added mo_shortname

NAMESPACE

@@ -95,6 +95,7 @@ export(mo_fullname)
 export(mo_genus)
 export(mo_gramstain)
 export(mo_property)
+export(mo_shortname)
 export(mo_species)
 export(mo_subspecies)
 export(mo_type)

NEWS.md

@@ -10,7 +10,7 @@
   * Column names of datasets `microorganisms` and `septic_patients`
   * All old syntaxes will still work with this version, but will throw warnings
 * Functions `as.atc` and `is.atc` to transform/look up antibiotic ATC codes as defined by the WHO. The existing function `guess_atc` is now an alias of `as.atc`.
-* Aliases for existing function `mo_property`: `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`, `mo_fullname`, `mo_aerobic`, `mo_type`, `mo_gramstain`. The last two functions have a `language` parameter, with support for Spanish, German and Dutch:
+* Aliases for existing function `mo_property`: `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`, `mo_fullname`, `mo_shortname`, `mo_aerobic`, `mo_type` and `mo_gramstain`. The last two functions have a `language` parameter, with support for Spanish, German and Dutch:
   ```r
   mo_gramstain("E. coli")
   # [1] "Negative rods"

R/mo.R

@@ -18,7 +18,7 @@
 
 #' 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.
+#' Use this function to determine a valid ID based on a genus (and species). Determination is done using Artificial Intelligence (AI), so the input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
 #' @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].
 #'
@@ -37,6 +37,7 @@
 #' \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}}
+#'   \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{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
 #' }
@@ -62,6 +63,10 @@
 #' as.mo("VISA") # Vancomycin Intermediate S. aureus
 #' as.mo("VRSA") # Vancomycin Resistant S. aureus
 #'
+#' as.mo("Streptococcus group A")
+#' as.mo("GAS") # Group A Streptococci
+#' as.mo("GBS") # Group B Streptococci
+#'
 #' # guess_mo is an alias of as.mo and works the same
 #' guess_mo("S. epidermidis")                 # will remain species: STAEPI
 #' guess_mo("S. epidermidis", Becker = TRUE)  # will not remain species: STACNS
@@ -172,6 +177,11 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
       x[i] <- 'STAAUR'
       next
     }
+    if (tolower(x[i]) == '^s.*pyo$') {
+      # avoid detection of Actinomyces pyogenes in case of Streptococcus pyogenes
+      x[i] <- 'STCPYO'
+      next
+    }
     if (tolower(x[i]) == '^p.*aer$') {
       # avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
       x[i] <- 'PSEAER'
@@ -192,7 +202,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
       next
     }
 
-    # translate known trivial names to genus+species
+    # translate known trivial abbreviations to genus+species
     if (!is.na(x_trimmed[i])) {
       if (toupper(x_trimmed[i]) == 'MRSA'
           | toupper(x_trimmed[i]) == 'VISA'
@@ -218,6 +228,10 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
         x[i] <- 'STCPNE'
         next
       }
+      if (toupper(x_trimmed[i]) %like% '^G[ABCDFHK]S$') {
+        x[i] <- gsub("G([ABCDFHK])S", "STCGR\\1", x_trimmed[i])
+        next
+      }
     }
 
     # try any match keeping spaces

R/mo_property.R

@@ -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")                  # "Staphylococcus epidermidis"
-#' mo_fullname("S. epidermidis", Becker = TRUE)  # "Coagulase Negative Staphylococcus (CoNS)"
+#' 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")                     # "Streptococcus pyogenes"
-#' mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
+#' 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") {

man/as.mo.Rd

@@ -33,7 +33,7 @@ guess_mo(x, Becker = FALSE, Lancefield = FALSE)
 Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
 }
 \description{
-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.
+Use this function to determine a valid ID based on a genus (and species). Determination is done using Artificial Intelligence (AI), so the input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
 }
 \details{
 \code{guess_mo} is an alias of \code{as.mo}.
@@ -44,6 +44,7 @@ Some exceptions have been built in to get more logical results, based on prevale
 \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}}
+  \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{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
 }
@@ -62,6 +63,10 @@ as.mo("MRSA") # Methicillin Resistant S. aureus
 as.mo("VISA") # Vancomycin Intermediate S. aureus
 as.mo("VRSA") # Vancomycin Resistant S. aureus
 
+as.mo("Streptococcus group A")
+as.mo("GAS") # Group A Streptococci
+as.mo("GBS") # Group B Streptococci
+
 # guess_mo is an alias of as.mo and works the same
 guess_mo("S. epidermidis")                 # will remain species: STAEPI
 guess_mo("S. epidermidis", Becker = TRUE)  # will not remain species: STACNS

man/mo_property.Rd

@@ -7,6 +7,7 @@
 \alias{mo_species}
 \alias{mo_subspecies}
 \alias{mo_fullname}
+\alias{mo_shortname}
 \alias{mo_type}
 \alias{mo_gramstain}
 \alias{mo_aerobic}
@@ -30,6 +31,8 @@ mo_subspecies(x, Becker = FALSE, Lancefield = FALSE)
 
 mo_fullname(x, Becker = FALSE, Lancefield = FALSE)
 
+mo_shortname(x, Becker = FALSE, Lancefield = FALSE)
+
 mo_type(x, language = "en")
 
 mo_gramstain(x, language = "en")
@@ -61,6 +64,7 @@ mo_genus("E. coli")           # "Escherichia"
 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
@@ -77,6 +81,7 @@ mo_gramstain("E. coli", "nl") # "Negatieve staven"
 # 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"
@@ -88,12 +93,14 @@ mo_genus("EHEC")              # "Escherichia"
 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
@@ -103,12 +110,16 @@ mo_aerobic("B. fragilis")     # FALSE
 
 
 # Becker classification, see ?as.mo
-mo_fullname("S. epidermidis")                 # "Staphylococcus epidermidis"
+mo_fullname("S. epidermidis")                  # "Staphylococcus epidermidis"
-mo_fullname("S. epidermidis", Becker = TRUE)  # "Coagulase Negative Staphylococcus (CoNS)"
+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")                     # "Streptococcus pyogenes"
-mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
+mo_fullname("S. pyogenes", Lancefield = TRUE)  # "Streptococcus group A"
+mo_shortname("S. pyogenes")                    # "S. pyogenes"
+mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS"
 }
 \seealso{
 \code{\link{microorganisms}}

tests/testthat/test-mo.R

@@ -14,6 +14,8 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
   expect_equal(as.character(as.mo("Bartonella")), "BAR")
 
+  expect_equal(as.character(as.mo("S. pyo")), "STCPYO") # not Actinomyces pyogenes
+
   expect_equal(as.character(as.mo("P. aer")), "PSEAER") # not Pasteurella aerogenes
 
   expect_equal(as.character(as.mo("Negative rods")), "GNR")

tests/testthat/test-mo_property.R

@@ -10,6 +10,12 @@ test_that("mo_property works", {
   expect_equal(mo_gramstain("E. coli"), "Negative rods")
   expect_equal(mo_aerobic("E. coli"), TRUE)
 
+  expect_equal(mo_shortname("MRSA"), "S. aureus")
+  expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
+  expect_equal(mo_shortname("MRSA", Becker = "all"), "CoPS")
+  expect_equal(mo_shortname("S. aga"), "S. agalactiae")
+  expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
+
   expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
   expect_equal(mo_gramstain("E. coli", language = "de"), "Negative Staebchen")