% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/class2tree.R
\name{class2tree}
\alias{class2tree}
\alias{plot.classtree}
\alias{print.classtree}
\title{Convert list of classifications to a tree.}
\usage{
class2tree(input, varstep = TRUE, check = TRUE, ...)

\method{plot}{classtree}(x, ...)

\method{print}{classtree}(x, ...)
}
\arguments{
\item{input}{List of classification data.frame's from the function
\code{\link{classification}}}

\item{varstep}{Vary step lengths between successive levels relative to
proportional loss of the number of distinct classes.}

\item{check}{If TRUE, remove all redundant levels which are different for
all rows or constant for all rows and regard each row as a different basal
taxon (species). If FALSE all levels are retained and basal taxa (species)
also must be coded as variables (columns). You will get a warning if
species are not coded, but you can ignore this if that was your intention.}

\item{...}{Further arguments passed on to hclust.}

\item{x}{Input object to print or plot - output from class2tree function.}
}
\value{
An object of class "classtree" with slots:
\itemize{
 \item phylo - The resulting object, a phylo object
 \item classification - The classification data.frame, with taxa as rows,
 and different classification levels as columns
 \item distmat - Distance matrix
 \item names - The names of the tips of the phylogeny
}

Note that when you execute the resulting object, you only get the phylo
object. You can get to the other 3 slots by calling them directly, like
output$names, etc.
}
\description{
This function converts a list of hierarchies for individual species into
a single species by taxonomic level matrix, then calculates a distance
matrix based on taxonomy alone, and outputs either a phylo or dist object.
See details for more information.
}
\details{
See \code{\link[vegan]{taxa2dist}}. Thanks to Jari Oksanen for
making the taxa2dist function and pointing it out, and Clarke & Warwick
(1998, 2001), which taxa2dist was based on.
}
\examples{
\dontrun{
spnames <- c('Quercus robur', 'Iris oratoria', 'Arachis paraguariensis',
 'Helianthus annuus','Madia elegans','Lupinus albicaulis',
 'Pinus lambertiana')
out <- classification(spnames, db='itis')
tr <- class2tree(out)
plot(tr)

spnames <- c('Klattia flava', 'Trollius sibiricus', 'Arachis paraguariensis',
 'Tanacetum boreale', 'Gentiana yakushimensis','Sesamum schinzianum',
 'Pilea verrucosa','Tibouchina striphnocalyx','Lycium dasystemum',
 'Berkheya echinacea','Androcymbium villosum',
 'Helianthus annuus','Madia elegans','Lupinus albicaulis',
 'Pinus lambertiana')
out <- classification(spnames, db='ncbi')
tr <- class2tree(out)
plot(tr)
}
}
