_name("ent_asb_clo")
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# its code:
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as.mo("Enterobacter asburiae/cloacae")
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# all internal algorithms will work as well:
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mo_name("Ent asburia cloacae")
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# and even the taxonomy was added based on the genus!
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mo_family("ent_asb_clo")
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mo_family("E. asburiae/cloacae")
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mo_gramstain("Enterobacter asburiae/cloacae")
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mo_info("ent_asb_clo")
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mo_info("Enterobacter asburiae/cloacae")
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}
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}
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\seealso{
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