% 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).  If a character is supplied
as a named list, and the names correspond to the names of the tips, then
this parameter will be ignored and the names of the characters will be used
to match them to the names of the tips.}
}
\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
}