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## rTrait.R (2021-12-15)
## Trait Evolution
## Copyright 2010-2021 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
rTraitDisc <-
function(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
rate = 0.1, states = LETTERS[1:k], freq = rep(1/k, k),
ancestor = FALSE, root.value = 1, ...)
{
if (is.null(phy$edge.length))
stop("tree has no branch length")
if (any(phy$edge.length < 0))
stop("at least one branch length negative")
if (is.character(model)) {
switch(toupper(model), "ER" = {
if (length(rate) != 1)
stop("`rate' must have one element")
Q <- matrix(rate, k, k)
}, "ARD" = {
if (length(rate) != k*(k - 1))
stop("`rate' must have k(k - 1) elements")
Q <- matrix(0, k, k)
Q[col(Q) != row(Q)] <- rate
}, "SYM" = {
if (length(rate) != k*(k - 1)/2)
stop("`rate' must have k(k - 1)/2 elements")
Q <- matrix(0, k, k)
sel <- col(Q) < row(Q)
Q[sel] <- rate
Q <- t(Q)
Q[sel] <- rate
})
}
if (is.matrix(model)) {
Q <- model
if (ncol(Q) != nrow(Q))
stop("the matrix given as `model' must be square")
}
phy <- reorder(phy, "postorder")
n <- length(phy$tip.label)
N <- dim(phy$edge)[1]
ROOT <- n + 1L
x <- integer(n + phy$Nnode)
x[ROOT] <- as.integer(root.value)
anc <- phy$edge[, 1]
des <- phy$edge[, 2]
el <- phy$edge.length
if (!is.function(model)) {
if (requireNamespace("expm", quietly = TRUE)) {
FOO <- expm::expm
} else {
warning("package expm not available, using ape::matexpo instead")
FOO <- matexpo
}
}
if (is.function(model)) {
environment(model) <- environment() # to find 'k'
for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i], ...)
} else {
freq <- rep(freq, each = k)
Q <- Q * freq
diag(Q) <- 0
diag(Q) <- -rowSums(Q)
for (i in N:1) {
p <- FOO(Q * el[i])[x[anc[i]], ]
x[des[i]] <- sample.int(k, size = 1, FALSE, prob = p)
}
}
if (ancestor) {
if (is.null(phy$node.label)) phy <- makeNodeLabel(phy)
names(x) <- c(phy$tip.label, phy$node.label)
} else {
x <- x[1:n]
names(x) <- phy$tip.label
}
class(x) <- "factor"
levels(x) <- states
x
}
rTraitCont <-
function(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
ancestor = FALSE, root.value = 0, ...)
{
if (is.null(phy$edge.length))
stop("tree has no branch length")
if (any(phy$edge.length < 0))
stop("at least one branch length negative")
phy <- reorder(phy, "postorder")
n <- length(phy$tip.label)
N <- dim(phy$edge)[1]
ROOT <- n + 1L
x <- numeric(n + phy$Nnode)
x[ROOT] <- root.value
anc <- phy$edge[, 1]
des <- phy$edge[, 2]
el <- phy$edge.length
if (is.function(model)) {
environment(model) <- environment()
for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i], ...)
} else {
model <- pmatch(toupper(model), c("BM", "OU"))
if (length(sigma) == 1) sigma <- rep(sigma, N)
else if (length(sigma) != N)
stop("'sigma' must have one or Nedge(phy) elements")
if (model == 2) { # "OU"
if (length(alpha) == 1) alpha <- rep(alpha, N)
else if (length(alpha) != N)
stop("'alpha' must have one or Nedge(phy) elements")
if (length(theta) == 1) theta <- rep(theta, N)
else if (length(theta) != N)
stop("'theta' must have one or Nedge(phy) elements")
}
x <- .C(C_rTraitCont, as.integer(model), as.integer(N),
as.integer(anc - 1L), as.integer(des - 1L), el,
as.double(sigma), as.double(alpha), as.double(theta),
x = x, NAOK = TRUE)$x
}
if (ancestor) {
if (is.null(phy$node.label)) phy <- makeNodeLabel(phy)
names(x) <- c(phy$tip.label, phy$node.label)
} else {
x <- x[1:n]
names(x) <- phy$tip.label
}
x
}
rTraitMult <-
function(phy, model, p = 1, root.value = rep(0, p), ancestor = FALSE,
asFactor = NULL, trait.labels = paste("x", 1:p, sep = ""), ...)
{
phy <- reorder(phy, "postorder")
n <- length(phy$tip.label)
m <- phy$Nnode
N <- dim(phy$edge)[1]
ROOT <- n + 1L
x <- matrix(0, n + m, p)
x[ROOT, ] <- root.value
anc <- phy$edge[, 1]
des <- phy$edge[, 2]
el <- phy$edge.length
if (is.null(el)) el <- numeric(N)
environment(model) <- environment() # to find 'p'
for (i in N:1) x[des[i], ] <- model(x[anc[i], ], el[i], ...)
if (ancestor) {
if (is.null(phy$node.label)) phy <- makeNodeLabel(phy)
rownames(x) <- c(phy$tip.label, phy$node.label)
} else {
x <- x[1:n, , drop = FALSE]
rownames(x) <- phy$tip.label
}
x <- as.data.frame(x)
names(x) <- trait.labels
if (!is.null(asFactor)) {
for (i in asFactor) {
y <- x[, i]
x[, i] <- factor(y, labels = LETTERS[1:length(unique(y))])
}
}
x
}
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