P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 13:42:04 +02:00
Code Releases Activity

(v0.7.1.9077) mo codes fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-09-20 14:18:29 +02:00
parent 3596adb295
commit 40e6b3e8f6
26 changed files with 256 additions and 256 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
man/as.mo.Rd
View File

@ -81,10 +81,11 @@ This function uses intelligent rules to help getting fast and logical results. I
\itemize{
\item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
\item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see \emph{Microbial prevalence of pathogens in humans} below)}
\item{Taxonomic kingdom: it first searches in Bacteria/Chromista, then Fungi, then Protozoa}
\item{Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa, then Archaea, then others}
\item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
}
A couple of effects because of these rules:
\itemize{
\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}

3
man/microorganisms.old.Rd
View File

@ -4,12 +4,13 @@
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{A \code{\link{data.frame}} with 24,246 observations and 4 variables:
\format{A \code{\link{data.frame}} with 24,246 observations and 5 variables:
\describe{
\item{\code{col_id}}{Catalogue of Life ID that was originally given}
\item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set}
\item{\code{fullname}}{Old full taxonomic name of the microorganism}
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).