mirror of
https://github.com/msberends/AMR.git
synced 2025-10-31 06:48:22 +01:00
remove MO_lookup from sysdata.rda
This commit is contained in:
@@ -32,7 +32,7 @@
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#' @description
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#' Welcome to the `AMR` package.
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#'
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#' The `AMR` package is a [free and open-source](https://msberends.github.io/AMR#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project!
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#' The `AMR` package is a [free and open-source](https://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project!
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#'
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#' This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
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#'
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@@ -225,6 +225,8 @@ search_type_in_df <- function(x, type, info = TRUE) {
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# -- mo
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if (type == "mo") {
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add_MO_lookup_to_AMR_env()
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if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) {
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# take first 'mo' column
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found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
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@@ -1379,6 +1381,38 @@ add_intrinsic_resistance_to_AMR_env <- function() {
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}
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}
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add_MO_lookup_to_AMR_env <- function() {
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# for all MO functions, saves a lot of time on package load and in package size
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if (is.null(AMR_env$MO_lookup)) {
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MO_lookup <- AMR::microorganisms
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MO_lookup$kingdom_index <- NA_real_
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MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
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MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
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MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
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MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
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# all the rest
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MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
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# the fullname lowercase, important for the internal algorithms in as.mo()
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MO_lookup$fullname_lower <- tolower(trimws(paste(
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MO_lookup$genus,
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MO_lookup$species,
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MO_lookup$subspecies
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)))
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ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
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MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
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MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
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# special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
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MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")] <- gsub(" enterica ", " ", MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")], fixed = TRUE)
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MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
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MO_lookup$species_first <- tolower(substr(MO_lookup$species, 1, 1)) # tolower for groups (Streptococcus, Salmonella)
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MO_lookup$subspecies_first <- tolower(substr(MO_lookup$subspecies, 1, 1)) # tolower for Salmonella serovars
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AMR_env$MO_lookup <- MO_lookup
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}
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}
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trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u0085\u00A0\u1680\u180E\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u200B\u200C\u200D\u2028\u2029\u202F\u205F\u2060\u3000\uFEFF]") {
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# this is even faster than trimws() itself which sets " \t\n\r".
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trimws(..., whitespace = whitespace)
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@@ -124,6 +124,8 @@ add_custom_microorganisms <- function(x) {
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meet_criteria(x, allow_class = "data.frame")
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stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'."))
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add_MO_lookup_to_AMR_env()
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# remove any extra class/type, such as grouped tbl, or data.table:
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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colnames(x) <- tolower(colnames(x))
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@@ -269,7 +271,11 @@ add_custom_microorganisms <- function(x) {
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#' @export
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clear_custom_microorganisms <- function() {
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n <- nrow(AMR_env$MO_lookup)
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AMR_env$MO_lookup <- create_MO_lookup()
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# reset
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AMR_env$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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@@ -182,6 +182,8 @@ eucast_rules <- function(x,
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
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add_MO_lookup_to_AMR_env()
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if ("custom" %in% rules && is.null(custom_rules)) {
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warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
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immediate = TRUE
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@@ -51,6 +51,8 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
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meet_criteria(string, allow_class = "character")
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
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add_MO_lookup_to_AMR_env()
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if (type == "markdown") {
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before <- "*"
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after <- "*"
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@@ -127,6 +127,8 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
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}
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join_microorganisms <- function(type, x, by, suffix, ...) {
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add_MO_lookup_to_AMR_env()
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if (!is.data.frame(x)) {
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if (pkg_is_available("tibble", also_load = FALSE)) {
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x <- import_fn("tibble", "tibble")(mo = x)
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188
R/mdro.R
188
R/mdro.R
@@ -325,7 +325,7 @@ mdro <- function(x = NULL,
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"No column found as input for `col_mo`, ",
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font_bold(paste0("assuming all rows contain ", font_italic("Mycobacterium tuberculosis"), "."))
