% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/NA.utilities.R
\name{make.states.matrix}
\alias{make.states.matrix}
\title{Sates matrix}
\usage{
make.states.matrix(tree, character, inapplicable = NULL,
  match.tip.char = FALSE)
}
\arguments{
\item{tree}{\code{phylo}, a tree}

\item{character}{Either vector of character states (\code{"numeric"} or \code{"character"}) or a list of the same length of than the tips in the tree (see details)}

\item{inapplicable}{When the intended reconstruction method is \code{"Fitch"}, how do deal with inapplicable data: \code{1}, \code{2} for respectively treating them as ? or an extra state (default = \code{NULL}).}

\item{match.tip.char}{\code{logical}, \code{TRUE} to match the character to the tip labels (e.g character 1 matches with tip "a" or "1") or \code{FALSE} (default) to match the character to the tips entry (e.g. character 1 matches with the first tip)}
}
\value{
A list of character states for each node and tip per pass:
-\code{$Char}: a \code{list} of character states for the tips.
-\code{$Dp1}: a \code{list} of the tips' and nodes' states after the first downpass.
-\code{$Up1}: a \code{list} of the tips' and nodes' states after the first uppass.
-\code{$Dp2}: a \code{list} of the tips' and nodes' states after the second downpass.
-\code{$Up2}: a \code{list} of the tips' and nodes' states after the second uppass.
-\code{$tracker}: a \code{list} tracking the applicable regions.
-\code{$regions}: a single \code{numeric} value counting the number of applicable regions.
-\code{$changes}: a \code{numeric} vector recording the node with state changes.
-\code{$score}: a \code{numeric} vector recording the score of the tree.
-\code{$tree}: a \code{phylo} object describing the tree.
-\code{$n_tip}: a \code{numeric} vector recording the number of tips.
-\code{$n_node}: a \code{numeric} vector recording the number of (internal) nodes within the tree.
}
\description{
Creates a states matrix
}
\details{
If \code{character} argument is a list, each element of the list must be a \code{"numeric"} vector with \code{"?"} being all states and \code{"-"} being \code{-1}.
}
\examples{
## A simple topology
tree <- ape::read.tree(text = "((a,b),(c,d));")

## A simple character
character <- "0101"

## Create a states matrix for reconstruction
make.states.matrix(tree, character)

## A complex character
character <- "0{01}-?"

}
\seealso{
\code{\link{apply.reconstruction}}.
}
\author{
Thomas Guillerme
}