Commit the man pages and make aggregate public again

man/extrapol.freq.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/distrib.extrapol.R
+\name{extrapol.freq}
+\alias{extrapol.freq}
+\title{Read frequencies krigging}
+\usage{
+extrapol.freq(x, min.coord, max.coord, grid.grain = 100, coords, otus.table,
+  cutoff = 0.001, return.metabarcoding.data = FALSE)
+}
+\arguments{
+\item{x}{a vector or matrix from a row-normalized read table 
+\code{\link{metabarcoding.data}} object}
+
+\item{min.coord}{a vector of length = 2 indicating the minimum values of x and y
+coordinates to be used for the predicted grid}
+
+\item{max.coord}{a vector of length = 2 indicating the maximum values of x and y
+coordinates to be used for the predicted grid}
+
+\item{grid.grain}{an integer indicating the resolution (i.e. nb of subpoints) in x and y
+coordinates required for the predicted grid}
+
+\item{coords}{a dataframe containing the x and y coordinates of the abundances 
+from x to be extrapolated.}
+
+\item{otus.table}{a motus data.frame containing motus informations of x}
+
+\item{cutoff}{a cutoff below which abundances are set to 0. 
+This threshold also determines the value to be added to 0 values for log10 
+transformation}
+
+\item{return.metabarcoding.data}{if \code{TRUE}, returns a \code{\link{metabarcoding.data}} object. Default is \code{FALSE}}
+}
+\value{
+either a dataframe or a S3 object with a structure similar to \code{\link{metabarcoding.data}} object. 
+        The number of samples corresponds to the predicted points.
+        The two last columns (if \code{return.metabarcoding.data==F}) or sample data.frame contains x y coordinates of the predicted grid
+        The all but last two columns (if \code{return.metabarcoding.data==F}) or read matrix contains the predicted log10 transformed relative abundances 
+        instead of reads counts
+        If \code{return.metabarcoding.data==F} the motus data.frame contains the motus informations from x
+}
+\description{
+Extrapolates read frequencies from a \code{\link{metabarcoding.data}} object in space for a finer resolution
+}
+\examples{
+
+data(termes)
+#Create dummy spatial coordinates
+attr(termes, "samples")[c("x", "y")] = expand.grid(1:7,1:3)
+
+#compute frequencies
+attr(termes, "layers")[["reads.freq"]] = normalize(termes, MARGIN=1)$reads
+
+# Getting extrapolations
+termes.pred = extrapol.freq(attr(termes, "layers")[["reads.freq"]], min.coord=c(1,1), max.coord=c(7,3), 
+                            grid.grain=100,termes$samples[,c("x", "y")], termes$motus, cutoff=1e-3)
+
+head(termes.pred$reads)
+}
+\seealso{
+\code{\link{map.extrapol.freq}} as well as \code{sp} and \code{gstat} packages
+}
+\author{
+Lucie Zinger
+}