]> git.donarmstrong.com Git - ape.git/log
ape.git
11 years agofinal commit for ape 3.0-8 master
paradis [Tue, 2 Apr 2013 10:44:43 +0000 (10:44 +0000)]
final commit for ape 3.0-8

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@213 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome news for ape 3.0-8
paradis [Sat, 30 Mar 2013 05:31:00 +0000 (05:31 +0000)]
some news for ape 3.0-8

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@212 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agomodified ace( method = ...)
paradis [Mon, 18 Mar 2013 10:51:36 +0000 (10:51 +0000)]
modified ace(  method = ...)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@211 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome changes done before the HD failure of my laptop... I presume
paradis [Mon, 18 Mar 2013 10:29:37 +0000 (10:29 +0000)]
some changes done before the HD failure of my laptop... I presume

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@210 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agocorrects previous error when moving files
paradis [Wed, 13 Feb 2013 06:53:44 +0000 (06:53 +0000)]
corrects previous error when moving files

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@209 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agofix from Pierre Legendre
paradis [Wed, 13 Feb 2013 06:52:04 +0000 (06:52 +0000)]
fix from Pierre Legendre

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@208 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agofix bug in prop.clades
paradis [Sat, 9 Feb 2013 12:43:50 +0000 (12:43 +0000)]
fix bug in prop.clades

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@207 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome modifs for ape 3.0-8
paradis [Thu, 31 Jan 2013 11:58:31 +0000 (11:58 +0000)]
some modifs for ape 3.0-8

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@206 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agomore corrections for ape 3.0-7
paradis [Mon, 21 Jan 2013 10:54:42 +0000 (10:54 +0000)]
more corrections for ape 3.0-7

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@205 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome updates for ape 3.0-7
paradis [Wed, 16 Jan 2013 02:07:27 +0000 (02:07 +0000)]
some updates for ape 3.0-7

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@204 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agonew chronos files and a bunch of various improvements
paradis [Fri, 4 Jan 2013 12:48:57 +0000 (12:48 +0000)]
new chronos files and a bunch of various improvements

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@203 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agonew code for reading FASTA files
paradis [Thu, 27 Dec 2012 09:48:23 +0000 (09:48 +0000)]
new code for reading FASTA files

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@202 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agoa few changes....
paradis [Wed, 19 Dec 2012 07:35:43 +0000 (07:35 +0000)]
a few changes....

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@201 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agoadding the new function 'where'
paradis [Wed, 28 Nov 2012 10:02:30 +0000 (10:02 +0000)]
adding the new function 'where'

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@200 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agofix in drop.tip() and new option in pic()
paradis [Thu, 22 Nov 2012 07:56:13 +0000 (07:56 +0000)]
fix in drop.tip() and new option in pic()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@199 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agofinal corrections for ape 3.0-6
paradis [Mon, 22 Oct 2012 10:13:38 +0000 (10:13 +0000)]
final corrections for ape 3.0-6

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@198 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome changes for ape 3.0-6
paradis [Fri, 12 Oct 2012 07:56:32 +0000 (07:56 +0000)]
some changes for ape 3.0-6

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@197 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome updates for ape 3.0-6
paradis [Tue, 2 Oct 2012 04:00:29 +0000 (04:00 +0000)]
some updates for ape 3.0-6

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@196 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agoupdated reorder.phylo.Rd
paradis [Fri, 7 Sep 2012 14:54:06 +0000 (14:54 +0000)]
updated reorder.phylo.Rd

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@195 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agoprovisional version of the new reorder.phylo()
paradis [Mon, 3 Sep 2012 09:09:07 +0000 (09:09 +0000)]
provisional version of the new reorder.phylo()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@194 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agochanges in reorder(, "cladewise")
paradis [Mon, 20 Aug 2012 08:45:48 +0000 (08:45 +0000)]
changes in reorder(, "cladewise")

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@193 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agonew dist.nodes() with C code
paradis [Thu, 16 Aug 2012 08:12:38 +0000 (08:12 +0000)]
new dist.nodes() with C code

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@192 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agobetter error-catching with ace()
paradis [Mon, 25 Jun 2012 07:18:05 +0000 (07:18 +0000)]
better error-catching with ace()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@191 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosmall moification on man page of as.phylo
paradis [Mon, 25 Jun 2012 02:52:46 +0000 (02:52 +0000)]
small moification on man page of as.phylo

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@190 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agosome small changes
paradis [Fri, 22 Jun 2012 08:15:03 +0000 (08:15 +0000)]
some small changes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@189 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agofix in read.dna and change in write.dna
paradis [Thu, 3 May 2012 08:41:44 +0000 (08:41 +0000)]
fix in read.dna and change in write.dna

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@188 6e262413-ae40-0410-9e79-b911bd7a66b7

