X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Face.R;h=b67549f9dccf4cd55b3d68b0fe5bd7ffb3f9ef8b;hb=3ece2ec76da287a8a86339827cc44e193fe16cdd;hp=c9a45110ca7eb926c0ca406494b30cf9cb9e9553;hpb=24fc6c03893f85a3f9ab3d088201b3731f3035b4;p=ape.git diff --git a/R/ace.R b/R/ace.R index c9a4511..b67549f 100644 --- a/R/ace.R +++ b/R/ace.R @@ -1,8 +1,8 @@ -## ace.R (2009-11-12) +## ace.R (2010-12-08) ## Ancestral Character Estimation -## Copyright 2005-2009 Emmanuel Paradis and Ben Bolker +## Copyright 2005-2010 Emmanuel Paradis and Ben Bolker ## This file is part of the R-package `ape'. ## See the file ../COPYING for licensing issues. @@ -12,7 +12,7 @@ ace <- function(x, phy, type = "continuous", method = "ML", CI = TRUE, scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1) { if (!inherits(phy, "phylo")) - stop('object "phy" is not of class "phylo".') + stop('object "phy" is not of class "phylo".') if (is.null(phy$edge.length)) stop("tree has no branch lengths") type <- match.arg(type, c("continuous", "discrete")) @@ -25,8 +25,7 @@ ace <- function(x, phy, type = "continuous", method = "ML", CI = TRUE, if (!is.null(names(x))) { if(all(names(x) %in% phy$tip.label)) x <- x[phy$tip.label] - else warning('the names of argument "x" and the tip labels of the tree -did not match: the former were ignored in the analysis.') + else warning("the names of 'x' and the tip labels of the tree do not match: the former were ignored in the analysis.") } obj <- list() if (kappa != 1) phy$edge.length <- phy$edge.length^kappa @@ -157,13 +156,14 @@ as the number of categories in `x'") phy <- reorder(phy, "pruningwise") Q <- matrix(0, nl, nl) - ## from Rich FitzJohn: - comp <- numeric(nb.tip + nb.node) # Storage... dev <- function(p, output.liks = FALSE) { + if (any(is.nan(p)) || any(is.infinite(p))) return(1e50) + ## from Rich FitzJohn: + comp <- numeric(nb.tip + nb.node) # Storage... Q[] <- c(p, 0)[rate] diag(Q) <- -rowSums(Q) for (i in seq(from = 1, by = 2, length.out = nb.node)) { - j <- i + 1 + j <- i + 1L anc <- phy$edge[i, 1] des1 <- phy$edge[i, 2] des2 <- phy$edge[j, 2] @@ -174,10 +174,11 @@ as the number of categories in `x'") liks[anc, ] <- v/comp[anc] } if (output.liks) return(liks[-TIPS, ]) - -2 * sum(log(comp[-TIPS])) + dev <- -2 * sum(log(comp[-TIPS])) + if (is.na(dev)) Inf else dev } out <- nlminb(rep(ip, length.out = np), function(p) dev(p), - lower = rep(0, np), upper = rep(Inf, np)) + lower = rep(0, np), upper = rep(1e50, np)) obj$loglik <- -out$objective/2 obj$rates <- out$par oldwarn <- options("warn") @@ -224,8 +225,36 @@ anova.ace <- function(object, ...) table <- data.frame(ll, df, ddf, dev, pchisq(dev, ddf, lower.tail = FALSE)) dimnames(table) <- list(1:length(X), c("Log lik.", "Df", - "Df change", "Deviance", + "Df change", "Resid. Dev", "Pr(>|Chi|)")) structure(table, heading = "Likelihood Ratio Test Table", class = c("anova", "data.frame")) } + +print.ace <- function(x, digits = 4, ...) +{ + cat("\n Ancestral Character Estimation\n\n") + cat("Call: ") + print(x$call) + cat("\n") + if (!is.null(x$loglik)) + cat(" Log-likelihood:", x$loglik, "\n\n") + ratemat <- x$index.matrix + if (is.null(ratemat)) { # to be improved + class(x) <- NULL + x$loglik <- x$call <- NULL + print(x) + } else { + dimnames(ratemat)[1:2] <- dimnames(x$lik.anc)[2] + cat("Rate index matrix:\n") + print(ratemat, na.print = ".") + cat("\n") + npar <- length(x$rates) + estim <- data.frame(1:npar, round(x$rates, digits), round(x$se, digits)) + cat("Parameter estimates:\n") + names(estim) <- c("rate index", "estimate", "std-err") + print(estim, row.names = FALSE) + cat("\nScaled likelihoods at the root (type '...$lik.anc' to get them for all nodes):\n") + print(x$lik.anc[1, ]) + } +}