Commit the man pages and make aggregate public again

man/get.classic.taxonomy.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/taxonomy_classic_table.R
+\name{get.classic.taxonomy}
+\alias{get.classic.taxonomy}
+\title{Get classical taxonomy format}
+\usage{
+get.classic.taxonomy(x, taxonomy, coltaxid)
+}
+\arguments{
+\item{x}{a \code{\link{metabarcoding.data}} object}
+
+\item{taxonomy}{a instance of \code{\linkS4class{taxonomy.obitools}}}
+
+\item{coltaxid}{a the name of the column containing taxids to be used for creating classical taxonomic description}
+}
+\value{
+returns a data.frame with the classical taxonomic description ("kingdom", "phylum", "class", "order", "family", "genus", "species"), as well as
+        sequence taxonomic assignment rank and scientific name for each sequences stored in the \code{\link{metabarcoding.data}} object
+}
+\description{
+Creates a table with the classical taxonomic description (from phylum to species)
+}
+\examples{
+
+data(termes)
+
+taxo=default.taxonomy()
+
+termes.taxo.table = get.classic.taxonomy(termes, taxo, "taxid")
+head(termes.taxo.table)
+
+attr(termes, "motus") = data.frame(termes$motus, termes.taxo.table)
+
+  
+}
+\seealso{
+\code{\linkS4class{taxonomy.obitools}}, and methods \code{\link{species}},\code{\link{genus}}, \code{\link{family}},\code{\link{kingdom}},
+         \code{\link{superkingdom}},\code{\link{taxonatrank}}, \code{\link{taxonmicank}}
+}
+\author{
+Lucie Zinger
+}
+\keyword{taxonomy}