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(v2.1.1.9230) deprecated resistance_predict(), data set folder name without space

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dr. M.S. (Matthijs) Berends
2025-03-28 16:48:56 +01:00
parent bd873ac1bc
commit b972bbb96f
25 changed files with 410 additions and 312 deletions
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2
man/clinical_breakpoints.Rd
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@ -50,7 +50,7 @@ The default is \code{"human"}, which can also be set with the package option \co
Clinical breakpoints in this package were validated through and imported from \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}. The developers of WHONET and this \code{AMR} package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.
Our import and reproduction script can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction scripts/reproduction_of_clinical_breakpoints.R>.
Our import and reproduction script can be found here: \url{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R}.
}
\subsection{Response From CLSI and EUCAST}{

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man/microorganisms.Rd
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@ -55,7 +55,7 @@ microorganisms
\description{
A data set containing the full microbial taxonomy (\strong{last updated: June 24th, 2024}) of six kingdoms. This data set is the backbone of this \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}} and microorganism properties can be looked up using any of the \code{\link[=mo_property]{mo_*}} functions.
This data set is carefully crafted, yet made 100\% reproducible from public and authoritative taxonomic sources (using \link{this script}(https://github.com/msberends/AMR/blob/main/data-raw/reproduction scripts/reproduction_of_microorganisms.R)), namely: \emph{List of Prokaryotic names with Standing in Nomenclature (LPSN)} for bacteria, \emph{MycoBank} for fungi, and \emph{Global Biodiversity Information Facility (GBIF)} for all others taxons.
This data set is carefully crafted, yet made 100\% reproducible from public and authoritative taxonomic sources (using \href{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R}{this script}), namely: \emph{List of Prokaryotic names with Standing in Nomenclature (LPSN)} for bacteria, \emph{MycoBank} for fungi, and \emph{Global Biodiversity Information Facility (GBIF)} for all others taxons.
}
\details{
Please note that entries are only based on LPSN, MycoBank, and GBIF (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.
@ -86,7 +86,7 @@ For convenience, some entries were added manually:
\item 8 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 \link{found here}(https://github.com/msberends/AMR/blob/main/data-raw/reproduction scripts/reproduction_of_microorganisms.R).
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}.
}
}