11 years agovarious fixes in C files
paradis [Tue, 1 May 2012 02:25:53 +0000 (02:25 +0000)]
various fixes in C files

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@187 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofix in birthdeath()
paradis [Fri, 20 Apr 2012 04:11:23 +0000 (04:11 +0000)]
fix in birthdeath()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@186 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofinal warp for ape 3.0-2
paradis [Thu, 5 Apr 2012 05:27:15 +0000 (05:27 +0000)]
final warp for ape 3.0-2

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@185 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agobunch of fixes for ape 3.0-2
paradis [Mon, 2 Apr 2012 02:35:39 +0000 (02:35 +0000)]
bunch of fixes for ape 3.0-2

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@184 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agovarious bug fixes
paradis [Sat, 31 Mar 2012 10:09:02 +0000 (10:09 +0000)]
various bug fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@183 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agovarious bug fixes
paradis [Sat, 24 Mar 2012 14:17:54 +0000 (14:17 +0000)]
various bug fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@182 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agoa few fixes
paradis [Mon, 5 Mar 2012 11:42:29 +0000 (11:42 +0000)]
a few fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@181 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agonew alex()
paradis [Tue, 28 Feb 2012 12:57:46 +0000 (12:57 +0000)]
new alex()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@180 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agovarious bug fixes since the release of ape 3.0
paradis [Fri, 17 Feb 2012 14:14:39 +0000 (14:14 +0000)]
various bug fixes since the release of ape 3.0

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@179 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agoa fix in cophyloplot()
paradis [Tue, 14 Feb 2012 04:15:37 +0000 (04:15 +0000)]
a fix in cophyloplot()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@178 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofinal commit for ape 3.0
paradis [Fri, 10 Feb 2012 06:53:03 +0000 (06:53 +0000)]
final commit for ape 3.0

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@177 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agonew files for ape 3.0
paradis [Wed, 8 Feb 2012 13:01:16 +0000 (13:01 +0000)]
new files for ape 3.0

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@176 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofinal wrap for ape 3.0
paradis [Fri, 13 Jan 2012 01:47:39 +0000 (01:47 +0000)]
final wrap for ape 3.0

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@175 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agonew option 'rotate.tree' in plot.phylo()
paradis [Sat, 17 Dec 2011 10:08:27 +0000 (10:08 +0000)]
new option 'rotate.tree' in plot.phylo()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@174 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofixes in mantel.test() and extract.clade()
paradis [Tue, 22 Nov 2011 07:38:09 +0000 (07:38 +0000)]
fixes in mantel.test() and extract.clade()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@173 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agoa few changes...
paradis [Thu, 10 Nov 2011 10:23:02 +0000 (10:23 +0000)]
a few changes...

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@172 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agobig update with files from Andrei
paradis [Thu, 20 Oct 2011 08:13:38 +0000 (08:13 +0000)]
big update with files from Andrei

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@171 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agonew LTT plot functions + updated reference in yule.time.Rd
paradis [Mon, 26 Sep 2011 08:34:50 +0000 (08:34 +0000)]
new LTT plot functions + updated reference in yule.time.Rd

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@170 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofinal fixes for ape 2.7-3
paradis [Tue, 9 Aug 2011 02:22:33 +0000 (02:22 +0000)]
final fixes for ape 2.7-3

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@169 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agobug fix in root()
paradis [Fri, 5 Aug 2011 05:05:00 +0000 (05:05 +0000)]
bug fix in root()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@168 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofix in c.multiPhylo()
paradis [Thu, 4 Aug 2011 11:00:29 +0000 (11:00 +0000)]
fix in c.multiPhylo()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@167 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agonew method = "REML" in ace() with continuous traits
paradis [Mon, 18 Jul 2011 04:05:06 +0000 (04:05 +0000)]
new method = "REML" in ace() with continuous traits

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@166 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agonew compute.brtime() + minor change in dist.topo.R
paradis [Fri, 15 Jul 2011 02:18:47 +0000 (02:18 +0000)]
new compute.brtime() + minor change in dist.topo.R

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@165 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agobug fix in chronopl()
paradis [Thu, 7 Jul 2011 04:07:56 +0000 (04:07 +0000)]
bug fix in chronopl()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@164 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agosome updates (including new CADM.global.Rd file)
paradis [Mon, 27 Jun 2011 09:18:33 +0000 (09:18 +0000)]
some updates (including new CADM.global.Rd file)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@163 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agocleaning of C files and update on simulation of OU process
paradis [Sat, 25 Jun 2011 01:01:05 +0000 (01:01 +0000)]
cleaning of C files and update on simulation of OU process

