From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Thu, 2 Oct 2008 15:40:07 +0000 (+0000)
Subject: bug corrected in del.gaps + small change in man page of theta.s
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=19e6ab24fb4e4b32cb867aef0b5bf57707344641;p=ape.git

bug corrected in del.gaps + small change in man page of theta.s

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@51 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/Changes b/Changes
index 0ca803e..854ae19 100644
--- a/Changes
+++ b/Changes
@@ -19,6 +19,9 @@ BUG FIXES
    o read.nexus() failed to read a file with a single tree with line
      breaks in the Newick string.
 
+   o del.gaps() returned a list of empty sequences when there were no
+     gaps.
+
 
 OTHER CHANGES
 
diff --git a/DESCRIPTION b/DESCRIPTION
index 1b4f9b9..6debdb3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.2-2
-Date: 2008-09-17
+Date: 2008-10-02
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
diff --git a/R/DNA.R b/R/DNA.R
index 90e841b..6704bbe 100644
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,4 +1,4 @@
-## DNA.R (2008-08-07)
+## DNA.R (2008-10-02)
 
 ##   Manipulations and Comparisons of DNA Sequences
 
@@ -11,7 +11,7 @@ del.gaps <- function(x)
 {
     deleteGaps <- function(x) {
         i <- which(x == 4)
-        x[-i]
+        if (length(i)) x[-i] else x
     }
 
     if (class(x) != "DNAbin") x <- as.DNAbin(x)
diff --git a/man/theta.s.Rd b/man/theta.s.Rd
index 70115d0..bd7a378 100644
--- a/man/theta.s.Rd
+++ b/man/theta.s.Rd
@@ -40,9 +40,8 @@ theta.s(s, n, variance = FALSE)
 }
 \examples{
 data(woodmouse)
-y <- seg.sites(woodmouse)
-s <- length(y)
-n <- length(woodmouse)
+s <- length(seg.sites(woodmouse))
+n <- nrow(woodmouse)
 theta.s(s, n)
 theta.s(s, n, variance = TRUE)
 }