various fixes in C files

[ape.git] / NEWS

diff --git a/NEWS b/NEWS
index de2da102a4fb09c042fc641ee32726b0accbf29d..6d74722e49d33a07139128b1f6bb68be65f6e75e 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,46 @@
+               CHANGES IN APE VERSION 3.0-4
+
+
+BUG FIXES
+
+    o read.dna() failed to read interleaved files if the first line
+      uses tabulations instead of white spaces.
+
+OTHER CHANGES
+
+    o The files ape-defunct.R and ape-defunct.Rd, which have not been
+      modified for almost two years, have been removed.
+
+    o The C code of bionj() has been reworked: it is more stable (by
+      avoiding passing character strings), slightly faster (by about
+      20%), and more accurate numerically.
+
+    o The C code of fastme.*() has been slightly modified and should
+      be more stable by avoiding passing character strings (the
+      results are identical to the previous versions).
+
+    o The file src/newick.c has been removed.
+
+
+
+               CHANGES IN APE VERSION 3.0-3
+
+
+BUG FIXES
+
+    o birthdeath() now catches errors and warnings much better so that
+      a result is returned in most cases.
+
+
+OTHER CHANGES
+
+    o Because of problems with character string manipulation in C, the
+      examples in ?bionj and in ?fastme have been disallowed. In the
+      meantime, these functions might be unstable. This will be solved
+      for the next release.
+
+
+
                CHANGES IN APE VERSION 3.0-2
 
 
@@ -17,14 +60,38 @@ BUG FIXES
 
     o mltt.plot(, backward = FALSE) did not set the x-axis correctly.
 
-    o A bug was introduced in prop.clades() with ape 3.0.
+    o A bug was introduced in prop.clades() with ape 3.0. The help page
+      has been clarified relative to the use of the option 'rooted'.
 
     o mantel.test() printed a useless warning message.
 
     o plot.phylo(, direction = "downward") ignored 'y.lim'.
 
     o is.monophyletic() did not work correctly if 'tips' was not stored
-      as integers
+      as integers.
+
+    o prop.part() could make R crash if the first tree had many
+      multichotomies.
+
+    o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'.
+
+    o SDM() did not work correctly. The code has also been generally
+      improved.
+
+
+OTHER CHANGES
+
+    o The DESCRIPTION file has been updated.
+
+    o The option 'original.data' of write.nexus() has been removed.
+
+    o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and
+      triangMtds.c have been improved which should fix some bugs in
+      the corresponding functions.
+
+    o dist.gene() now coerces input data frame as matrix resulting in
+      much faster calculations (thanks to a suggestion by Markus
+      Schlegel).