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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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21
man/mo_property.Rd
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@ -270,7 +270,7 @@ mo_property(
\item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'}
@ -278,7 +278,7 @@ mo_property(
\item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}}
\item{property}{one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed", or must be \code{"shortname"}}
\item{property}{one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be \code{"shortname"}}
}
\value{
\itemize{
@ -317,7 +317,7 @@ The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the o
SNOMED codes (\code{\link[=mo_snomed]{mo_snomed()}}) are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info.
Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}}, the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names.
Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}} (which will have the scientific reference as \link[base:names]{name}), the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names.
All output \link[=translate]{will be translated} where possible.
}
@ -380,12 +380,12 @@ mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
# scientific reference -----------------------------------------------------
mo_ref("Klebsiella pneumoniae")
mo_authors("Klebsiella pneumoniae")
mo_year("Klebsiella pneumoniae")
mo_lpsn("Klebsiella pneumoniae")
mo_gbif("Klebsiella pneumoniae")
mo_synonyms("Klebsiella pneumoniae")
mo_ref("Klebsiella aerogenes")
mo_authors("Klebsiella aerogenes")
mo_year("Klebsiella aerogenes")
mo_lpsn("Klebsiella aerogenes")
mo_gbif("Klebsiella aerogenes")
mo_synonyms("Klebsiella aerogenes")
# abbreviations known in the field -----------------------------------------
@ -396,7 +396,8 @@ mo_shortname("VISA")
mo_gramstain("VISA")
mo_genus("EHEC")
mo_species("EHEC")
mo_species("EIEC")
mo_name("UPEC")
# known subspecies ---------------------------------------------------------