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abname improvement, small fixes
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.2.0.9023
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Date: 2018-08-12
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Date: 2018-08-13
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -37,10 +37,7 @@ Authors@R: c(
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family = "Sinha",
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email = "b.sinha@umcg.nl",
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role = "ths",
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comment = c(ORCID = "0000-0003-1634-0010")),
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person(
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family = "University of Groningen",
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role = "uvp"))
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comment = c(ORCID = "0000-0003-1634-0010")))
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Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR)
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of microbial isolates, by using new S3 classes and applying EUCAST expert rules
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on antibiograms according to Leclercq (2013)
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@ -54,7 +51,6 @@ Imports:
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dplyr (>= 0.7.0),
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xml2 (>= 1.0.0),
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knitr (>= 1.0.0),
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Rcpp (>= 0.12.14),
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readr,
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rvest (>= 0.3.2),
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tibble
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5
NEWS.md
5
NEWS.md
@ -35,13 +35,14 @@
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* Possibility to globally set the default for the amount of items to print, with `options(max.print.freq = n)` where *n* is your preset value
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#### Changed
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* Improvements for forcasting with `resistance_predict` and added more examples
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* More antibiotics for EUCAST rules
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* Improvements for forecasting with `resistance_predict` and added more examples
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* More antibiotics added as parameters for EUCAST rules
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* Updated version of the `septic_patients` data set to better reflect the reality
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* Pretty printing for tibbles removed as it is not really the scope of this package
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* Printing of `mic` and `rsi` classes now returns all values - use `freq` to check distributions
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* Improved speed of key antibiotics comparison for determining first isolates
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* Column names for the `key_antibiotics` function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs
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* Speed improvement for the `abname` function
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* `%like%` now supports multiple patterns
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* Frequency tables are now actual `data.frame`s with altered console printing to make it look like a frequency table. Because of this, the parameter `toConsole` is not longer needed.
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* Fix for `freq` where the class of an item would be lost
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163
R/abname.R
Normal file
163
R/abname.R
Normal file
@ -0,0 +1,163 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Name of an antibiotic
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#'
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#' Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{antibiotics}}.
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#' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
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#' @param from,to type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be searched using \code{\link{guess_atc}}.
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#' @param textbetween text to put between multiple returned texts
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#' @param tolower return output as lower case with function \code{\link{tolower}}.
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#' @keywords ab antibiotics
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#' @source \code{\link{antibiotics}}
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#' @export
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#' @importFrom dplyr %>% pull
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#' @examples
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#' abname("AMCL")
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#' # "amoxicillin and enzyme inhibitor"
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#'
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#' # It is quite flexible at default (having `from = "guess"`)
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#' abname(c("amox", "J01CA04", "Trimox", "dispermox", "Amoxil"))
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#' # "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"
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#'
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#' # Multiple antibiotics can be combined with "+".
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#' # The second antibiotic will be set to lower case when `tolower` was not set:
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#' abname("AMCL+GENT", textbetween = "/")
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#' # "amoxicillin and enzyme inhibitor/gentamicin"
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#'
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#' abname(c("AMCL", "GENT"))
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#' # "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"
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#'
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#' abname("AMCL", to = "trivial_nl")
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#' # "Amoxicilline/clavulaanzuur"
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#'
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#' abname("AMCL", to = "atc")
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#' # "J01CR02"
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#'
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#' # specific codes for University Medical Center Groningen (UMCG):
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#' abname("J01CR02", from = "atc", to = "umcg")
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#' # "AMCL"
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abname <- function(abcode,
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from = c("guess", "atc", "molis", "umcg"),
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to = 'official',
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textbetween = ' + ',
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tolower = FALSE) {
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if (length(to) != 1L) {
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stop('`to` must be of length 1', call. = FALSE)
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}
