1 ## phymltest.R (2009-03-29)
3 ## Fits a Bunch of Models with PhyML
5 ## Copyright 2004-2009 Emmanuel Paradis
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
11 c("JC69", "JC69+I", "JC69+G", "JC69+I+G",
12 "K80", "K80+I", "K80+G", "K80+I+G",
13 "F81", "F81+I", "F81+G", "F81+I+G",
14 "F84", "F84+I", "F84+G", "F84+I+G",
15 "HKY85", "HKY85+I", "HKY85+G", "HKY85+I+G",
16 "TN93", "TN93+I", "TN93+G", "TN93+I+G",
17 "GTR", "GTR+I", "GTR+G", "GTR+I+G")
20 c(1, 2, 2, 3, 2, 3, 3, 4, 4, 5, 5, 6, 5, 6, 6, 7,
21 5, 6, 6, 7, 6, 7, 7, 8, 9, 10, 10, 11)
23 phymltest <- function(seqfile, format = "interleaved", itree = NULL,
24 exclude = NULL, execname = NULL, append = TRUE)
27 ## default names of PhyML:
28 if (is.null(execname)) {
29 if (os == "Linux") execname <- "phyml_3.0.1_linux32"
30 if (os == "Darwin") execname <- "phyml_3.0.1_macintel"
31 if (os == "Windows") execname <- "phyml_3.0.1_win32"
33 if (is.null(execname))
34 stop("you must give an executable file name for PHYML")
35 N <- length(.phymltest.model)
36 format <- match.arg(format, c("interleaved", "sequential"))
38 if (format != "interleaved") fmt[] <- "-q"
39 boot <- rep("-b 0", N) # to avoid any testing
40 mdl <- paste("-m", rep(c("JC69", "K80", "F81", "HKY85", "F84", "TN93", "GTR"), each = 4))
41 tstv <- rep("-t e", N) # ignored by PhyML with JC69 or F81
42 inv <- rep(c("", "-v e"), length.out = N)
43 ## no need to use the -c option of PhyML (4 categories by default if '-a e' is set):
44 alpha <- rep(rep(c("-c 1", "-a e"), each = 2), length.out = N)
46 if (!is.null(itree)) tree[] <- paste("-u ", itree)
48 cmd <- paste(execname, "-i", seqfile, fmt, boot, mdl, tstv, inv, alpha, tree, "--append ")
49 outfile <- paste(seqfile, "_phyml_stats.txt", sep = "")
52 unlink(paste(seqfile, "_phyml_tree.txt", sep = ""))
55 if (!is.null(exclude)) imod <- imod[!.phymltest.model %in% exclude]
57 for (i in imod) system(cmd[i])
59 l <- readLines(outfile)
60 l <- grep("Log-likelihood:", l, value = TRUE)
61 ## in case there were already some results in the output file:
62 if (dd <- length(l) - length(imod)) l <- l[-(1:dd)]
63 loglik <- as.numeric(sub(". Log-likelihood:", "", l))
64 names(loglik) <- .phymltest.model[imod]
65 class(loglik) <- "phymltest"
69 print.phymltest <- function(x, ...)
71 nfp <- .phymltest.nfp[.phymltest.model %in% names(x)]
72 X <- cbind(nfp, x, 2 * (nfp - x))
73 rownames(X) <- names(x)
74 colnames(X) <- c("nb.free.para", "loglik", "AIC")
78 summary.phymltest <- function(object, ...)
80 nfp <- .phymltest.nfp[.phymltest.model %in% names(object)]
82 model1 <- model2 <- character(0)
83 chi2 <- df <- P.val <- numeric(0)
84 for (i in 1:(N - 1)) {
85 for (j in (i + 1):N) {
86 if (nfp[i] >= nfp[j]) next
87 m1 <- unlist(strsplit(names(object)[i], "\\+"))
88 m2 <- unlist(strsplit(names(object)[j], "\\+"))
89 if (m1[1] == "K80" && m2[1] == "F81") next
90 ## à vérifier que ds les 2 lignes suivantes les conversions
91 ## se font bien correctement!!!!
92 if (length(grep("\\+I", names(object)[i])) > 0 && length(grep("\\+I", names(object)[j])) == 0) next
93 if (length(grep("\\+G", names(object)[i])) > 0 && length(grep("\\+G", names(object)[j])) == 0) next
94 ## Now we should be sure that m1 is nested in m2.
95 chi2 <- c(chi2, 2 * (object[j] - object[i]))
96 df <- c(df, nfp[j] - nfp[i])
97 P.val <- c(P.val, 1 - pchisq(2 * (object[j] - object[i]), nfp[j] - nfp[i]))
98 model1 <- c(model1, names(object)[i])
99 model2 <- c(model2, names(object)[j])
102 data.frame(model1, model2, chi2, df, P.val = round(P.val, 4))
105 plot.phymltest <- function(x, main = NULL, col = "blue", ...)
107 nfp <- .phymltest.nfp[.phymltest.model %in% names(x)]
111 main <- paste("Akaike information criterion for",
112 deparse(substitute(x)))
113 plot(rep(1, N), aic, bty = "n", xaxt = "n", yaxt = "n",
114 type = "n", xlab = "", ylab = "", main = main, ...)
115 axis(side = 2, pos = 0.85, las = 2)
117 y.lab <- seq(min(aic), max(aic), length = N)
118 segments(0.85, sort(aic), 1.1, y.lab, col = col)
120 parse(text = sub("\\+G", "\\+Gamma", names(sort(aic)))),