X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fsummary.phylo.R;h=f390b24d25bbb936331e26fea1e25aa51a45dd5a;hb=0d2caf41f13f7a3e8a313274cf819147940eac69;hp=bf01266aec96cc2c82d40fe7ff62c0f63b1fc83e;hpb=0875d81d5ba5e6dfe79d42c21b0284b674c73949;p=ape.git

diff --git a/R/summary.phylo.R b/R/summary.phylo.R
index bf01266..f390b24 100644
--- a/R/summary.phylo.R
+++ b/R/summary.phylo.R
@@ -1,8 +1,8 @@
-## summary.phylo.R (2010-05-25)
+## 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.
@@ -70,18 +70,6 @@ summary.phylo <- function(object, ...)
 
         }
     }
-    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:
@@ -97,10 +85,10 @@ print.phylo <- function(x, printlen = 6,...)
                               collapse=", "), ", ...\n", sep = ""))
     } else print(x$tip.label)
     if (!is.null(x$node.label)) {
-        cat("\tNode labels:\n")
+        cat("Node 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"
@@ -118,7 +106,6 @@ print.multiPhylo <- function(x, details = FALSE, ...)
     if (details)
       for (i in 1:N)
         cat("tree", i, ":", length(x[[i]]$tip.label), "tips\n")
-    cat("\n")
 }
 
 "[[.multiPhylo" <- function(x, i)
@@ -158,8 +145,8 @@ c.multiPhylo <- function(..., recursive = FALSE)
     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: