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(v0.7.1.9080) new LIS codes

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dr. M.S. (Matthijs) Berends
2019-09-22 17:19:59 +02:00
parent 57b0bd92a0
commit 66d405ff57
24 changed files with 239 additions and 222 deletions
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2
man/filter_ab_class.Rd
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@ -51,7 +51,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
\item{...}{parameters passed on to \code{\link[dplyr]{filter_at}}}
\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
}
\description{
Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.

3
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,454 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,465 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
@ -33,6 +33,7 @@ Manually added were:
\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel et al. 2005, PMID 15634993)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
}

2
man/microorganisms.codes.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Translation table for common microorganism codes}
\format{A \code{\link{data.frame}} with 4,927 observations and 2 variables:
\format{A \code{\link{data.frame}} with 5,006 observations and 2 variables:
\describe{
\item{\code{code}}{Commonly used code of a microorganism}
\item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}