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if (to == "atc") {
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return(guess_atc(abcode))
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}
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#antibiotics <- AMR::antibiotics
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abx <- AMR::antibiotics
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from <- from[1]
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# if (from == "guess") {
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# for (i in 1:3) {
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# if (abcode[1] %in% (antibiotics %>% pull(i))) {
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# from <- colnames(antibiotics)[i]
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# }
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# }
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# if (from == "guess") {
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# from <- "umcg"
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# }
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# }
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colnames(abx) <- colnames(abx) %>% tolower()
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from <- from %>% tolower()
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to <- to %>% tolower()
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if (!(from %in% colnames(abx) | from == "guess") |
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!to %in% colnames(abx)) {
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stop(paste0('Invalid `from` or `to`. Choose one of ',
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colnames(abx) %>% paste(collapse = ", "), '.'), call. = FALSE)
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}
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abcode <- as.character(abcode)
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abcode.bak <- abcode
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for (i in 1:length(abcode)) {
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if (abcode[i] %like% "[+]") {
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# support for multiple ab's with +
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parts <- trimws(strsplit(abcode[i], split = "+", fixed = TRUE)[[1]])
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ab1 <- abname(parts[1], from = from, to = to)
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ab2 <- abname(parts[2], from = from, to = to)
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if (missing(tolower)) {
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ab2 <- tolower(ab2)
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}
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abcode[i] <- paste0(ab1, textbetween, ab2)
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next
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}
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if (from %in% c("atc", "guess")) {
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if (abcode[i] %in% abx$atc) {
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abcode[i] <- abx[which(abx$atc == abcode[i]),] %>% pull(to)
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next
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}
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}
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if (from %in% c("molis", "guess")) {
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if (abcode[i] %in% abx$molis) {
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abcode[i] <- abx[which(abx$molis == abcode[i]),] %>% pull(to)
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next
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}
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}
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if (from %in% c("umcg", "guess")) {
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if (abcode[i] %in% abx$umcg) {
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abcode[i] <- abx[which(abx$umcg == abcode[i]),] %>% pull(to)
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next
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}
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}
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if (from %in% c("trade_name", "guess")) {
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if (abcode[i] %in% abx$trade_name) {
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abcode[i] <- abx[which(abx$trade_name == abcode[i]),] %>% pull(to)
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next
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}
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if (sum(abx$trade_name %like% abcode[i]) > 0) {
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abcode[i] <- abx[which(abx$trade_name %like% abcode[i]),] %>% pull(to)
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next
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}
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}
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if (from != "guess") {
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# when not found, try any `from`
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abcode[i] <- abx[which(abx[,from] == abcode[i]),] %>% pull(to) %>% .[1]
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}
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# when nothing found, try first chars of official name
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# if (is.na(abcode[i])) {
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# abcode[i] <- antibiotics %>%
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# filter(official %like% paste0('^', abcode.bak[i])) %>%
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# pull(to) %>%
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# .[1]
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# next
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# }
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if (is.na(abcode[i]) | length(abcode[i] == 0)) {
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abcode[i] <- abcode.bak[i]
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warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE)
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}
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}
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if (tolower == TRUE) {
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abcode <- abcode %>% tolower()
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}
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abcode
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}
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133
R/atc.R
133
R/atc.R
@ -203,139 +203,6 @@ atc_ddd <- function(atc_code, ...) {
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atc_property(atc_code = atc_code, property = "ddd", ...)
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}
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#' Name of an antibiotic
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#'
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#' Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{antibiotics}}.
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#' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
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#' @param from,to type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be search using \code{\link{guess_atc}}.
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#' @param textbetween text to put between multiple returned texts
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#' @param tolower return output as lower case with function \code{\link{tolower}}.
