## phymltest.R (2009-03-29)
## Fits a Bunch of Models with PhyML
## Copyright 2004-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
.phymltest.model <-
c("JC69", "JC69+I", "JC69+G", "JC69+I+G",
"K80", "K80+I", "K80+G", "K80+I+G",
"F81", "F81+I", "F81+G", "F81+I+G",
"F84", "F84+I", "F84+G", "F84+I+G",
"HKY85", "HKY85+I", "HKY85+G", "HKY85+I+G",
"TN93", "TN93+I", "TN93+G", "TN93+I+G",
"GTR", "GTR+I", "GTR+G", "GTR+I+G")
.phymltest.nfp <-
c(1, 2, 2, 3, 2, 3, 3, 4, 4, 5, 5, 6, 5, 6, 6, 7,
5, 6, 6, 7, 6, 7, 7, 8, 9, 10, 10, 11)
phymltest <- function(seqfile, format = "interleaved", itree = NULL,
exclude = NULL, execname = NULL, append = TRUE)
{
os <- Sys.info()[1]
## default names of PhyML:
if (is.null(execname)) {
if (os == "Linux") execname <- "phyml_3.0.1_linux32"
if (os == "Darwin") execname <- "phyml_3.0.1_macintel"
if (os == "Windows") execname <- "phyml_3.0.1_win32"
}
if (is.null(execname))
stop("you must give an executable file name for PHYML")
N <- length(.phymltest.model)
format <- match.arg(format, c("interleaved", "sequential"))
fmt <- rep("", N)
if (format != "interleaved") fmt[] <- "-q"
boot <- rep("-b 0", N) # to avoid any testing
mdl <- paste("-m", rep(c("JC69", "K80", "F81", "HKY85", "F84", "TN93", "GTR"), each = 4))
tstv <- rep("-t e", N) # ignored by PhyML with JC69 or F81
inv <- rep(c("", "-v e"), length.out = N)
## no need to use the -c option of PhyML (4 categories by default if '-a e' is set):
alpha <- rep(rep(c("-c 1", "-a e"), each = 2), length.out = N)
tree <- rep("", N)
if (!is.null(itree)) tree[] <- paste("-u ", itree)
cmd <- paste(execname, "-i", seqfile, fmt, boot, mdl, tstv, inv, alpha, tree, "--append ")
outfile <- paste(seqfile, "_phyml_stats.txt", sep = "")
if (!append) {
unlink(outfile)
unlink(paste(seqfile, "_phyml_tree.txt", sep = ""))
}
imod <- 1:N
if (!is.null(exclude)) imod <- imod[!.phymltest.model %in% exclude]
for (i in imod) system(cmd[i])
l <- readLines(outfile)
l <- grep("Log-likelihood:", l, value = TRUE)
## in case there were already some results in the output file:
if (dd <- length(l) - length(imod)) l <- l[-(1:dd)]
loglik <- as.numeric(sub(". Log-likelihood:", "", l))
names(loglik) <- .phymltest.model[imod]
class(loglik) <- "phymltest"
loglik
}
print.phymltest <- function(x, ...)
{
nfp <- .phymltest.nfp[.phymltest.model %in% names(x)]
X <- cbind(nfp, x, 2 * (nfp - x))
rownames(X) <- names(x)
colnames(X) <- c("nb.free.para", "loglik", "AIC")
print(X)
}
summary.phymltest <- function(object, ...)
{
nfp <- .phymltest.nfp[.phymltest.model %in% names(object)]
N <- length(object)
model1 <- model2 <- character(0)
chi2 <- df <- P.val <- numeric(0)
for (i in 1:(N - 1)) {
for (j in (i + 1):N) {
if (nfp[i] >= nfp[j]) next
m1 <- unlist(strsplit(names(object)[i], "\\+"))
m2 <- unlist(strsplit(names(object)[j], "\\+"))
if (m1[1] == "K80" && m2[1] == "F81") next
## à vérifier que ds les 2 lignes suivantes les conversions
## se font bien correctement!!!!
if (length(grep("\\+I", names(object)[i])) > 0 && length(grep("\\+I", names(object)[j])) == 0) next
if (length(grep("\\+G", names(object)[i])) > 0 && length(grep("\\+G", names(object)[j])) == 0) next
## Now we should be sure that m1 is nested in m2.
chi2 <- c(chi2, 2 * (object[j] - object[i]))
df <- c(df, nfp[j] - nfp[i])
P.val <- c(P.val, 1 - pchisq(2 * (object[j] - object[i]), nfp[j] - nfp[i]))
model1 <- c(model1, names(object)[i])
model2 <- c(model2, names(object)[j])
}
}
data.frame(model1, model2, chi2, df, P.val = round(P.val, 4))
}
plot.phymltest <- function(x, main = NULL, col = "blue", ...)
{
nfp <- .phymltest.nfp[.phymltest.model %in% names(x)]
N <- length(x)
aic <- 2 * (nfp - x)
if (is.null(main))
main <- paste("Akaike information criterion for",
deparse(substitute(x)))
plot(rep(1, N), aic, bty = "n", xaxt = "n", yaxt = "n",
type = "n", xlab = "", ylab = "", main = main, ...)
axis(side = 2, pos = 0.85, las = 2)
abline(v = 0.85)
y.lab <- seq(min(aic), max(aic), length = N)
segments(0.85, sort(aic), 1.1, y.lab, col = col)
text(1.1, y.lab,
parse(text = sub("\\+G", "\\+Gamma", names(sort(aic)))),
adj = 0)
}
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