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emph guess_bactid

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dr. M.S. (Matthijs) Berends
2018-08-01 08:03:31 +02:00
parent 36a5493099
commit 7c667eb732
5 changed files with 19 additions and 23 deletions
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26
R/bactid.R
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@ -21,7 +21,9 @@
#' Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
#' @param x a character vector or a dataframe with one or two columns
#' @rdname as.bactid
#' @details Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
#' @details \code{guess_bactid} does exactly the same as \code{as.bactid}.
#'
#' Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
#' \itemize{
#' \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
#' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
@ -53,17 +55,16 @@
#' library(dplyr)
#' df$bactid <- df %>%
#' select(microorganism_name) %>%
#' as.bactid()
#' guess_bactid()
#'
#' # and can even contain 2 columns, which is convenient for genus/species combinations:
#' df$bactid <- df %>%
#' select(genus, species) %>%
#' as.bactid()
#' guess_bactid()
#'
#' # same result:
#' df <- df %>%
#' mutate(bactid = paste(genus, species) %>%
#' as.bactid())
#' mutate(bactid = guess_bactid(paste(genus, species)))
#' }
as.bactid <- function(x) {
@ -158,7 +159,8 @@ as.bactid <- function(x) {
next
}
if (toupper(x.backup[i]) == 'MRSE') {
x[i] <- 'Staphylococcus epidermidis'
x[i] <- 'STAEPI'
next
}
if (toupper(x.backup[i]) == 'VRE') {
x[i] <- 'ENC'
@ -169,15 +171,9 @@ as.bactid <- function(x) {
x[i] <- 'PSEAER'
next
}
if (toupper(x.backup[i]) == 'PISP'
| toupper(x.backup[i]) == 'PRSP') {
# peni resistant S. pneumoniae
x[i] <- 'Streptococcus pneumoniae'
}
if (toupper(x.backup[i]) == 'VISP'
| toupper(x.backup[i]) == 'VRSP') {
# vanco resistant S. pneumoniae
x[i] <- 'Streptococcus pneumoniae'
if (toupper(x.backup[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
# peni R, peni I, vanco I, vanco R: S. pneumoniae
x[i] <- 'STCPNE'
}
}