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#' @keywords ab antibiotics
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#' @source \code{\link{antibiotics}}
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#' @export
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#' @importFrom dplyr %>% filter select slice
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#' @examples
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#' abname("AMCL")
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#' # "amoxicillin and enzyme inhibitor"
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#'
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#' abname("AMCL+GENT")
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#' # "amoxicillin and enzyme inhibitor + gentamicin"
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#'
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#' abname(c("AMCL", "GENT"))
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#' # "amoxicillin and enzyme inhibitor" "gentamicin"
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#'
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#' abname("AMCL", to = "trivial_nl")
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#' # "Amoxicilline/clavulaanzuur"
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#'
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#' abname("AMCL", to = "atc")
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#' # "J01CR02"
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#'
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#' abname("J01CR02", from = "atc", to = "umcg")
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#' # "AMCL"
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abname <- function(abcode, from = c("guess", "atc", "molis", "umcg"), to = 'official', textbetween = ' + ', tolower = FALSE) {
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if (length(to) != 1L) {
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stop('`to` must be of length 1', call. = FALSE)
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}
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if (to == "atc") {
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return(guess_atc(abcode))
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}
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antibiotics <- AMR::antibiotics
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from <- from[1]
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if (from == "guess") {
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for (i in 1:3) {
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if (abcode[1] %in% (antibiotics %>% pull(i))) {
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from <- colnames(antibiotics)[i]
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}
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}
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if (from == "guess") {
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from <- "umcg"
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}
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}
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colnames(antibiotics) <- colnames(antibiotics) %>% tolower()
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from <- from %>% tolower()
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to <- to %>% tolower()
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if (!from %in% colnames(antibiotics) |
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!to %in% colnames(antibiotics)) {
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stop(paste0('Invalid `from` or `to`. Choose one of ',
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colnames(antibiotics) %>% paste(collapse = ", "), '.'), call. = FALSE)
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}
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abcode <- as.character(abcode)
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abcode.bak <- abcode
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for (i in 1:length(abcode)) {
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abcode[i] <- abcode[i]
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if (!grepl('+', abcode[i], fixed = TRUE) & !grepl(' en ', abcode[i], fixed = TRUE)) {
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# only 1 drug
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if (abcode[i] %in% (antibiotics %>% pull(from))) {
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abcode[i] <-
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antibiotics %>%
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filter(.[, from] == abcode[i]) %>%
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select(to) %>%
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slice(1) %>%
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as.character()
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} else {
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# not found
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abcode[i] <- NA
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}
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} else {
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# more than 1 drug
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if (grepl('+', abcode[i], fixed = TRUE)) {
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abcode.group <-
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strsplit(abcode[i], '+', fixed = TRUE) %>%
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unlist() %>%
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trimws('both')
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} else if (grepl(' en ', abcode[i], fixed = TRUE)) {
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abcode.group <-
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strsplit(abcode[i], ' en ', fixed = TRUE) %>%
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unlist() %>%
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trimws('both')
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} else {
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warning('Invalid concat.')
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abcode[i] <- NA
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next
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}
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for (j in 1:length(abcode.group)) {
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abcode.group[j] <-
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antibiotics %>%
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filter(.[, from] == abcode.group[j]) %>%
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select(to) %>%
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slice(1) %>%
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as.character()
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if (j > 1 & to %in% c('official', 'trivial_nl')) {
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abcode.group[j] <- abcode.group[j] %>% tolower()
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}
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}
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abcode[i] <- paste(abcode.group, collapse = textbetween)
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}
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# when nothing found, try first chars of official name
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if (is.na(abcode[i])) {
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abcode[i] <- antibiotics %>%
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filter(official %like% paste0('^', abcode.bak[i])) %>%
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pull(to) %>%
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.[1]
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}
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if (is.na(abcode[i])) {
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warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE)
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}
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}
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if (tolower == TRUE) {
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abcode <- abcode %>% tolower()
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}
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abcode
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}
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#' Find ATC code based on antibiotic property
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#'
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@ -71,7 +71,7 @@
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#' select(hospital_id, amox, cipr) %>%
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#' group_by(hospital_id) %>%
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#' ggplot_rsi() +
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#' facet_grid("hospital_id") +
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#' facet_wrap("hospital_id", nrow = 1) +
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#' labs(title = "AMR of Amoxicillin And Ciprofloxacine Per Hospital")
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ggplot_rsi <- function(data,
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position = "stack",
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17
man/abname.Rd
Executable file → Normal file
17
man/abname.Rd
Executable file → Normal file
@ -1,5 +1,5 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/atc.R
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% Please edit documentation in R/abname.R
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\name{abname}
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\alias{abname}
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\title{Name of an antibiotic}
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@ -13,7 +13,7 @@ abname(abcode, from = c("guess", "atc", "molis", "umcg"),
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\arguments{
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\item{abcode}{a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}}
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\item{from, to}{type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be search using \code{\link{guess_atc}}.}
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\item{from, to}{type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be searched using \code{\link{guess_atc}}.}
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\item{textbetween}{text to put between multiple returned texts}
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@ -26,11 +26,17 @@ Convert antibiotic codes (from a laboratory information system like MOLIS or GLI
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abname("AMCL")
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# "amoxicillin and enzyme inhibitor"
|
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abname("AMCL+GENT")
|
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# "amoxicillin and enzyme inhibitor + gentamicin"
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# It is quite flexible at default (having `from = "guess"`)
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abname(c("amox", "J01CA04", "Trimox", "dispermox", "Amoxil"))
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# "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"
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# Multiple antibiotics can be combined with "+".
