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(v1.4.0.9013) is_gram_negative/positive update

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dr. M.S. (Matthijs) Berends
2020-11-09 13:07:02 +01:00
parent 423879c034
commit d3b1d33210
22 changed files with 149 additions and 82 deletions
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2
man/antibiotic_class_selectors.Rd
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@ -85,7 +85,7 @@ if (require("dplyr")) {
# get bug/drug combinations for only macrolides in Gram-positives:
example_isolates \%>\%
filter(mo \%>\% is_gram_positive()) \%>\%
filter(is_gram_positive()) \%>\%
select(mo, macrolides()) \%>\%
bug_drug_combinations() \%>\%
format()

2
man/as.mo.Rd
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@ -31,7 +31,7 @@ mo_renamed()
\arguments{
\item{x}{a character vector or a \link{data.frame} with one or two columns}
\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into coagulase-negative \emph{Staphylococci} ("CoNS") and coagulase-positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2,3).
\item{Becker}{a logical to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2,3).
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}

8
man/mo_property.Rd
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@ -116,7 +116,7 @@ The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always ret
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}. Functions \code{\link[=is_gram_negative]{is_gram_negative()}} and \code{\link[=is_gram_positive]{is_gram_positive()}} always return \code{TRUE} or \code{FALSE}, even for species outside the kingdom of Bacteria.
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}. Functions \code{\link[=is_gram_negative]{is_gram_negative()}} and \code{\link[=is_gram_positive]{is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (except when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
All output will be \link{translate}d where possible.
@ -241,7 +241,7 @@ mo_shortname("S. pyo") # "S. pyogenes"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" (='Group A Streptococci')
# language support for German, Dutch, Spanish, Portuguese, Italian and French
# language support --------------------------------------------------------
mo_gramstain("E. coli", language = "de") # "Gramnegativ"
mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
mo_gramstain("E. coli", language = "es") # "Gram negativo"
@ -258,7 +258,11 @@ mo_fullname("S. pyogenes",
Lancefield = TRUE,
language = "nl") # "Streptococcus groep A"
# gram stains can be used as a filter
example_isolates \%>\%
filter(is_gram_positive())
# other --------------------------------------------------------------------
# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("E. coli")
# get a list with the taxonomy, the authors, Gram-stain and URL to the online database