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as.mo
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2
NEWS.md
2
NEWS.md
@ -9,7 +9,7 @@
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* New functions `set_mo_source()` and `get_mo_source()` to use your own predefined MO codes as input for `as.mo()` and consequently all `mo_*` functions
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* Support for the upcoming [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
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* New function `guess_ab_col()` to find an antibiotic column in a table
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* New function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values.
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* New function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 10 uncoerced values and will refer to `mo_failures()`.
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* New function `mo_renamed()` to get a list of all returned values from `as.mo()` that have had taxonomic renaming
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* New function `age()` to calculate the (patients) age in years
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* New function `age_groups()` to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.
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63
R/mo.R
63
R/mo.R
@ -316,18 +316,21 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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next
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}
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# no nonsense text
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if (toupper(x_trimmed[i]) %in% c('OTHER', 'NONE', 'UNKNOWN')) {
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x[i] <- NA_character_
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failures <- c(failures, x_backup[i])
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next
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}
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# translate known trivial abbreviations to genus + species ----
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if (!is.na(x_trimmed[i])) {
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if (toupper(x_trimmed[i]) == 'MRSA'
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| toupper(x_trimmed[i]) == 'MSSA'
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| toupper(x_trimmed[i]) == 'VISA'
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| toupper(x_trimmed[i]) == 'VRSA') {
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if (toupper(x_trimmed[i]) %in% c('MRSA', 'MSSA', 'VISA', 'VRSA')) {
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x[i] <- microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'MRSE'
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| toupper(x_trimmed[i]) == 'MSSE') {
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if (toupper(x_trimmed[i]) %in% c('MRSE', 'MSSE')) {
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x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
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next
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}
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@ -508,7 +511,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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}
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# try fullname without start and stop regex, to also find subspecies ----
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# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
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# like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
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found <- microorganisms.prevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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@ -579,7 +582,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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}
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# try fullname without start and stop regex, to also find subspecies ----
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# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
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# like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
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found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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@ -627,8 +630,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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} else {
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x <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
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}
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warning(red(paste0('UNCERTAIN - "',
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a.x_backup, '" -> ', italic(found[1, name]))),
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warning(red(paste0('(UNCERTAIN) "',
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a.x_backup, '" >> ', italic(found[1, name]), " (TSN ", found[1, tsn], ")")),
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call. = FALSE, immediate. = FALSE)
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notes <<- c(notes,
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renamed_note(name_old = found[1, name],
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@ -644,9 +647,10 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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a.x_backup_stripped <- trimws(gsub(" ", " ", a.x_backup_stripped, fixed = TRUE))
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found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, clear_options = FALSE, allow_uncertain = FALSE)))
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if (!is.na(found) & nchar(b.x_trimmed) >= 6) {
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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warning(red(paste0('UNCERTAIN - "',
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a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
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warning(red(paste0('(UNCERTAIN) "',
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a.x_backup, '" >> ', italic(microorganismsDT[mo == found_result[1L], fullname][[1]]), " (", found_result[1L], ")")),
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call. = FALSE, immediate. = FALSE)
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return(found[1L])
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}
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@ -658,9 +662,10 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")
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found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE, allow_uncertain = FALSE)))
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if (!is.na(found)) {
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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warning(red(paste0('UNCERTAIN - "',
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a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
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warning(red(paste0('(UNCERTAIN) "',
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a.x_backup, '" >> ', italic(microorganismsDT[mo == found_result[1L], fullname][[1]]), " (", found_result[1L], ")")),
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call. = FALSE, immediate. = FALSE)
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return(found[1L])
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}
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@ -668,11 +673,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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}
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# (4) not yet implemented taxonomic changes in ITIS
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found <- suppressMessages(suppressWarnings(exec_as.mo(temp_changes(b.x_trimmed), clear_options = FALSE, allow_uncertain = FALSE)))
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found <- suppressMessages(suppressWarnings(exec_as.mo(TEMPORARY_TAXONOMY(b.x_trimmed), clear_options = FALSE, allow_uncertain = FALSE)))
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if (!is.na(found)) {
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found_result <- found
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found <- microorganismsDT[mo == found, ..property][[1]]
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warning(red(paste0('UNCERTAIN - "',
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a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
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warning(red(paste0('(UNCERTAIN) "',
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a.x_backup, '" >> ', italic(microorganismsDT[mo == found_result[1L], fullname][[1]]), " (", found_result[1L], ")")),
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call. = FALSE, immediate. = FALSE)
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return(found[1L])
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}
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@ -697,17 +703,19 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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failures <- failures[!failures %in% c(NA, NULL, NaN)]
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if (length(failures) > 0) {
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options(mo_failures = sort(unique(failures)))
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if (n_distinct(failures) > 25) {
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warning(n_distinct(failures), " different values could not be coerced to a valid MO code. See mo_failures() to review them.",
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call. = FALSE)
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} else {
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warning(red(paste0("These ", length(failures) , " values could not be coerced to a valid MO code: ",
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paste('"', unique(failures), '"', sep = "", collapse = ', '),
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". See mo_failures() to review them.")),
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plural <- ""
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if (n_distinct(failures) > 1) {
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plural <- "s"
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}
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msg <- paste0("\n", n_distinct(failures), " unique value", plural, " could not be coerced to a valid MO code")
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if (n_distinct(failures) <= 10) {
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msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ', '))
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}
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msg <- paste0(msg, ". Use mo_failures() to review failured input.")
