Commit the man pages and make aggregate public again

man/extracts-obiclean-methods.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/obiclean.R
+\docType{methods}
+\name{extracts.obiclean,metabarcoding.data-method}
+\alias{extracts.obiclean,metabarcoding.data-method}
+\alias{extracts.obiclean-methods,metabarcoding.data}
+\title{Extracts the obiclean results}
+\usage{
+\S4method{extracts.obiclean}{metabarcoding.data}(obj)
+}
+\arguments{
+\item{obj}{the \code{\linkS4class{metabarcoding.data}} to analyze}
+}
+\value{
+the modified \code{\linkS4class{metabarcoding.data}} instance
+}
+\description{
+The method \code{extracts.obiclean} of the class \code{\linkS4class{metabarcoding.data}}
+extracts \code{obiclean} results from the MOTUs descriptions include in the 
+\code{\linkS4class{metabarcoding.data}} instance. 
+When an \code{obitab} file is imported using the \code{\link{import.metabarcoding.data}}
+if \code{obiclean} results are present in the file they are stored in the 
+\code{motu} data.frame. By calling this methods, MOTU descriptors describing 
+the \code{obiclean} status are moved to a set of layers.
+}
+\examples{
+
+# load termite data set from the ROBITools sample data
+data(termes)
+
+# shows the initial list of layer names
+layer.names(t)
+
+# extracts the obiclean status
+termes = extracts.obiclean(termes)
+
+# shows the name of the newly created layers
+layer.names(t)
+
+
+
+}
+\seealso{
+\code{\linkS4class{metabarcoding.data}}, \code{\link{threshold.mask}}, \code{\link{normalize}}
+}
+\author{
+Eric Coissac
+}