fixing various bugs + news in cophyloplot

[ape.git] / R / DNA.R

diff --git a/R/DNA.R b/R/DNA.R
index 72e12582617e0927bdc5d9a2a884d5784b6c46fb..e7c0e3a85d74a51518b2a12b1a6593614877d6dc 100644 (file)
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,8 +1,8 @@
-## DNA.R (2009-09-18)
+## DNA.R (2010-03-16)
 
 ##   Manipulations and Comparisons of DNA Sequences
 
-## Copyright 2002-2009 Emmanuel Paradis
+## Copyright 2002-2010 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -90,6 +90,9 @@ rbind.DNAbin <- function(...)
     obj <- list(...)
     n <- length(obj)
     if (n == 1) return(obj[[1]])
+    for (i in 1:n)
+        if (!is.matrix(obj[[1]]))
+            stop("the 'rbind' method for \"DNAbin\" accepts only matrices")
     NC <- unlist(lapply(obj, ncol))
     if (length(unique(NC)) > 1)
         stop("matrices do not have the same number of columns.")
@@ -106,6 +109,9 @@ cbind.DNAbin <-
     obj <- list(...)
     n <- length(obj)
     if (n == 1) return(obj[[1]])
+    for (i in 1:n)
+        if (!is.matrix(obj[[1]]))
+            stop("the 'cbind' method for \"DNAbin\" accepts only matrices")
     NR <- unlist(lapply(obj, nrow))
     for (i in 1:n) class(obj[[i]]) <- NULL
     if (check.names) {
@@ -144,7 +150,11 @@ cbind.DNAbin <-
 }
 
 c.DNAbin <- function(..., recursive = FALSE)
+{
+    if (!all(unlist(lapply(list(...), is.list))))
+        stop("the 'c' method for \"DNAbin\" accepts only lists")
     structure(NextMethod("c"), class = "DNAbin")
+}
 
 print.DNAbin <- function(x, ...)
 {
@@ -292,7 +302,10 @@ dist.dna <- function(x, model = "K80", variance = FALSE, gamma = FALSE,
 {
     MODELS <- c("RAW", "JC69", "K80", "F81", "K81", "F84", "T92", "TN93",
                 "GG95", "LOGDET", "BH87", "PARALIN", "N")
-    imod <- which(MODELS == toupper(model))
+    imod <- pmatch(toupper(model), MODELS)
+    if (is.na(imod))
+        stop(paste("'model' must be one of:",
+                   paste("\"", MODELS, "\"", sep = "", collapse = " ")))
     if (imod == 11 && variance) {
         warning("computing variance temporarily not available for model BH87.")
         variance <- FALSE