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  1. 2
      NAMESPACE
  2. 101
      R/atc.R
  3. 8
      README.md
  4. 46
      man/abname.Rd
  5. BIN
      man/figures/logo_en.png

2
NAMESPACE

@ -10,6 +10,7 @@ S3method(print,rsi) @@ -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) @@ -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)

101
R/atc.R

@ -119,3 +119,104 @@ atc_property <- function(atc_code, @@ -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
}

8
README.md

@ -1,10 +1,14 @@ @@ -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`: @@ -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:

46
man/abname.Rd

@ -0,0 +1,46 @@ @@ -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}

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