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(v3.0.1.9066) fix documentation

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dr. M.S. (Matthijs) Berends
2026-06-24 19:34:47 +02:00
parent 39b6a250de
commit a88150ca4a
7 changed files with 38 additions and 28 deletions
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5
man/microorganisms.Rd
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@@ -59,11 +59,10 @@ Included taxonomic data from \href{https://lpsn.dsmz.de}{LPSN}, \href{https://ww
For convenience, some entries were added manually:
\itemize{
\item All 37 groups and complexes of the \link{microorganisms.groups} data set, for cross-reference (examples include beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.)
\item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H
\item 37 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
\item 1 entry of \emph{Blastocystis} (\emph{B. hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
\item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
\item 9 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
}
The syntax used to transform the original data to a cleansed \R format, can be \href{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R}{found here}.

12
man/mo_property.Rd
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@@ -401,6 +401,7 @@ Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct
\examples{
# taxonomic tree -----------------------------------------------------------
mo_domain("Klebsiella pneumoniae")
mo_kingdom("Klebsiella pneumoniae")
mo_phylum("Klebsiella pneumoniae")
mo_class("Klebsiella pneumoniae")
@@ -410,6 +411,8 @@ mo_genus("Klebsiella pneumoniae")
mo_species("Klebsiella pneumoniae")
mo_subspecies("Klebsiella pneumoniae")
# all in one go
mo_taxonomy("Klebsiella pneumoniae")
# full names and short names -----------------------------------------------
@@ -430,6 +433,7 @@ mo_rank("Klebsiella pneumoniae")
mo_url("Klebsiella pneumoniae")
mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
mo_group_members("Streptococcus group A")
mo_group_members(c(
"Streptococcus group A",
"Streptococcus group C",
@@ -473,6 +477,7 @@ mo_shortname("K. pneu rh")
mo_fullname("Staph epidermidis")
mo_fullname("Staph epidermidis", Becker = TRUE)
mo_shortname("Staph epidermidis")
mo_shortname("Staph epidermidis", Becker = TRUE)
@@ -481,6 +486,7 @@ mo_shortname("Staph epidermidis", Becker = TRUE)
mo_fullname("Strep agalactiae")
mo_fullname("Strep agalactiae", Lancefield = TRUE)
mo_shortname("Strep agalactiae")
mo_shortname("Strep agalactiae", Lancefield = TRUE)
@@ -493,10 +499,10 @@ 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 untranslated
mo_kingdom("Klebsiella pneumoniae")
# mo_type is equal to mo_domain, but mo_domain will remain untranslated
mo_domain("Klebsiella pneumoniae")
mo_type("Klebsiella pneumoniae")
mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")