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# The second antibiotic will be set to lower case when `tolower` was not set:
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abname("AMCL+GENT", textbetween = "/")
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# "amoxicillin and enzyme inhibitor/gentamicin"
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abname(c("AMCL", "GENT"))
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# "amoxicillin and enzyme inhibitor" "gentamicin"
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# "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"
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abname("AMCL", to = "trivial_nl")
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# "Amoxicilline/clavulaanzuur"
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@ -38,6 +44,7 @@ abname("AMCL", to = "trivial_nl")
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abname("AMCL", to = "atc")
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# "J01CR02"
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# specific codes for University Medical Center Groningen (UMCG):
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abname("J01CR02", from = "atc", to = "umcg")
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# "AMCL"
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}
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@ -84,6 +84,6 @@ septic_patients \%>\%
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select(hospital_id, amox, cipr) \%>\%
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group_by(hospital_id) \%>\%
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ggplot_rsi() +
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facet_grid("hospital_id") +
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facet_wrap("hospital_id", nrow = 1) +
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labs(title = "AMR of Amoxicillin And Ciprofloxacine Per Hospital")
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}
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||||
19
tests/testthat/test-abname.R
Normal file
19
tests/testthat/test-abname.R
Normal file
@ -0,0 +1,19 @@
|
||||
context("abname.R")
|
||||
|
||||
test_that("abname works", {
|
||||
expect_equal(abname("AMOX"), "Amoxicillin")
|
||||
expect_equal(abname(c("AMOX", "GENT")), c("Amoxicillin", "Gentamicin"))
|
||||
expect_equal(abname(c("AMOX+GENT")), "Amoxicillin + gentamicin")
|
||||
expect_equal(abname("AMOX", from = 'umcg'), "Amoxicillin")
|
||||
expect_equal(abname("amox", from = 'molis', tolower = TRUE), "amoxicillin")
|
||||
expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
|
||||
expect_equal(abname(c("amox", "J01CA04", "Trimox", "dispermox", "Amoxil")),
|
||||
rep("Amoxicillin", 5))
|
||||
expect_equal(abname("AMOX", to = 'atc'), "J01CA04")
|
||||
|
||||
expect_error(abname("AMOX", to = c(1:3)))
|
||||
expect_error(abname("AMOX", to = "test"))
|
||||
expect_warning(abname("TEST
|
||||
"))
|
||||
expect_warning(abname("AMOX or GENT"))
|
||||
})
|
||||
@ -4,7 +4,6 @@ test_that("atc_property works", {
|
||||
if (!is.null(curl::nslookup("www.whocc.no", error = FALSE))) {
|
||||
expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
|
||||
expect_equal(atc_property("J01CA04", property = "unit"), "g")
|
||||
|
||||
expect_equal(atc_property("J01CA04", property = "DDD"),
|
||||
atc_ddd("J01CA04"))
|
||||
|
||||
@ -19,22 +18,6 @@ test_that("atc_property works", {
|
||||
}
|
||||
})
|
||||
|
||||
test_that("abname works", {
|
||||
expect_equal(abname("AMOX"), "Amoxicillin")
|
||||
expect_equal(abname(c("AMOX", "GENT")), c("Amoxicillin", "Gentamicin"))
|
||||
expect_equal(abname(c("AMOX+GENT")), "Amoxicillin + gentamicin")
|
||||
expect_equal(abname("AMOX", from = 'umcg'), "Amoxicillin")
|
||||
expect_equal(abname("amox", from = 'molis', tolower = TRUE), "amoxicillin")
|
||||
expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
|
||||
expect_equal(abname("AMOX", to = 'atc'), "J01CA04")
|
||||
expect_equal(abname("AMOX en GENT"), "Amoxicillin + gentamicin")
|
||||
expect_error(abname("AMOX", to = c(1:3)))
|
||||
expect_error(abname("AMOX", to = "test"))
|
||||
expect_warning(abname("TEST
|
||||
"))
|
||||
expect_warning(abname("AMOX or GENT"))
|
||||
})
|
||||
|
||||
test_that("guess_atc works", {
|
||||
expect_equal(guess_atc(c("J01FA01",
|
||||
"Erythromycin",
|
||||
|
||||
Loading…
Reference in New Issue
Block a user