# TOOD - write quick function to build a nexus file from read in matrix + text
#' @param x list containing, minimimally, data matrix (in matrix form)
#' @param data the data matrix
# mattext <- readLines("data/theropods/brusatte2014_matrix.txt")
# chartext <- readLines("data/theropods/brusatte2014_charlist.txt")
# mat <- text2mat(mattext)
# charlabs <- text2charlabels(chartext)
# twig1 <- buildnex2(data=mat, charlabels=charlabs)
buildnex2 <- function(data, charlabels=NULL, charnums=NULL, statelabels=NULL, taxlabels=NULL, filename=NULL) {
if (is.null(taxlabels)) {
if (is.null(rownames(data))) {
taxlabels <- rep('', nrow(data))
} else {
taxlabels <- rownames(data)
}
}
if (is.null(statelabels)) {
statelabels <- rep('', ncol(data))
}
if (is.null(charlabels)) {
charlabels <- rep('', ncol(data))
}
if (is.null(charnums)) {
charnums <- 1:ncol(data)
}
if (is.null(filename)) {
filename <- "file"
}
file <- rep(filename, ncol(data))
dimnames(data) <- NULL
res <- list(data = data, file = file, taxlabels = taxlabels, charlabels = charlabels, statelabels = statelabels, charnums = charnums, missing = "?", gap="-")
class(res) <- c("nex", "list")
res
}
# mattext <- readLines("/Users/chadeliason/Documents/UT/projects/phenome/data/theropods/brusatte2014_matrix.txt")
# chartext <- readLines("/Users/chadeliason/Documents/UT/projects/phenome/data/theropods/brusatte2014_charlist.txt")
# mat <- text2mat(mattext)
# charlabs <- text2charlabels(chartext)
# length(charlabs)
# twig1 <- buildnex2(data=mat, charlabels=charlabs)
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