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small fix for microorganisms data set

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dr. M.S. (Matthijs) Berends 2018-09-06 16:50:03 +02:00
parent de36b0be23
commit c5073f2fd1
2 changed files with 7 additions and 6 deletions
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13
R/mo.R
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@ -37,7 +37,6 @@
#' \itemize{ #' \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{"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}} #' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
#' \item{Something like \code{"s pyo"} will return the ID of \emph{Streptococcus pyogenes} and not \emph{Actinomyes pyogenes}}
#' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}} #' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
#' \item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}} #' \item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
#' } #' }
@ -139,6 +138,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
# add start en stop regex # add start en stop regex
x <- paste0('^', x, '$') x <- paste0('^', x, '$')
x_withspaces_all <- x_withspaces x_withspaces_all <- x_withspaces
x_withspaces_start <- paste0('^', x_withspaces)
x_withspaces <- paste0('^', x_withspaces, '$') x_withspaces <- paste0('^', x_withspaces, '$')
for (i in 1:length(x)) { for (i in 1:length(x)) {
@ -177,11 +177,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
x[i] <- 'STAAUR' x[i] <- 'STAAUR'
next next
} }
if (tolower(x[i]) == '^s.*pyo$') {
# avoid detection of Actinomyces pyogenes in case of Streptococcus pyogenes
x[i] <- 'STCPYO'
next
}
if (tolower(x[i]) == '^p.*aer$') { if (tolower(x[i]) == '^p.*aer$') {
# avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa # avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
x[i] <- 'PSEAER' x[i] <- 'PSEAER'
@ -240,6 +235,12 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
x[i] <- found[1L] x[i] <- found[1L]
next next
} }
# try any match keeping spaces, not ending with $
found <- MOs[which(MOs$fullname %like% x_withspaces_start[i]),]$mo
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match diregarding spaces # try any match diregarding spaces
found <- MOs[which(MOs$fullname %like% x[i]),]$mo found <- MOs[which(MOs$fullname %like% x[i]),]$mo

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data/microorganisms.rda
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