Commit the man pages and make aggregate public again

man/m.univariate.test.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mstat.R
+\name{m.univariate.test}
+\alias{m.univariate.test}
+\title{Test the significance of the M statistics by Monte-Carlo}
+\usage{
+m.univariate.test(w, groups, resampling = 100, alternative = "two.sided")
+}
+\arguments{
+\item{w}{the weigth matrix indicating the presence probability of each motu
+in each samples. Each line corresponds to a sample and each column
+to a MOTU. \code{rownames} of the \code{w} matrix must be the sample
+names.}
+
+\item{groups}{the list of considered groups as computed by the \code{\link{dist.center.group}}
+function}
+
+\item{resampling}{the number of simulation to establish the null distribution}
+
+\item{alternative}{a character value in \code{c('two.sided','less','greater')}
+- two.sided : the m stat is check against the two side of the empirical
+              M distribution
+- less : test if the M stat is lesser than the M observed in the the empirical
+              M distribution (exlusion hypothesis)
+- greater : test if the M stat is greater than the M observed in the the empirical
+              M distribution (aggregation hypothesis)}
+}
+\value{
+a vector of p.value with an attribute \code{m.stat} containing the actual M stat
+        for each MOTUs
+}
+\description{
+Computes computes the p.value the M statistics asociated to a MOTU
+by shuffling MOTUs among location.
+}
+\examples{
+      
+data(termes)
+termes.ok = termes[,colSums(termes$reads)>0]
+pos = expand.grid(1:3 * 10,1:7 * 10)
+labels = rownames(termes.ok)
+d = dist.grid(pos[,1],pos[2],labels)
+groups = dist.center.group(d,20)
+w = m.weight(termes.ok)
+pval = m.univariate.test(w,groups)
+
+}