Commit the man pages and make aggregate public again

man/summary.taxores.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/taxonomic.resolution.R
+\name{summary.taxores}
+\alias{summary.taxores}
+\title{Dataset taxonomic resolution summary.}
+\usage{
+\method{summary}{taxores}(x, colranks, colscores, thresh = 0.7)
+}
+\arguments{
+\item{x}{a \code{\link{metabarcoding.data}} object}
+
+\item{colranks}{a string indicating column name where ranks are stored in \code{x}}
+
+\item{colscores}{a string indicating column name where taxonomic identification scores are stored in \code{x}}
+
+\item{thresh}{a threshold for defining at which taxonomic identification scores a sequence can be considered as "not assigned". 
+Default is \code{0.7}}
+}
+\value{
+returns a data.frame and piecharts of the number/proportion of MOTUs/reads assigned to each taxonomic levels
+}
+\description{
+Summarizes the taxonomic relution of reads and MOTUs over the entire dataset
+}
+\examples{
+
+data(termes)
+taxo=default.taxonomy()
+
+termes.taxo.table = get.classic.taxonomy(termes, taxo, "taxid")
+attr(termes, "motus") = data.frame(termes$motus, termes.taxo.table)
+attr(termes, "motus")["count"] = colSums(termes$reads)
+
+summary.taxores(termes, "taxonomic_rank_ok","best_identity")
+
+}
+\seealso{
+\code{\linkS4class{taxonomy.obitools}}, and method \code{\link{taxonmicank}}
+}
+\author{
+Lucie Zinger
+}
+\keyword{taxonomy}