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)
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x$mo <- as.mo("Mycobacterium tuberculosis") # consider overkill at all times: AMR_env$MO_lookup[which(AMR_env$MO_lookup$fullname == "Mycobacterium tuberculosis"), "mo", drop = TRUE]
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x$mo <- as.mo("Mycobacterium tuberculosis", keep_synonyms = TRUE)
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col_mo <- "mo"
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}
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stop_if(is.null(col_mo), "`col_mo` must be set")
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@@ -382,120 +382,16 @@ mdro <- function(x = NULL,
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cols_ab <- get_column_abx(
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x = x,
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soft_dependencies = c(
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# [table] 1 (S aureus):
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"GEN",
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"RIF",
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"CPT",
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"OXA",
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"CIP",
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"MFX",
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"SXT",
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"FUS",
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"VAN",
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"TEC",
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"TLV",
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"TGC",
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"CLI",
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"DAP",
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"ERY",
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"LNZ",
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"CHL",
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"FOS",
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"QDA",
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"TCY",
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"DOX",
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"MNO",
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# [table] 1 (S aureus)
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"GEN", "RIF", "CPT", "OXA", "CIP", "MFX", "SXT", "FUS", "VAN", "TEC", "TLV", "TGC", "CLI", "DAP", "ERY", "LNZ", "CHL", "FOS", "QDA", "TCY", "DOX", "MNO",
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# [table] 2 (Enterococcus)
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"GEH",
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"STH",
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"IPM",
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"MEM",
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"DOR",
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"CIP",
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"LVX",
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"MFX",
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"VAN",
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"TEC",
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"TGC",
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"DAP",
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"LNZ",
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"AMP",
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"QDA",
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"DOX",
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"MNO",
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"GEH", "STH", "IPM", "MEM", "DOR", "CIP", "LVX", "MFX", "VAN", "TEC", "TGC", "DAP", "LNZ", "AMP", "QDA", "DOX", "MNO",
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# [table] 3 (Enterobacteriaceae)
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"GEN",
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"TOB",
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"AMK",
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"NET",
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"CPT",
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"TCC",
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"TZP",
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"ETP",
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"IPM",
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"MEM",
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"DOR",
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"CZO",
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"CXM",
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"CTX",
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"CAZ",
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"FEP",
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"FOX",
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"CTT",
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"CIP",
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"SXT",
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"TGC",
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"ATM",
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"AMP",
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"AMC",
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"SAM",
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"CHL",
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"FOS",
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"COL",
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"TCY",
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"DOX",
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"MNO",
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"GEN", "TOB", "AMK", "NET", "CPT", "TCC", "TZP", "ETP", "IPM", "MEM", "DOR", "CZO", "CXM", "CTX", "CAZ", "FEP", "FOX", "CTT", "CIP", "SXT", "TGC", "ATM", "AMP", "AMC", "SAM", "CHL", "FOS", "COL", "TCY", "DOX", "MNO",
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# [table] 4 (Pseudomonas)
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"GEN",
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"TOB",
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"AMK",
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"NET",
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"IPM",
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"MEM",
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"DOR",
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"CAZ",
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"FEP",
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"CIP",
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"LVX",
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"TCC",
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"TZP",
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"ATM",
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"FOS",
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"COL",
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"PLB",
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"GEN", "TOB", "AMK", "NET", "IPM", "MEM", "DOR", "CAZ", "FEP", "CIP", "LVX", "TCC", "TZP", "ATM", "FOS", "COL", "PLB",
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# [table] 5 (Acinetobacter)
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"GEN",
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"TOB",
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"AMK",
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"NET",
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"IPM",
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"MEM",
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"DOR",
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"CIP",
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"LVX",
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"TZP",
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"TCC",
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"CTX",
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"CRO",
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"CAZ",
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"FEP",
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"SXT",
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"SAM",
