(v0.7.1.9032) eucast_rules() improvements

R/mo_property.R

@@ -21,7 +21,7 @@
 
 #' Property of a microorganism
 #'
-#' Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
+#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link{as.mo}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
 #' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
 #' @param property one of the column names of the \code{\link{microorganisms}} data set or \code{"shortname"}
 #' @param language language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.
@@ -53,7 +53,7 @@
 #' @seealso \code{\link{microorganisms}}
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' ## taxonomic tree
+#' # taxonomic tree -----------------------------------------------------------
 #' mo_kingdom("E. coli")         # "Bacteria"
 #' mo_phylum("E. coli")          # "Proteobacteria"
 #' mo_class("E. coli")           # "Gammaproteobacteria"
@@ -63,35 +63,33 @@
 #' mo_species("E. coli")         # "coli"
 #' mo_subspecies("E. coli")      # ""
 #'
-#' ## colloquial properties
+#' # colloquial properties ----------------------------------------------------
 #' mo_name("E. coli")            # "Escherichia coli"
 #' mo_fullname("E. coli")        # "Escherichia coli", same as mo_name()
 #' mo_shortname("E. coli")       # "E. coli"
 #'
-#' ## other properties
+#' # other properties ---------------------------------------------------------
 #' mo_gramstain("E. coli")       # "Gram-negative"
 #' mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
 #' mo_rank("E. coli")            # "species"
 #' mo_url("E. coli")             # get the direct url to the online database entry
 #' mo_synonyms("E. coli")        # get previously accepted taxonomic names
 #'
-#' ## scientific reference
+#' # scientific reference -----------------------------------------------------
 #' mo_ref("E. coli")             # "Castellani et al., 1919"
 #' mo_authors("E. coli")         # "Castellani et al."
 #' mo_year("E. coli")            # 1919
 #'
-#'
-#' # Abbreviations known in the field
+#' # abbreviations known in the field -----------------------------------------
 #' mo_genus("MRSA")              # "Staphylococcus"
 #' mo_species("MRSA")            # "aureus"
-#' mo_shortname("MRSA")          # "S. aureus"
-#' mo_gramstain("MRSA")          # "Gram-positive"
+#' mo_shortname("VISA")          # "S. aureus"
+#' mo_gramstain("VISA")          # "Gram-positive"
 #'
-#' mo_genus("VISA")              # "Staphylococcus"
-#' mo_species("VISA")            # "aureus"
+#' mo_genus("EHEC")              # "Escherichia"
+#' mo_species("EHEC")            # "coli"
 #'
-#'
-#' # Known subspecies
+#' # known subspecies ---------------------------------------------------------
 #' mo_name("doylei")             # "Campylobacter jejuni doylei"
 #' mo_genus("doylei")            # "Campylobacter"
 #' mo_species("doylei")          # "jejuni"
@@ -100,14 +98,14 @@
 #' mo_fullname("K. pneu rh")     # "Klebsiella pneumoniae rhinoscleromatis"
 #' mo_shortname("K. pneu rh")    # "K. pneumoniae"
 #'
-#'
-#' # Becker classification, see ?as.mo
+#' \donttest{
+#' # Becker classification, see ?as.mo ----------------------------------------
 #' mo_fullname("S. epi")                     # "Staphylococcus epidermidis"
 #' mo_fullname("S. epi", Becker = TRUE)      # "Coagulase-negative Staphylococcus (CoNS)"
 #' mo_shortname("S. epi")                    # "S. epidermidis"
 #' mo_shortname("S. epi", Becker = TRUE)     # "CoNS"
 #'
-#' # Lancefield classification, see ?as.mo
+#' # Lancefield classification, see ?as.mo ------------------------------------
 #' mo_fullname("S. pyo")                     # "Streptococcus pyogenes"
 #' mo_fullname("S. pyo", Lancefield = TRUE)  # "Streptococcus group A"
 #' mo_shortname("S. pyo")                    # "S. pyogenes"
@@ -136,6 +134,7 @@
 #' mo_taxonomy("E. coli")
 #' # get a list with the taxonomy, the authors and the URL to the online database
 #' mo_info("E. coli")
+#' }
 mo_name <- function(x, language = get_locale(), ...) {
   translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE)
 }