phylogeny/sunplin-functions.r

In Between-the-Fjords/seedclim-data: Code for Cleaning SeedClim data

library(ape)

sunplin.read.nexus <- function ( localFile ) {
	return ( read.nexus(localFile) );
}

sunplin.tree2newick <- function( Tree ){
	return (write.tree(Tree))
}

sunplin.n.tree <- function ( fileOrText, nth, typeInput ){
	if( typeInput == "tree" ){
		write(fileOrText, "temp", sep = "\n")
		fileOrText = "temp"
	}
	ret <- strsplit(scan(fileOrText, what = character(), skip = nth, nlines = 1 ), " ")[[4]]
	return (read.tree(text=ret))
}

sunplin.n.mat <- function ( fileName, nth ){
	ret <- scan(fileName, what = character(), nlines = 1)
	if( is.numeric(ret[1]) == TRUE ) qtdNodes <- as.numeric(ret[1])
	else qtdNodes <- as.numeric(ret[2])
	ret <- scan(fileName, what = character(), sep = '\n', skip = (((nth-1)*(qtdNodes+1) + 1)), nlines =(qtdNodes) + 1)
	ret <- strsplit(ret,"\t")
	mat <- round(lower.tri(matrix(1,qtdNodes+1,qtdNodes+1)))
	for(i in 1 : qtdNodes+1 )
		mat[1,i] <- ret[[1]][i]
	for(i in 2 : qtdNodes+1){
		for(j in 1 : i-1 ){
			mat[i,j] <- ret[[i]][j]
		}
	}
	return (mat)
}

sunplin.expd <- function( fileTree, filePuts, numTree, method ){
    dyn.load("sunplin.spn")
	return (.Call("expd", fileTree, filePuts, numTree, method))
}

sunplin.dist <- function( fileOrText, typeInput ){
    dyn.load("sunplin.spn")
	return (.Call("dist", fileOrText, typeInput))
}