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fix documentation

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dr. M.S. (Matthijs) Berends
2022-10-06 11:33:30 +02:00
parent 0d8b098220
commit b9342d103e
8 changed files with 64 additions and 67 deletions
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43
R/mo_property.R
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@ -98,6 +98,7 @@
#' mo_authors("Klebsiella pneumoniae")
#' mo_year("Klebsiella pneumoniae")
#' mo_lpsn("Klebsiella pneumoniae")
#' mo_gbif("Klebsiella pneumoniae")
#'
#' # abbreviations known in the field -----------------------------------------
#' mo_genus("MRSA")
@ -109,20 +110,15 @@
#' mo_species("EHEC")
#'
#' # known subspecies ---------------------------------------------------------
#' mo_name("doylei")
#' mo_genus("doylei")
#' mo_species("doylei")
#' mo_subspecies("doylei")
#'
#' mo_fullname("K. pneu rh")
#' mo_shortname("K. pneu rh")
#'
#' \donttest{
#' # Becker classification, see ?as.mo ----------------------------------------
#' mo_fullname("S. epi")
#' mo_fullname("S. epi", Becker = TRUE)
#' mo_shortname("S. epi")
#' mo_shortname("S. epi", Becker = TRUE)
#' mo_fullname("Staph. epi")
#' mo_fullname("Staph. epi", Becker = TRUE)
#' mo_shortname("Staph. epi")
#' mo_shortname("Staph. epi", Becker = TRUE)
#'
#' # Lancefield classification, see ?as.mo ------------------------------------
#' mo_fullname("S. pyo")
@ -132,23 +128,19 @@
#'
#'
#' # language support --------------------------------------------------------
#' mo_gramstain("Klebsiella pneumoniae", language = "de")
#' mo_gramstain("Klebsiella pneumoniae", language = "nl")
#' mo_gramstain("Klebsiella pneumoniae", language = "es")
#' mo_gramstain("Klebsiella pneumoniae", language = "de") # German
#' mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
#' mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
#' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
#' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
#'
#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
#' mo_kingdom("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae")
#' mo_type("Klebsiella pneumoniae", language = "nl")
#'
#' mo_fullname("S. pyogenes",
#' Lancefield = TRUE,
#' language = "de"
#' )
#' mo_fullname("S. pyogenes",
#' Lancefield = TRUE,
#' language = "nl"
#' )
#' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
#' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
#'
#'
#' # other --------------------------------------------------------------------
@ -158,10 +150,13 @@
#' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
#' if (require("dplyr")) {
#' example_isolates %>%
#' filter(mo_is_gram_positive())
#'
#' filter(mo_is_gram_positive()) %>%
#' count(mo_genus(), count = TRUE)
#' }
#' if (require("dplyr")) {
#' example_isolates %>%
#' filter(mo_is_intrinsic_resistant(ab = "vanco"))
#' filter(mo_is_intrinsic_resistant(ab = "vanco")) %>%
#' count(mo_genus(), count = TRUE)
#' }
#'
#'