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@162 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agovarious bug fixes
paradis [Tue, 21 Jun 2011 11:31:21 +0000 (11:31 +0000)]
various bug fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@161 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agovarious updates for ape 2.7-2 (fixed)
paradis [Thu, 16 Jun 2011 03:02:16 +0000 (03:02 +0000)]
various updates for ape 2.7-2 (fixed)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@160 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agovarious fixes and small news
paradis [Fri, 3 Jun 2011 04:08:54 +0000 (04:08 +0000)]
various fixes and small news

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@159 6e262413-ae40-0410-9e79-b911bd7a66b7

12 years agofixing drop.tip and bionj
paradis [Thu, 19 May 2011 16:42:58 +0000 (16:42 +0000)]
fixing drop.tip and bionj

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@158 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agochange file name ChangeLog to NEWS
paradis [Mon, 18 Apr 2011 02:51:28 +0000 (02:51 +0000)]
change file name ChangeLog to NEWS

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@157 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agosmall update in rTrait.R (coercing parameters as double)
paradis [Mon, 18 Apr 2011 02:49:11 +0000 (02:49 +0000)]
small update in rTrait.R (coercing parameters as double)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@156 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew option 'draw' in plot.phylo()
paradis [Tue, 29 Mar 2011 09:19:17 +0000 (09:19 +0000)]
new option 'draw' in plot.phylo()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@155 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agofinal update for ape 2.7-1
paradis [Sat, 26 Mar 2011 08:41:35 +0000 (08:41 +0000)]
final update for ape 2.7-1

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@154 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew trex() + kronoviz() and bug fixing in identify.phylo()
paradis [Wed, 23 Mar 2011 12:28:30 +0000 (12:28 +0000)]
new trex() + kronoviz() and bug fixing in identify.phylo()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@153 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agosome big fixes for ape 2.7-1
paradis [Mon, 21 Mar 2011 12:08:02 +0000 (12:08 +0000)]
some big fixes for ape 2.7-1

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@152 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agofinal packing for ape 2.7
paradis [Thu, 17 Mar 2011 03:00:02 +0000 (03:00 +0000)]
final packing for ape 2.7

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@151 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoa bunch of new stuff (see ChangeLog)
paradis [Wed, 16 Mar 2011 08:50:32 +0000 (08:50 +0000)]
a bunch of new stuff (see ChangeLog)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@150 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew image.DNAbin()
paradis [Wed, 16 Mar 2011 02:47:44 +0000 (02:47 +0000)]
new image.DNAbin()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@149 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agofixes in bind.tree()
paradis [Wed, 2 Mar 2011 06:47:44 +0000 (06:47 +0000)]
fixes in bind.tree()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@148 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agobug fixing in read.nexus() + Others....
paradis [Tue, 1 Mar 2011 10:02:08 +0000 (10:02 +0000)]
bug fixing in read.nexus() + Others....

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@147 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agobug fixes in plot.phylo
paradis [Thu, 17 Feb 2011 17:04:12 +0000 (17:04 +0000)]
bug fixes in plot.phylo

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@146 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoa few bug fixes especially in plot.phylo()
paradis [Fri, 11 Feb 2011 12:54:50 +0000 (12:54 +0000)]
a few bug fixes especially in plot.phylo()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@145 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agobug fix in read.dna + change the default of tol in drop.fossil
paradis [Tue, 1 Feb 2011 03:15:05 +0000 (03:15 +0000)]
bug fix in read.dna + change the default of tol in drop.fossil

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@144 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agosome bug fixes and '...' in rTrait*()
paradis [Fri, 24 Dec 2010 17:32:05 +0000 (17:32 +0000)]
some bug fixes and '...' in rTrait*()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@143 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoseveral fixes
paradis [Tue, 14 Dec 2010 15:51:09 +0000 (15:51 +0000)]
several fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@142 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agobug fix in write.tree()
paradis [Tue, 7 Dec 2010 10:35:25 +0000 (10:35 +0000)]
bug fix in write.tree()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@141 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agofix a bug in as.hclust.phylo + a few typos in man pages
paradis [Tue, 30 Nov 2010 08:07:19 +0000 (08:07 +0000)]
fix a bug in as.hclust.phylo + a few typos in man pages

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@140 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agovarious bug fixes
paradis [Wed, 24 Nov 2010 09:26:27 +0000 (09:26 +0000)]
various bug fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@139 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agobug fix in mcmc.popsize()
paradis [Thu, 18 Nov 2010 01:53:39 +0000 (01:53 +0000)]
bug fix in mcmc.popsize()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@138 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew pic.ortho() and varCompPhylip() + fix in dist.nodes()
paradis [Mon, 15 Nov 2010 13:56:37 +0000 (13:56 +0000)]
new pic.ortho() and varCompPhylip() + fix in dist.nodes()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@137 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agobug fixed in write.tree
paradis [Mon, 8 Nov 2010 08:11:11 +0000 (08:11 +0000)]
bug fixed in write.tree

