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(v0.9.0.9020) as.mo() improvement

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dr. M.S. (Matthijs) Berends
2020-02-09 22:04:29 +01:00
parent 4e1c16c5a5
commit c7a76ba713
35 changed files with 70179 additions and 70116 deletions
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4
man/antibiotics.Rd
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@ -60,8 +60,8 @@ Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and co
These data sets are available as 'flat files' for use even without R - you can find the files here:
\itemize{
\item \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R}
\item \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R}
\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt}
\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt}
}
}
}

4
man/as.mo.Rd
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@ -68,7 +68,7 @@ A microorganism ID from this package (class: \code{\link{mo}}) typically looks l
Values that cannot be coered will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
Use the \code{\link[=mo_property]{mo_property_*}} functions to get properties based on the returned code, see Examples.
Use the \code{\link[=mo_property]{mo_*}} functions to get properties based on the returned code, see Examples.
The algorithm uses data from the Catalogue of Life (see below) and from one other source (see \link{microorganisms}).
@ -79,7 +79,7 @@ The \code{\link[=as.mo]{as.mo()}} function uses several coercion rules for fast
\item Breakdown of input values to identify possible matches.
}
This will lead to the effect that e.g. \code{"E. coli"} (a highly prevalent microorganism found in humans) will return the microbial ID of \emph{Escherichia coli} and not \emph{Entamoeba coli} (a less prevalent microorganism in humans), although the latter would alphabetically come first.
This will lead to the effect that e.g. \code{"E. coli"} (a microorganism highly prevalent in humans) will return the microbial ID of \emph{Escherichia coli} and not \emph{Entamoeba coli} (a microorganism less prevalent in humans), although the latter would alphabetically come first.
}
\subsection{Coping with uncertain results}{

2
man/microorganisms.Rd
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@ -43,7 +43,7 @@ Manually added were:
This data set is available as 'flat file' for use even without R - you can find the file here:
\itemize{
\item \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R}
\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
}
}
}

4
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 5,433 observations and 2 variables:
\format{A \code{\link{data.frame}} with 5,450 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
@ -13,7 +13,7 @@
microorganisms.codes
}
\description{
A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link[=set_mo_source]{set_mo_source()}}.
A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link[=set_mo_source]{set_mo_source()}}. They will all be searched when using \code{\link[=as.mo]{as.mo()}} and consequently all the \code{\link[=mo_property]{mo_*}} functions.
}
\section{Catalogue of Life}{