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"COL",
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"PLB",
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"TCY",
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"DOX",
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"MNO"
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"GEN", "TOB", "AMK", "NET", "IPM", "MEM", "DOR", "CIP", "LVX", "TZP", "TCC", "CTX", "CRO", "CAZ", "FEP", "SXT", "SAM", "COL", "PLB", "TCY", "DOX", "MNO"
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),
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verbose = verbose,
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info = info,
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@@ -506,30 +402,7 @@ mdro <- function(x = NULL,
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} else if (guideline$code == "eucast3.2") {
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cols_ab <- get_column_abx(
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x = x,
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soft_dependencies = c(
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"AMP",
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"AMX",
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"CIP",
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"DAL",
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"DAP",
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"ERV",
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"FDX",
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"GEN",
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"LNZ",
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"MEM",
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"MTR",
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"OMC",
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"ORI",
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"PEN",
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"QDA",
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"RIF",
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"TEC",
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"TGC",
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"TLV",
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"TOB",
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"TZD",
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"VAN"
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),
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soft_dependencies = c("AMP", "AMX", "CIP", "DAL", "DAP", "ERV", "FDX", "GEN", "LNZ", "MEM", "MTR", "OMC", "ORI", "PEN", "QDA", "RIF", "TEC", "TGC", "TLV", "TOB", "TZD", "VAN"),
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verbose = verbose,
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info = info,
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only_sir_columns = only_sir_columns,
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@@ -539,30 +412,7 @@ mdro <- function(x = NULL,
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} else if (guideline$code == "eucast3.3") {
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cols_ab <- get_column_abx(
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x = x,
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soft_dependencies = c(
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"AMP",
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"AMX",
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"CIP",
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"DAL",
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"DAP",
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"ERV",
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"FDX",
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"GEN",
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"LNZ",
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"MEM",
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"MTR",
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"OMC",
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"ORI",
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"PEN",
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"QDA",
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"RIF",
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"TEC",
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"TGC",
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"TLV",
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"TOB",
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"TZD",
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"VAN"
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),
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soft_dependencies = c("AMP", "AMX", "CIP", "DAL", "DAP", "ERV", "FDX", "GEN", "LNZ", "MEM", "MTR", "OMC", "ORI", "PEN", "QDA", "RIF", "TEC", "TGC", "TLV", "TOB", "TZD", "VAN"),
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verbose = verbose,
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info = info,
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only_sir_columns = only_sir_columns,
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@@ -572,16 +422,7 @@ mdro <- function(x = NULL,
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} else if (guideline$code == "tb") {
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cols_ab <- get_column_abx(
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x = x,
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soft_dependencies = c(
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"CAP",
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"ETH",
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"GAT",
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"INH",
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"PZA",
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"RIF",
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"RIB",
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"RFP"
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),
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soft_dependencies = c("CAP", "ETH", "GAT", "INH", "PZA", "RIF", "RIB", "RFP"),
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verbose = verbose,
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info = info,
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only_sir_columns = only_sir_columns,
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@@ -591,14 +432,7 @@ mdro <- function(x = NULL,
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} else if (guideline$code == "mrgn") {
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cols_ab <- get_column_abx(
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x = x,
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soft_dependencies = c(
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"PIP",
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"CTX",
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"CAZ",
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"IPM",
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"MEM",
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"CIP"
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),
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soft_dependencies = c("PIP", "CTX", "CAZ", "IPM", "MEM", "CIP"),
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verbose = verbose,
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info = info,
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only_sir_columns = only_sir_columns,
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12
R/mo.R
12
R/mo.R
@@ -164,6 +164,8 @@ as.mo <- function(x,
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language <- validate_language(language)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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add_MO_lookup_to_AMR_env()
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if (tryCatch(all(x %in% c(AMR_env$MO_lookup$mo, NA)) &&
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isFALSE(Becker) &&
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isFALSE(Lancefield), error = function(e) FALSE)) {
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@@ -492,6 +494,7 @@ mo_uncertainties <- function() {
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#' @rdname as.mo
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#' @export
