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added mo_shortname

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dr. M.S. (Matthijs) Berends
2018-09-05 10:51:46 +02:00
parent 790bd1622d
commit e39a9a8b05
8 changed files with 88 additions and 12 deletions
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45
R/mo_property.R
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@ -38,6 +38,7 @@
#' mo_species("E. coli") # "coli"
#' mo_subspecies("E. coli") # <NA>
#' mo_fullname("E. coli") # "Escherichia coli"
#' mo_shortname("E. coli") # "E. coli"
#' mo_type("E. coli") # "Bacteria"
#' mo_gramstain("E. coli") # "Negative rods"
#' mo_aerobic("E. coli") # TRUE
@ -54,6 +55,7 @@
#' # Abbreviations known in the field
#' mo_genus("MRSA") # "Staphylococcus"
#' mo_species("MRSA") # "aureus"
#' mo_shortname("MRSA") # "S. aureus"
#' mo_gramstain("MRSA") # "Positive cocci"
#'
#' mo_genus("VISA") # "Staphylococcus"
@ -65,12 +67,14 @@
#' mo_species("EHEC") # "coli"
#' mo_subspecies("EHEC") # "EHEC"
#' mo_fullname("EHEC") # "Escherichia coli (EHEC)"
#' mo_shortname("EHEC") # "E. coli"
#'
#' mo_genus("doylei") # "Campylobacter"
#' mo_species("doylei") # "jejuni"
#' mo_fullname("doylei") # "Campylobacter jejuni (doylei)"
#'
#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae (rhinoscleromatis)"
#' mo_shortname("K. pneu rh") # "K. pneumoniae"
#'
#'
#' # Anaerobic bacteria
@ -80,12 +84,16 @@
#'
#'
#' # Becker classification, see ?as.mo
#' mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
#' mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
#' mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
#' mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
#' mo_shortname("S. epidermidis") # "S. epidermidis"
#' mo_shortname("S. epidermidis", Becker = TRUE) # "CoNS"
#'
#' # Lancefield classification, see ?as.mo
#' mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
#' mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
#' mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
#' mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
#' mo_shortname("S. pyogenes") # "S. pyogenes"
#' mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS"
mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE) {
property <- tolower(property[1])
if (!property %in% colnames(microorganisms)) {
@ -129,6 +137,35 @@ mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE) {
mo_property(x, "fullname", Becker = Becker, Lancefield = Lancefield)
}
#' @rdname mo_property
#' @export
mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
res1 <- as.mo(x)
res2 <- as.mo(x, Becker = Becker, Lancefield = Lancefield)
res2_fullname <- mo_fullname(res2)
res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
res2_fullname <- gsub("Streptococcus group (.*)",
"G\\1S",
res2_fullname) # turn "Streptococcus group A" to "GAS"
res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname), 1, 1),
". ",
mo_species(res2_fullname))
if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ",
mo_species(res1[res1 == res2]))
}
res1[res1 != res2] <- res2_fullname
as.character(res1)
} else {
# return G. species
paste0(substr(mo_genus(x), 1, 1), ". ", mo_species(x))
}
}
#' @rdname mo_property
#' @export
mo_type <- function(x, language = "en") {