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(v1.5.0.9029) added missing families and orders

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dr. M.S. (Matthijs) Berends
2021-03-05 01:31:46 +01:00
parent ddf88345f1
commit 0e0e3c4ffa
30 changed files with 61003 additions and 60523 deletions
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2
man/catalogue_of_life.Rd
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@ -18,7 +18,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
Included are:
\itemize{
\item All ~57,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa
\item All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa
\item All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).
\item All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as \emph{Strongyloides} and \emph{Taenia})
\item All ~14,000 previously accepted names of all included (sub)species (these were taxonomically renamed)

4
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 69,625 Microorganisms}
\title{Data Set with 70,026 Microorganisms}
\format{
A \link{data.frame} with 69,625 observations and 16 variables:
A \link{data.frame} with 70,026 observations and 16 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}