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@136 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoa bunch of modifications and fixes
paradis [Thu, 4 Nov 2010 08:38:08 +0000 (08:38 +0000)]
a bunch of modifications and fixes

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@135 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agofinal version for ape 2.6-1
paradis [Mon, 1 Nov 2010 17:33:56 +0000 (17:33 +0000)]
final version for ape 2.6-1

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@134 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew speciesTree()
paradis [Wed, 20 Oct 2010 15:42:48 +0000 (15:42 +0000)]
new speciesTree()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@133 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoa few changes and one bug fix
paradis [Tue, 19 Oct 2010 14:38:43 +0000 (14:38 +0000)]
a few changes and one bug fix

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@132 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agocorrecting a bug in write.tree + error in MPR examples
paradis [Thu, 7 Oct 2010 10:04:09 +0000 (10:04 +0000)]
correcting a bug in write.tree + error in MPR examples

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@131 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoa few changes....
paradis [Thu, 7 Oct 2010 09:21:18 +0000 (09:21 +0000)]
a few changes....

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@130 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoadding bd.time
paradis [Mon, 27 Sep 2010 16:01:03 +0000 (16:01 +0000)]
adding bd.time

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@129 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agomany changes!
paradis [Thu, 16 Sep 2010 15:12:58 +0000 (15:12 +0000)]
many changes!

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@128 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoimprovements to compar.gee + bug fix in extract.clade
paradis [Wed, 21 Jul 2010 08:43:53 +0000 (08:43 +0000)]
improvements to compar.gee + bug fix in extract.clade

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@127 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoBOTHlabels(... hozir = TRUE)
paradis [Mon, 19 Jul 2010 11:50:40 +0000 (11:50 +0000)]
BOTHlabels(... hozir = TRUE)

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@126 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew as.list.DNAbin
paradis [Tue, 13 Jul 2010 12:21:24 +0000 (12:21 +0000)]
new as.list.DNAbin

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@125 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agosmall changes in PGLS.R
paradis [Mon, 14 Jun 2010 14:58:27 +0000 (14:58 +0000)]
small changes in PGLS.R

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@124 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew mixedFontLabel() + bug fix in rTraitCont.c
paradis [Thu, 27 May 2010 15:25:40 +0000 (15:25 +0000)]
new mixedFontLabel() + bug fix in rTraitCont.c

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@123 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew operators for "multiPhylo" + fixed small bug in bind.tree()
paradis [Tue, 25 May 2010 15:53:24 +0000 (15:53 +0000)]
new operators for "multiPhylo" + fixed small bug in bind.tree()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@122 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agovarious changes to DNAbin functions + new labels.DNAbin()
paradis [Mon, 17 May 2010 08:38:00 +0000 (08:38 +0000)]
various changes to DNAbin functions + new labels.DNAbin()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@121 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agoremoving NPRS + change bind.tree.Rd to avoid crash during R CMD check ape
paradis [Mon, 17 May 2010 07:02:07 +0000 (07:02 +0000)]
removing NPRS + change bind.tree.Rd to avoid crash during R CMD check ape

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@120 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years ago2nd try!!
paradis [Thu, 6 May 2010 16:48:18 +0000 (16:48 +0000)]
2nd try!!

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@119 6e262413-ae40-0410-9e79-b911bd7a66b7

13 years agonew faster nj.c
paradis [Sat, 24 Apr 2010 10:05:16 +0000 (10:05 +0000)]
new faster nj.c

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@118 6e262413-ae40-0410-9e79-b911bd7a66b7

14 years agoremoving evolve.phylo + bug fix in as.phylo.hclust
paradis [Wed, 7 Apr 2010 14:39:56 +0000 (14:39 +0000)]
removing evolve.phylo + bug fix in as.phylo.hclust

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@117 6e262413-ae40-0410-9e79-b911bd7a66b7

14 years agovarious corrections
paradis [Fri, 2 Apr 2010 15:36:35 +0000 (15:36 +0000)]
various corrections

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@116 6e262413-ae40-0410-9e79-b911bd7a66b7

14 years agofixing various bugs + news in cophyloplot
paradis [Fri, 19 Mar 2010 16:51:48 +0000 (16:51 +0000)]
fixing various bugs + news in cophyloplot

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@115 6e262413-ae40-0410-9e79-b911bd7a66b7

14 years agofixes in compar.ou and plot.phylo + new bind.tree
paradis [Tue, 16 Mar 2010 09:54:18 +0000 (09:54 +0000)]
fixes in compar.ou and plot.phylo + new bind.tree

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@114 6e262413-ae40-0410-9e79-b911bd7a66b7