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warning(red(msg),
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call. = FALSE,
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immediate. = TRUE) # thus will always be shown, even if >= warnings
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}
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}
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# Becker ----
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if (Becker == TRUE | Becker == "all") {
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@ -792,8 +800,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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x
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}
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temp_changes <- function(x) {
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TEMPORARY_TAXONOMY <- function(x) {
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x[x %like% 'Cutibacterium'] <- gsub('Cutibacterium', 'Propionibacterium', x[x %like% 'Cutibacterium'])
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x
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}
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#' @importFrom crayon blue italic
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@ -815,7 +824,7 @@ renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "", mo = ""
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}
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msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
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msg <- gsub("et al.", italic("et al."), msg)
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msg_plain <- paste0(name_old, ref_old, " -> ", name_new, ref_new)
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msg_plain <- paste0(name_old, ref_old, " >> ", name_new, ref_new)
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msg_plain <- c(getOption("mo_renamed", character(0)), msg_plain)
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options(mo_renamed = sort(msg_plain))
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return(blue(paste("Note:", msg)))
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@ -21,9 +21,6 @@
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# ==================================================================== #
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*/
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// Keep GitLab as original source
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// window.location.replace("github", "gitlab");
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// Add updated Font Awesome 5.6.3 library
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$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">');
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@ -34,7 +31,7 @@ $( document ).ready(function() {
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var url_old = window.location.href;
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var url_new = url_old.replace("github", "gitlab");
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if (url_old != url_new) {
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window.location.replace(url);
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window.location.replace(url_new);
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}
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$('footer').html('<p>' +
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@ -47,4 +44,4 @@ $( document ).ready(function() {
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$('.template-reference-index h1').text('Manual');
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});
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$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR','*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");
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$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");
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@ -238,7 +238,7 @@
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<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
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<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
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<li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
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<li>New function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 25 uncoerced values.</li>
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<li>New function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 10 uncoerced values and will refer to <code><a href="../reference/mo_failures.html">mo_failures()</a></code>.</li>
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<li>New function <code><a href="../reference/mo_renamed.html">mo_renamed()</a></code> to get a list of all returned values from <code><a href="../reference/as.mo.html">as.mo()</a></code> that have had taxonomic renaming</li>
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<li>New function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</li>
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<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
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@ -21,9 +21,6 @@
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# ==================================================================== #
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*/
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// Keep GitLab as original source
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// window.location.replace("github", "gitlab");
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// Add updated Font Awesome 5.6.3 library
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$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">');
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@ -34,7 +31,7 @@ $( document ).ready(function() {
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var url_old = window.location.href;
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var url_new = url_old.replace("github", "gitlab");
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if (url_old != url_new) {
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window.location.replace(url);
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window.location.replace(url_new);
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}
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$('footer').html('<p>' +
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@ -47,4 +44,4 @@ $( document ).ready(function() {
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$('.template-reference-index h1').text('Manual');
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});
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$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR','*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");
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$('head').append("<!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.gitlab.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s); })();</script><!-- End Matomo Code -->");
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