stop(paste("'model' must be one of:",
paste("\"", MODELS, "\"", sep = "", collapse = " ")))
if (imod == 11 && variance) {
- warning("computing variance temporarily not available for model BH87.")
+ warning("computing variance not available for model BH87.")
variance <- FALSE
}
if (gamma && imod %in% c(1, 5:7, 9:15)) {
-## compute.brtime.R (2011-07-15)
+## compute.brtime.R (2011-07-26)
## Compute and Set Branching Times
## x: branching times (aka, node ages or heights)
if (identical(method, "coalescent")) { # the default
- x <- 2 * rexp(n - 1)/(as.double(n:2) * as.double((n - 1):1))
- if (is.null(force.positive))
- force.positive <- TRUE
+ x <- 2 * rexp(m)/(as.double((m + 1):2) * as.double(m:1))
+ ## x <- 2 * rexp(n - 1)/(as.double(n:2) * as.double((n - 1):1))
+ if (is.null(force.positive)) force.positive <- TRUE
} else if (is.numeric(method)) {
x <- as.vector(method)
if (length(x) != m)
-## summary.phylo.R (2010-11-03)
+## summary.phylo.R (2011-08-04)
## Print Summary of a Phylogeny and "multiPhylo" operators
-## Copyright 2003-2010 Emmanuel Paradis, and 2006 Ben Bolker
+## Copyright 2003-2011 Emmanuel Paradis, and 2006 Ben Bolker
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
}
}
- if (!is.null(attr(object, "loglik"))) {
- cat("Phylogeny estimated by maximum likelihood.\n")
- cat(" log-likelihood:", attr(object, "loglik"), "\n\n")
- npart <- length(attr(object, "para"))
- for (i in 1:npart) {
- cat("partition ", i, ":\n", sep = "")
- print(attr(object, "para")[[i]])
- if (i == 1) next
- else cat(" contrast parameter (xi):",
- attr(object, "xi")[i - 1], "\n")
- }
- }
}
### by BB:
cat("\tNode labels:\n")
if (nb.node > printlen) {
cat(paste("\t", paste(x$node.label[1:printlen],
- collapse=", "), ",...\n", sep = ""))
+ collapse=", "), ", ...\n", sep = ""))
} else print(x$node.label)
}
rlab <- if (is.rooted(x)) "Rooted" else "Unrooted"
n <- length(obj)
x <- obj[[1L]]
N <- length(x)
- i <- 1L
- while (i < n) {
+ i <- 2L
+ while (i <= n) {
a <- N + 1L
N <- N + length(obj[[i]])
## x is of class "multiPhylo", so this uses the operator below: