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Support for German and Spanish microorganism properties, cleanup

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dr. M.S. (Matthijs) Berends
2018-09-04 11:33:30 +02:00
parent 5405002119
commit b388e3fee7
20 changed files with 256 additions and 157 deletions
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37
R/mo.R
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@ -19,15 +19,19 @@
#' Transform to microorganism ID
#'
#' 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
#' @param Becker a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1]. This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".
#' @param Lancefield a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, i.e. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L. Groups D and E will be ignored, since they are \emph{Enterococci}.
#' @param x a character vector or a \code{data.frame} with one or two columns
#' @param Becker a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].
#'
#' This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".
#' @param Lancefield a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, i.e. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
#'
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
#' @rdname as.mo
#' @aliases mo
#' @keywords mo Becker becker Lancefield lancefield guess
#' @details \code{guess_mo} is an alias of \code{as.mo}.
#'
#' Use the \code{\link{mo_property}} functions to get properties based on the returned mo, see Examples.
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
#'
#' Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are:
#' \itemize{
@ -39,10 +43,9 @@
#' Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
#' For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
#' @source
#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \cr
#' \url{https://dx.doi.org/10.1128/CMR.00109-13} \cr
#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \cr
#' \url{https://dx.doi.org/10.1084/jem.57.4.571}
#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
#'
#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
#' @export
#' @importFrom dplyr %>% pull left_join
#' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
@ -63,7 +66,7 @@
#' guess_mo("S. epidermidis") # will remain species: STAEPI
#' guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: STACNS
#'
#' guess_mo("S. pyogenes") # will remain species: STCAGA
#' guess_mo("S. pyogenes") # will remain species: STCPYO
#' guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
#'
#' # Use mo_* functions to get a specific property based on `mo`
@ -177,10 +180,17 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
if (tolower(x[i]) %like% 'coagulase negative'
| tolower(x[i]) %like% 'cns'
| tolower(x[i]) %like% 'cons') {
# coerce S. coagulase negative, also as CNS and CoNS
# coerce S. coagulase negative
x[i] <- 'STACNS'
next
}
if (tolower(x[i]) %like% 'coagulase positive'
| tolower(x[i]) %like% 'cps'
| tolower(x[i]) %like% 'cops') {
# coerce S. coagulase positive
x[i] <- 'STACPS'
next
}
# translate known trivial names to genus+species
if (!is.na(x_trimmed[i])) {
@ -204,7 +214,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
next
}
if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
# peni R, peni I, vanco I, vanco R: S. pneumoniae
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- 'STCPNE'
next
}
@ -327,7 +337,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
}
}
if (Lancefield == TRUE) {
if (Lancefield == TRUE | Lancefield == "all") {
# group A
x[x == "STCPYO"] <- "STCGRA" # S. pyogenes
# group B
@ -338,6 +348,9 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
"zooepidemicus", "dysgalactiae")) %>%
pull(mo)
x[x %in% S_groupC] <- "STCGRC" # S. agalactiae
if (Lancefield == "all") {
x[substr(x, 1, 3) == "ENC"] <- "STCGRD" # all Enterococci
}
# group F
x[x == "STCANG"] <- "STCGRF" # S. anginosus
# group H