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mo_renamed <- function() {
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add_MO_lookup_to_AMR_env()
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x <- AMR_env$mo_renamed
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x$new <- synonym_mo_to_accepted_mo(x$old)
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@@ -547,6 +550,7 @@ mo_cleaning_regex <- function() {
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# will be exported using s3_register() in R/zzz.R
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pillar_shaft.mo <- function(x, ...) {
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add_MO_lookup_to_AMR_env()
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out <- format(x)
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# grey out the kingdom (part until first "_")
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out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
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@@ -664,6 +668,7 @@ get_skimmers.mo <- function(column) {
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#' @export
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#' @noRd
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print.mo <- function(x, print.shortnames = FALSE, ...) {
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add_MO_lookup_to_AMR_env()
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cat("Class 'mo'\n")
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x_names <- names(x)
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if (is.null(x_names) & print.shortnames == TRUE) {
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@@ -704,6 +709,7 @@ summary.mo <- function(object, ...) {
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#' @export
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#' @noRd
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as.data.frame.mo <- function(x, ...) {
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add_MO_lookup_to_AMR_env()
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if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
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||||
warning_(
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||||
"The data contains old MO codes (from a previous AMR package version). ",
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||||
@@ -741,6 +747,7 @@ as.data.frame.mo <- function(x, ...) {
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y <- NextMethod()
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||||
attributes(y) <- attributes(i)
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||||
# must only contain valid MOs
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||||
add_MO_lookup_to_AMR_env()
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||||
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
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||||
}
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||||
#' @method [[<- mo
|
||||
@@ -750,6 +757,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
y <- NextMethod()
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||||
attributes(y) <- attributes(i)
|
||||
# must only contain valid MOs
|
||||
add_MO_lookup_to_AMR_env()
|
||||
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
|
||||
}
|
||||
#' @method c mo
|
||||
@@ -759,6 +767,7 @@ c.mo <- function(...) {
|
||||
x <- list(...)[[1L]]
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
add_MO_lookup_to_AMR_env()
|
||||
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
|
||||
}
|
||||
|
||||
@@ -788,6 +797,8 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
cat(word_wrap("No uncertainties to show. Only uncertainties of the last call of `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue))
|
||||
return(invisible(NULL))
|
||||
}
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
|
||||
if (has_colour()) {
|
||||
@@ -1049,6 +1060,7 @@ replace_old_mo_codes <- function(x, property) {
|
||||
# B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
|
||||
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% AMR_env$MO_lookup$mo
|
||||
if (any(ind, na.rm = TRUE)) {
|
||||
add_MO_lookup_to_AMR_env()
|
||||
# get the ones that match
|
||||
affected <- x[ind]
|
||||
affected_unique <- unique(affected)
|
||||
|
||||
@@ -84,6 +84,8 @@ mo_matching_score <- function(x, n) {
|
||||
meet_criteria(x, allow_class = c("character", "data.frame", "list"))
|
||||
meet_criteria(n, allow_class = "character")
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
x <- parse_and_convert(x)
|
||||
# no dots and other non-whitespace characters
|
||||
x <- gsub("[^a-zA-Z0-9 \\(\\)]+", "", x)
|
||||
|
||||
@@ -417,6 +417,8 @@ mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = get
|
||||
language <- validate_language(language)
|
||||
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
|
||||
metadata <- get_mo_uncertainties()
|
||||
|
||||
@@ -725,6 +727,8 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
language <- validate_language(language)
|
||||
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
|
||||
metadata <- get_mo_uncertainties()
|
||||
@@ -811,6 +815,8 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
language <- validate_language(language)
|
||||
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...)
|
||||
metadata <- get_mo_uncertainties()
|
||||
@@ -847,7 +853,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
|
||||
x <- find_mo_col(fn = "mo_property")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR_env$MO_lookup))
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms))
|
||||
language <- validate_language(language)
|
||||
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
|
||||
|
||||
@@ -855,7 +861,8 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
|
||||
}
|
||||
|
||||
mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ...) {
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]),
|
||||
|
||||
@@ -261,6 +261,8 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
|
||||
}
|
||||
|
||||
check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_on_error = TRUE) {
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
if (paste(deparse(substitute(x)), collapse = "") == "get_mo_source()") {
|
||||
return(TRUE)
|
||||
}
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@@ -95,6 +95,7 @@ vec_cast.character.mo <- function(x, to, ...) {
|
||||
as.character(x)
|
||||
}
|
||||
vec_cast.mo.character <- function(x, to, ...) {
|
||||
add_MO_lookup_to_AMR_env()
|
||||
return_after_integrity_check(x, "microorganism code", as.character(AMR_env$MO_lookup$mo))
|
||||
}
|
||||
|
||||
|
||||
40
R/zzz.R
40
R/zzz.R
@@ -181,11 +181,10 @@ if (utf8_supported && !is_latex) {
|
||||
try(loadNamespace("tibble"), silent = TRUE)
|
||||
}
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
# reference data - they have additional to improve algorithm speed
|
||||
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
|
||||
AMR_env$AB_lookup <- create_AB_lookup()
|
||||
AMR_env$AV_lookup <- create_AV_lookup()
|
||||
AMR_env$MO_lookup <- create_MO_lookup()
|
||||
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
|
||||
AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
|
||||
}
|
||||
|
||||
.onAttach <- function(lib, pkg) {
|
||||
@@ -208,36 +207,3 @@ if (utf8_supported && !is_latex) {
|
||||
}, error = function(e) packageStartupMessage("Failed: ", e$message))
|
||||
}
|
||||
}
|
||||
|
||||
# Helper functions --------------------------------------------------------
|
||||
|
||||
create_AB_lookup <- function() {
|
||||
cbind(AMR::antibiotics, AB_LOOKUP)
|
||||
}
|
||||
|
||||
create_AV_lookup <- function() {
|
||||
cbind(AMR::antivirals, AV_LOOKUP)
|
||||
}
|
||||
|
||||
create_MO_lookup <- function() {
|
||||
MO_lookup <- AMR::microorganisms
|
||||
|
||||
MO_lookup$kingdom_index <- NA_real_
|
||||
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
|
||||
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
|
||||
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
|
||||
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
|
||||
# all the rest
|
||||
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
|
||||
|
||||
if (length(MO_FULLNAME_LOWER) != nrow(MO_lookup)) {
|
||||
packageStartupMessage("fullname_lower not same size - applied tolower(), update sysdata.rda!")
