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(v0.7.1.9077) mo codes fix
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@ -81,10 +81,11 @@ This function uses intelligent rules to help getting fast and logical results. I
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\itemize{
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\item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
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\item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see \emph{Microbial prevalence of pathogens in humans} below)}
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\item{Taxonomic kingdom: it first searches in Bacteria/Chromista, then Fungi, then Protozoa}
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\item{Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa, then Archaea, then others}
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\item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
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}
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A couple of effects because of these rules:
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\itemize{
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\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
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@ -4,12 +4,13 @@
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\name{microorganisms.old}
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\alias{microorganisms.old}
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\title{Data set with previously accepted taxonomic names}
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\format{A \code{\link{data.frame}} with 24,246 observations and 4 variables:
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\format{A \code{\link{data.frame}} with 24,246 observations and 5 variables:
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\describe{
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\item{\code{col_id}}{Catalogue of Life ID that was originally given}
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\item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set}
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\item{\code{fullname}}{Old full taxonomic name of the microorganism}
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\item{\code{ref}}{Author(s) and year of concerning scientific publication}
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\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
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}}
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\source{
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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}()}).
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