# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # (2022). AMR: An R Package for Working with Antimicrobial Resistance # # Data. Journal of Statistical Software, 104(3), 1-31. # # https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # # colleagues from around the world, see our website. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # #' Add Custom Microorganisms #' #' 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*. #' #' **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. #' #' There are two ways to circumvent this and automate the process of adding microorganisms: #' #' **Method 1:** Using the [package option][AMR-options] [`AMR_custom_mo`][AMR-options], which is the preferred method. To use this method: #' #' 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. #' #' 2. Set the file location to the [package option][AMR-options] [`AMR_custom_mo`][AMR-options]: `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: #' #' ```r #' # Add custom microorganism codes: #' options(AMR_custom_mo = "~/my_custom_mo.rds") #' ``` #' #' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function. #' #' **Method 2:** Loading the microorganism directly from your `.Rprofile` file. Note that the definitions will be stored in a user-specific \R file, which is a suboptimal workflow. To use this method: #' #' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`. #' #' 2. Add a text like below and save the file: #' #' ```r #' # Add custom antibiotic drug codes: #' AMR::add_custom_microorganisms( #' data.frame(genus = "Enterobacter", #' species = "asburiae/cloacae") #' ) #' ``` #' #' Use [clear_custom_microorganisms()] to clear the previously added microorganisms. #' @seealso [add_custom_antimicrobials()] to add custom antimicrobials. #' @rdname add_custom_microorganisms #' @export #' @examples #' \donttest{ #' # a combination of species is not formal taxonomy, so #' # this will result in "Enterobacter cloacae cloacae", #' # since it resembles the input best: #' mo_name("Enterobacter asburiae/cloacae") #' #' # now add a custom entry - it will be considered by as.mo() and #' # all mo_*() functions #' add_custom_microorganisms( #' data.frame( #' genus = "Enterobacter", #' species = "asburiae/cloacae" #' ) #' ) #' #' # E. asburiae/cloacae is now a new microorganism: #' mo_name("Enterobacter asburiae/cloacae") #' #' # its code: #' as.mo("Enterobacter asburiae/cloacae") #' #' # all internal algorithms will work as well: #' mo_name("Ent asburia cloacae") #' #' # and even the taxonomy was added based on the genus! #' mo_family("E. asburiae/cloacae") #' mo_gramstain("Enterobacter asburiae/cloacae") #' #' mo_info("Enterobacter asburiae/cloacae") #' #' #' # the function tries to be forgiving: #' add_custom_microorganisms( #' data.frame( #' GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE", #' SPECIES = "SPECIES" #' ) #' ) #' mo_name("BACTEROIDES / PARABACTEROIDES") #' mo_rank("BACTEROIDES / PARABACTEROIDES") #' #' # taxonomy still works, even though a slashline genus was given as input: #' mo_family("Bacteroides/Parabacteroides") #' #' #' # for groups and complexes, set them as species or subspecies: #' add_custom_microorganisms( #' 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") stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'.")) add_MO_lookup_to_AMR_env() # remove any extra class/type, such as grouped tbl, or data.table: x <- as.data.frame(x, stringsAsFactors = FALSE) colnames(x) <- tolower(colnames(x)) # rename 'name' to 'fullname' if it's in the data set if ("name" %in% colnames(x) && !"fullname" %in% colnames(x)) { colnames(x)[colnames(x) == "name"] <- "fullname" } # keep only columns available in the microorganisms data set x <- x[, colnames(AMR_env$MO_lookup)[colnames(AMR_env$MO_lookup) %in% colnames(x)], drop = FALSE] # clean the input ---- for (col in c("genus", "species", "subspecies")) { if (!col %in% colnames(x)) { x[, col] <- "" } if (is.factor(x[, col, drop = TRUE])) { x[, col] <- as.character(x[, col, drop = TRUE]) } col_ <- x[, col, drop = TRUE] 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 col_ <- gsub(" group( |$)", " Group\\1", col_, perl = TRUE) col_[is.na(col_)] <- "" if (col == "genus") { substr(col_, 1, 1) <- toupper(substr(col_, 1, 1)) col_ <- gsub("/([a-z])", "/\\U\\1", col_, perl = TRUE) stop_if(any(col_ == ""), "the 'genus' column cannot be empty") stop_if(any(col_ %like% " "), "the 'genus' column must not contain spaces") } x[, col] <- col_ } # if subspecies is a group or complex, add it to the species and empty the subspecies x$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), "the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank) ) } else { x$rank <- ifelse(x$subspecies != "", "subspecies", ifelse(x$species != "", "species", ifelse(x$genus != "", "genus", stop("in add_custom_microorganisms(): only microorganisms up to the genus level can be added", call. = FALSE ) ) ) ) } x$source <- "Added by user" if (!"fullname" %in% colnames(x)) { x$fullname <- trimws2(paste(x$genus, x$species, x$subspecies)) } if (!"kingdom" %in% colnames(x)) x$kingdom <- "" if (!"phylum" %in% colnames(x)) x$phylum <- "" if (!"class" %in% colnames(x)) x$class <- "" if (!"order" %in% colnames(x)) x$order <- "" if (!"family" %in% colnames(x)) x$family <- "" x$kingdom[is.na(x$kingdom)] <- "" x$phylum[is.na(x$phylum)] <- "" x$class[is.na(x$class)] <- "" x$order[is.na(x$order)] <- "" x$family[is.na(x$family)] <- "" for (col in colnames(x)) { if (is.factor(x[, col, drop = TRUE])) { x[, col] <- as.character(x[, col, drop = TRUE]) } if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) { x[, col] <- as.list(x[, col, drop = TRUE]) } } # fill in taxonomy based on genus genus_to_check <- gsub("^(.*)[^a-zA-Z].*", "\\1", x$genus, perl = TRUE) 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$genus)] x$phylum[which(x$phylum == "" & genus_to_check != "")] <- AMR_env$MO_lookup$phylum[match(genus_to_check[which(x$phylum == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)] 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$genus)] x$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)] 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$genus)] # fill in other columns that are used in internal algorithms x$prevalence <- NA_real_ x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)] x$prevalence[is.na(x$prevalence)] <- 1.25 x$status <- "accepted" x$ref <- paste("Self-added,", format(Sys.Date(), "%Y")) x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)] # complete missing kingdom index, so mo_matching_score() will not return NA x$kingdom_index[is.na(x$kingdom_index)] <- 1 x$fullname_lower <- tolower(x$fullname) x$full_first <- substr(x$fullname_lower, 1, 1) x$species_first <- tolower(substr(x$species, 1, 1)) x$subspecies_first <- tolower(substr(x$subspecies, 1, 1)) if (!"mo" %in% colnames(x)) { # create the mo code x$mo <- NA_character_ } x$mo <- trimws2(as.character(x$mo)) x$mo[x$mo == ""] <- NA_character_ current <- sum(AMR_env$MO_lookup$source == "Added by user", na.rm = TRUE) x$mo[is.na(x$mo)] <- paste0( "CUSTOM", seq.int(from = current + 1, to = current + nrow(x), by = 1), "_", trimws( paste(abbreviate_mo(x$genus, 5), abbreviate_mo(x$species, 4, hyphen_as_space = TRUE), abbreviate_mo(x$subspecies, 4, hyphen_as_space = TRUE), sep = "_"), whitespace = "_")) stop_if(anyDuplicated(c(as.character(AMR_env$MO_lookup$mo), x$mo)), "MO codes must be unique and not match existing MO codes of the AMR package") # add to package ---- AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo) class(AMR_env$MO_lookup$mo) <- "character" new_df <- AMR_env$MO_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE] rownames(new_df) <- NULL list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list) for (l in which(list_cols)) { # prevent binding NULLs in lists, replace with NA new_df[, l] <- as.list(NA_character_) } for (col in colnames(x)) { # assign new values new_df[, col] <- x[, col, drop = TRUE] } # clear previous coercions suppressMessages(mo_reset_session()) AMR_env$MO_lookup <- unique(rbind_AMR(AMR_env$MO_lookup, new_df)) class(AMR_env$MO_lookup$mo) <- c("mo", "character") if (nrow(x) <= 3) { message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal `microorganisms` data set.") } else { message_("Added ", nr2char(nrow(x)), " records to the internal `microorganisms` data set.") } } #' @rdname add_custom_microorganisms #' @export clear_custom_microorganisms <- function() { n <- nrow(AMR_env$MO_lookup) # reset AMR_env$MO_lookup <- NULL add_MO_lookup_to_AMR_env() # clear previous coercions suppressMessages(mo_reset_session()) n2 <- nrow(AMR_env$MO_lookup) AMR_env$custom_mo_codes <- character(0) 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] AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, , drop = FALSE] message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `microorganisms` data set.") } abbreviate_mo <- function(x, minlength = 5, prefix = "", hyphen_as_space = FALSE, ...) { if (hyphen_as_space == TRUE) { x <- gsub("-", " ", x, fixed = TRUE) } # keep a starting Latin ae suppressWarnings( gsub("(\u00C6|\u00E6)+", "AE", toupper( paste0(prefix, abbreviate( gsub("^ae", "\u00E6\u00E6", x, ignore.case = TRUE), minlength = minlength, use.classes = TRUE, method = "both.sides", ... )))) ) }