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(v1.0.1.9005) as.mo() improvements

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dr. M.S. (Matthijs) Berends
2020-04-13 21:09:56 +02:00
parent 219cff403f
commit d1cb7d3b6f
97 changed files with 2849 additions and 2098 deletions
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2
man/WHONET.Rd
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@ -32,7 +32,7 @@ A \code{\link{data.frame}} with 500 observations and 53 variables:
\item \verb{Inducible clindamycin resistance}\cr Clindamycin can be induced?
\item \code{Comment}\cr Other comments
\item \verb{Date of data entry}\cr Date this data was entered in WHONET
\item \code{AMP_ND10:CIP_EE}\cr 27 different antibiotics. You can lookup the abbreviatons in the \link{antibiotics} data set, or use e.g. \code{\link[=ab_name]{ab_name("AMP")}} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link[=as.rsi]{as.rsi()}}.
\item \code{AMP_ND10:CIP_EE}\cr 28 different antibiotics. You can lookup the abbreviations in the \link{antibiotics} data set, or use e.g. \code{\link[=ab_name]{ab_name("AMP")}} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link[=as.rsi]{as.rsi()}}.
}
}
\usage{

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man/antibiotics.Rd
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@ -4,7 +4,7 @@
\name{antibiotics}
\alias{antibiotics}
\alias{antivirals}
\title{Data sets with ~550 antimicrobials}
\title{Data sets with 554 antimicrobials}
\format{
\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 14 variables:}{
\itemize{

2
man/ggplot_pca.Rd
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@ -99,7 +99,7 @@ ggplot_pca(
\item{...}{Parameters passed on to functions}
}
\description{
This function is to produce a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function.
Produces a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function.
}
\details{
The colours for labels and points can be changed by adding another scale layer for colour, like \code{\link[=scale_colour_viridis_d]{scale_colour_viridis_d()}} or \code{\link[=scale_colour_brewer]{scale_colour_brewer()}}.

4
man/microorganisms.Rd
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@ -3,7 +3,7 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\title{Data set with 69,447 microorganisms}
\format{
A \code{\link{data.frame}} with 69,447 observations and 17 variables:
\itemize{
@ -38,7 +38,7 @@ Manually added were:
\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 \emph{et al.} 2005, PMID 15634993)
\item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
\item 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
}
\subsection{Direct download}{

2
man/microorganisms.codes.Rd
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@ -5,7 +5,7 @@
\alias{microorganisms.codes}
\title{Translation table for common microorganism codes}
\format{
A \code{\link{data.frame}} with 5,450 observations and 2 variables:
A \code{\link{data.frame}} with 5,585 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set

2
man/microorganisms.old.Rd
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@ -5,7 +5,7 @@
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{
A \code{\link{data.frame}} with 24,246 observations and 5 variables:
A \code{\link{data.frame}} with 24,253 observations and 5 variables:
\itemize{
\item \code{col_id}\cr Catalogue of Life ID that was originally given
\item \code{col_id_new}\cr New Catalogue of Life ID that responds to an entry in the \link{microorganisms} data set

3
man/rsi_translation.Rd
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@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data set for R/SI interpretation}
\format{
A \code{\link{data.frame}} with 13,975 observations and 9 variables:
A \code{\link{data.frame}} with 15,745 observations and 10 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "MIC" or "DISK"
@ -16,6 +16,7 @@ A \code{\link{data.frame}} with 13,975 observations and 9 variables:
\item \code{disk_dose}\cr Dose of the used disk diffusion method
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
\item \code{uti}\cr A logical value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
}
}
\usage{