abname, logo

NAMESPACE

@@ -10,6 +10,7 @@ S3method(print,rsi)
 S3method(summary,mic)
 S3method(summary,rsi)
 export(EUCAST_rules)
+export(abname)
 export(anti_join_bactlist)
 export(as.mic)
 export(as.rsi)
@@ -56,6 +57,7 @@ importFrom(dplyr,progress_estimated)
 importFrom(dplyr,pull)
 importFrom(dplyr,row_number)
 importFrom(dplyr,select)
+importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tibble)
 importFrom(dplyr,vars)

R/atc.R

@@ -119,3 +119,104 @@ atc_property <- function(atc_code,
   returnvalue
   
 }
+
+#' Name of an antibiotic
+#'
+#' 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{ablist}}.
+#' @param abcode a code or name, like \code{"amox"}, \code{"cftr"} or \code{"J01CA04"}
+#' @param from,to type to transform from and to. See \code{\link{ablist}} for its column names.
+#' @param textbetween text to put between multiple returned texts
+#' @param tolower return output as lower case with function \code{\link{tolower}}.
+#' @keywords ab antibiotics
+#' @export
+#' @importFrom dplyr %>% filter select slice 
+#' @examples
+#' abname("AMCL")
+#' # "amoxicillin and enzyme inhibitor"
+#'
+#' abname("AMCL+GENT")
+#' # "amoxicillin and enzyme inhibitor + gentamicin"
+#'
+#' abname(c("AMCL", "GENT"))
+#' # "amoxicillin and enzyme inhibitor" "gentamicin" 
+#'
+#' abname("AMCL", to = "trivial")
+#' # "Amoxicilline/clavulaanzuur"
+#'
+#' abname("AMCL", to = "atc")
+#' # "J01CR02"
+#'
+#' abname("J01CR02", from = "atc", to = "umcg")
+#' # "AMCL"
+#'
+#' @source \code{\link{ablist}}
+abname <- function(abcode, from = 'umcg', to = 'official', textbetween = ' + ', tolower = FALSE) {
+  
+  ablist <- AMR::ablist
+  colnames(ablist) <- colnames(ablist) %>% tolower()
+  from <- from %>% tolower()
+  to <- to %>% tolower()
+  
+  if (!from %in% colnames(ablist) |
+      !to %in% colnames(ablist)) {
+    stop(paste0('Invalid `from` or `to`. Choose one of ', 
+                colnames(ablist) %>% paste(collapse = ","), '.'), call. = FALSE)
+  }
+  
+  abcode <- as.character(abcode)
+  
+  for (i in 1:length(abcode)) {
+    drug <- abcode[i]
+    if (!grepl('+', drug, fixed = TRUE) & !grepl(' en ', drug, fixed = TRUE)) {
+      # bestaat maar uit 1 middel
+      if (any(ablist[, from] == drug)) {
+        abcode[i] <-
+          ablist %>%
+          filter(.[, from] == drug) %>%
+          select(to) %>%
+          slice(1) %>%
+          as.character()
+      } else {
+        # niet gevonden
+        warning('Code "', drug, '" not found in antibiotics list.', call. = FALSE)
+        abcode[i] <- NA
+      }
+    } else {
+      # meerdere middelen
+      if (grepl('+', drug, fixed = TRUE)) {
+        drug.group <-
+          strsplit(drug, '+', fixed = TRUE) %>%
+          unlist() %>%
+          trimws('both')
+      } else if (grepl(' en ', drug, fixed = TRUE)) {
+        drug.group <-
+          strsplit(drug, ' en ', fixed = TRUE) %>%
+          unlist() %>%
+          trimws('both')
+      } else {
+        warning('Invalid concat.')
+        abcode[i] <- NA
+        next
+      }
+      
+      for (j in 1:length(drug.group)) {
+        drug.group[j] <-
+          ablist %>%
+          filter(.[, from] == drug.group[j]) %>%
+          select(to) %>%
+          slice(1) %>%
+          as.character()
+        if (j > 1 & to %in% c('official', 'trivial')) {
+          drug.group[j] <- drug.group[j] %>% tolower()
+        }
+      }
+      abcode[i] <- paste(drug.group, collapse = textbetween)
+    }
+  }
+  
+  if (tolower == TRUE) {
+    abcode <- abcode %>% tolower()
+  }
+  
+  abcode
+}

README.md

@@ -1,10 +1,14 @@
 # `AMR`
 This is an [R package](https://www.r-project.org) to simplify the analysis of Antimicrobial Resistance (AMR).
 
+![logo](man/figures/logo_en.png)
+
+This R package was created for academic research by PhD students of the Medical Microbiology & Infection Prevention (mmb) department of the [University of Groningen](https://www.rug.nl/) who also maintain this package, see [#authors].
+
 ## Why this package?
 This R package contains functions to make microbiological, epidemiological data analysis easier. It allows the use of some new S3 classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).
 
-This R package was created for academic research by PhD students of the [University of Groningen](https://www.rug.nl/).
+AMR can also be predicted for the forthcoming years with the `rsi_predict` function. For use with the `dplyr` package, the `rsi` can be used in conjunction with `summarise` to calculate the resistance percentages of different antibiotic columns of a table.
 
 ## How to use it?
 ```r
@@ -63,7 +67,7 @@ A plot of `rsi_data`:
 plot(rsi_data)
 ```
 
-![plot2_ex4](man/figures/rsi_example.png)
+![example](man/figures/rsi_example.png)
 
 Other epidemiological functions:
 

man/abname.Rd

@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atc.R
+\name{abname}
+\alias{abname}
+\title{Name of an antibiotic}
+\source{
+\code{\link{ablist}}
+}
+\usage{
+abname(abcode, from = "umcg", to = "official", textbetween = " + ",
+  tolower = FALSE)
+}
+\arguments{
+\item{abcode}{a code or name, like \code{"amox"}, \code{"cftr"} or \code{"J01CA04"}}
+
+\item{from, to}{type to transform from and to. See \code{\link{ablist}} for its column names.}
+
+\item{textbetween}{text to put between multiple returned texts}
+
+\item{tolower}{return output as lower case with function \code{\link{tolower}}.}
+}
+\description{
+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{ablist}}.
+}
+\examples{
+abname("AMCL")
+# "amoxicillin and enzyme inhibitor"
+
+abname("AMCL+GENT")
+# "amoxicillin and enzyme inhibitor + gentamicin"
+
+abname(c("AMCL", "GENT"))
+# "amoxicillin and enzyme inhibitor" "gentamicin" 
+
+abname("AMCL", to = "trivial")
+# "Amoxicilline/clavulaanzuur"
+
+abname("AMCL", to = "atc")
+# "J01CR02"
+
+abname("J01CR02", from = "atc", to = "umcg")
+# "AMCL"
+
+}
+\keyword{ab}
+\keyword{antibiotics}