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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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5
man/as.mo.Rd
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@ -170,9 +170,8 @@ as.mo(c(
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"Staphylococcus aureus (MRSA,",
"Zthafilokkoockus oureuz", # handles incorrect spelling
"Sthafilokkockus aureus", # handles incorrect spelling
"Staphylococcus aureus (MRSA)",
"MRSA", # Methicillin Resistant S. aureus
"VISA", # Vancomycin Intermediate S. aureus
"VRSA", # Vancomycin Resistant S. aureus

43
man/mo_property.Rd
View File

@ -383,6 +383,7 @@ mo_ref("Klebsiella pneumoniae")
mo_authors("Klebsiella pneumoniae")
mo_year("Klebsiella pneumoniae")
mo_lpsn("Klebsiella pneumoniae")
mo_gbif("Klebsiella pneumoniae")
# abbreviations known in the field -----------------------------------------
mo_genus("MRSA")
@ -394,20 +395,15 @@ mo_genus("EHEC")
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")
@ -417,23 +413,19 @@ mo_shortname("S. pyo", Lancefield = TRUE)
# 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 --------------------------------------------------------------------
@ -443,10 +435,13 @@ mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
# 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)
}