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## pic.R (2017-08-22)
## Phylogenetically Independent Contrasts
## Copyright 2002-2017 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
pic <- function(x, phy, scaled = TRUE, var.contrasts = FALSE, rescaled.tree = FALSE)
{
if (!inherits(phy, "phylo")) stop("object 'phy' is not of class \"phylo\"")
if (is.null(phy$edge.length)) stop("your tree has no branch lengths")
nb.tip <- length(phy$tip.label)
nb.node <- phy$Nnode
if (nb.node != nb.tip - 1)
stop("'phy' is not rooted and fully dichotomous")
if (length(x) != nb.tip)
stop("length of phenotypic and of phylogenetic data do not match")
if (any(is.na(x)))
stop("missing data in 'x': you may consider removing the species with missing data from your tree with the function 'drop.tip'.")
phy <- reorder(phy, "postorder")
phenotype <- numeric(nb.tip + nb.node)
if (is.null(names(x))) {
phenotype[1:nb.tip] <- x
} else {
if (all(names(x) %in% phy$tip.label))
phenotype[1:nb.tip] <- x[phy$tip.label]
else {
phenotype[1:nb.tip] <- x
warning("the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis.")
}
}
## No need to copy the branch lengths: they are rescaled
## in the C code, so it's important to leave the default
## `DUP = TRUE' of .C.
ans <- .C(C_pic, as.integer(nb.tip),
as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
as.double(phy$edge.length), as.double(phenotype),
double(nb.node), double(nb.node),
as.integer(var.contrasts), as.integer(scaled))
contr <- ans[[6]]
lbls <-
if (is.null(phy$node.label)) as.character(1:nb.node + nb.tip)
else phy$node.label
if (var.contrasts) {
contr <- cbind(contr, ans[[7]])
dimnames(contr) <- list(lbls, c("contrasts", "variance"))
} else names(contr) <- lbls
if (rescaled.tree) {
phy$edge.length <- ans[[4]]
contr <- list(contr = contr, rescaled.tree = phy)
}
contr
}
pic.ortho <- function(x, phy, var.contrasts = FALSE, intra = FALSE)
{
n <- length(x)
m <- n - 1L # number of nodes
phy <- reorder(phy, "postorder")
xx <- unlist(lapply(x, mean)) # 'x' in Felsenstein's paper
xx <- c(xx, numeric(m))
delta.v <- numeric(n + m)
s <- 1/lengths(x)
s <- c(s, numeric(m))
contrast <- var.cont <- numeric(m)
i <- 1L
while (i < m + n) {
d1 <- phy$edge[i, 2]
d2 <- phy$edge[i + 1L, 2]
a <- phy$edge[i, 1]
tmp1 <- 1/(phy$edge.length[i] + delta.v[d1])
tmp2 <- 1/(phy$edge.length[i + 1L] + delta.v[d2])
xx[a] <- (tmp1 * xx[d1] + tmp2 * xx[d2])/(tmp1 + tmp2)
delta.v[a] <- 1/(tmp1 + tmp2)
f1 <- tmp1/(tmp1 + tmp2)
f2 <- tmp2/(tmp1 + tmp2)
s[a] <- f1*f1 * s[d1] + f2*f2 * s[d2]
tmp <- 1/(s[d1] + s[d2])
contrast[a - n] <- (xx[d1] - xx[d2]) * sqrt(tmp)
var.cont[a - n] <- (1/tmp1 + 1/tmp2) * tmp
i <- i + 2L
}
lbls <-
if (is.null(phy$node.label)) as.character(1:m + n)
else phy$node.label
if (var.contrasts) {
contrast <- cbind(contrast, var.cont)
dimnames(contrast) <- list(lbls, c("contrasts", "variance"))
} else names(contrast) <- lbls
if (intra) {
intraspe.ctr <- function(x) {
k <- length(x) - 1L
if (!k) return(NULL)
ctr <- numeric(k)
ctr[1L] <- x[1L] - x[2L]
if (k > 1)
for (i in 2:k)
ctr[i] <- x[i + 1L] - mean(x[1:i])
sqrt((1:k)/(1:k + 1)) * ctr
}
tmp <- lapply(x, intraspe.ctr)
names(tmp) <- phy$tip.label
attr(contrast, "intra") <- tmp
}
contrast
}
varCompPhylip <- function(x, phy, exec = NULL)
{
n <- Ntip(phy)
if (is.vector(x)) x <- as.list(x)
if (is.matrix(x) || is.data.frame(x)) {
tmpx <- vector("list", n)
for (i in 1:n) tmpx[[i]] <- x[i, , drop = FALSE]
names(tmpx) <- rownames(x)
x <- tmpx
}
p <- if (is.vector(x[[1]])) 1L else ncol(x[[1]])
if (!is.null(names(x))) x <- x[phy$tip.label]
phy <- makeLabel(phy, len = 10)
lbs <- phy$tip.label
ni <- sapply(x, function(xx) if (is.vector(xx)) 1L else nrow(xx))
pfx <- tempdir()
write.tree(phy, file = paste(pfx, "intree", sep = "/"))
infile <- paste(pfx, "infile", sep = "/")
file.create(infile)
cat(n, " ", p, "\n", sep = "", file = infile, append = TRUE)
for (i in 1:n) {
cat(lbs[i], file = infile, append = TRUE)
## can surely be better but OK for the moment:
cat(paste(rep(" ", 11 - nchar(lbs[i])), collapse = ""),
file = infile, append = TRUE)
cat(ni[i], "\n", sep = "", file = infile, append = TRUE)
if (ni[i] == 1) {
cat(x[[i]], sep = " ", file = infile, append = TRUE)
cat("\n", file = infile, append = TRUE)
} else write(t(x[[i]]), file = infile, ncolumns = p, append = TRUE)
}
if (is.null(exec))
exec <-
if (.Platform$OS.type == "unix") "phylip contrast"
else "contrast"
odir <- setwd(pfx)
on.exit(setwd(odir))
if (file.exists("outfile")) unlink("outfile")
system(exec, intern = TRUE, input = c("W", "A", "Y"))
varA <- scan("outfile", skip = 7, nlines = p, quiet = TRUE)
varE <- scan("outfile", skip = 11 + p, nlines = p, quiet = TRUE)
if (p > 1) {
varA <- matrix(varA, p, p, byrow = TRUE)
varE <- matrix(varE, p, p, byrow = TRUE)
}
list(varA = varA, varE = varE)
}
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