P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:41:58 +02:00
Code Releases Activity

(v1.2.0.9011) mo_domain(), improved error handling

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
man/mo_property.Rd
View File

@ -13,6 +13,7 @@
\alias{mo_class}
\alias{mo_phylum}
\alias{mo_kingdom}
\alias{mo_domain}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_snomed}
@ -48,6 +49,8 @@ mo_phylum(x, language = get_locale(), ...)
mo_kingdom(x, language = get_locale(), ...)
mo_domain(x, language = get_locale(), ...)
mo_type(x, language = get_locale(), ...)
mo_gramstain(x, language = get_locale(), ...)
@ -96,16 +99,18 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link[=as.mo]{as.mo()}}, which makes it possible to use microbial abbreviations, codes and names as input. Please see \emph{Examples}.
}
\details{
All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{mo_year()}}. This leads to the following results:
All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{mo_year()}}. Please refer to this example, knowing that \emph{Escherichia blattae} was renamed to \emph{Shimwellia blattae} in 2010:
\itemize{
\item \code{mo_name("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)
\item \code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)
\item \code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)
\item \code{mo_name("Escherichia blattae")} will return \code{"Shimwellia blattae"} (with a message about the renaming)
\item \code{mo_ref("Escherichia blattae")} will return \code{"Burgess et al., 1973"} (with a message about the renaming)
\item \code{mo_ref("Shimwellia blattae")} will return \code{"Priest et al., 2010"} (without a message)
}
The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \emph{"E. coli"}. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like \emph{"CoNS"} (Coagulase-Negative Staphylococci) and \emph{"GBS"} (Group B Streptococci).
The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \code{"E. coli"}. Exceptions are abbreviations of staphylococci (like \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. In other words, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results.
The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318}{PMID 11837318}), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
All output will be \link{translate}d where possible.