|
||||
MO_lookup$fullname_lower <- tolower(MO_lookup$fullname)
|
||||
} else {
|
||||
MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
|
||||
}
|
||||
MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
|
||||
MO_lookup$species_first <- tolower(substr(MO_lookup$species, 1, 1)) # tolower for groups (Streptococcus, Salmonella)
|
||||
MO_lookup$subspecies_first <- tolower(substr(MO_lookup$subspecies, 1, 1)) # tolower for Salmonella serovars
|
||||
MO_lookup
|
||||
}
|
||||
|
||||
@@ -144,21 +144,6 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
]
|
||||
}
|
||||
}
|
||||
create_MO_fullname_lower <- function() {
|
||||
AMR_env$MO_lookup <- AMR::microorganisms
|
||||
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
|
||||
AMR_env$MO_lookup$fullname_lower <- tolower(trimws(paste(
|
||||
AMR_env$MO_lookup$genus,
|
||||
AMR_env$MO_lookup$species,
|
||||
AMR_env$MO_lookup$subspecies
|
||||
)))
|
||||
ind <- AMR_env$MO_lookup$genus == "" | grepl("^[(]unknown ", AMR_env$MO_lookup$fullname, perl = TRUE)
|
||||
AMR_env$MO_lookup[ind, "fullname_lower"] <- tolower(AMR_env$MO_lookup[ind, "fullname", drop = TRUE])
|
||||
AMR_env$MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", AMR_env$MO_lookup$fullname_lower, perl = TRUE))
|
||||
# special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
|
||||
AMR_env$MO_lookup$fullname_lower[which(AMR_env$MO_lookup$subspecies %like_case% "^[A-Z]")] <- gsub(" enterica ", " ", AMR_env$MO_lookup$fullname_lower[which(AMR_env$MO_lookup$subspecies %like_case% "^[A-Z]")], fixed = TRUE)
|
||||
AMR_env$MO_lookup$fullname_lower
|
||||
}
|
||||
MO_CONS <- create_species_cons_cops("CoNS")
|
||||
MO_COPS <- create_species_cons_cops("CoPS")
|
||||
MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptococcus" &
|
||||
@@ -166,7 +151,6 @@ MO_STREP_ABCG <- AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$genus == "Streptoc
|
||||
"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
|
||||
"group A", "group B", "group C", "group G"
|
||||
))]
|
||||
MO_FULLNAME_LOWER <- create_MO_fullname_lower()
|
||||
MO_PREVALENT_GENERA <- c(
|
||||
"Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
|
||||
"Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
|
||||
@@ -298,7 +282,6 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
MO_STREP_ABCG,
|
||||
MO_FULLNAME_LOWER,
|
||||
MO_PREVALENT_GENERA,
|
||||
AB_LOOKUP,
|
||||
AV_LOOKUP,
|
||||
|
||||
@@ -28,7 +28,7 @@ A BibTeX entry for LaTeX users is:
|
||||
\description{
|
||||
Welcome to the \code{AMR} package.
|
||||
|
||||
The \code{AMR} package is a \href{https://msberends.github.io/AMR#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
|
||||
The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
|
||||
|
||||
This work was published in the Journal of Statistical Software (Volume 104(3); \href{https://doi.org/10.18637/jss.v104.i03}{DOI 10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\href{https://doi.org/10.33612/diss.177417131}{DOI 10.33612/diss.177417131} and \href{https://doi.org/10.33612/diss.192486375}{DOI 10.33612/diss.192486375}).
|
||||
|
||||
|
||||
Reference in New Issue
Block a user