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paradis [Mon, 27 Jul 2009 13:23:14 +0000 (13:23 +0000)]
fixing write.nexus()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@86
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 27 Jul 2009 07:46:47 +0000 (07:46 +0000)]
fixing zoom()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@85
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 23 Jul 2009 08:13:39 +0000 (08:13 +0000)]
fixing add.scale.bar()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@84
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 20 Jul 2009 07:37:14 +0000 (07:37 +0000)]
faster nj()!!!
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@83
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 14 Jul 2009 04:40:09 +0000 (04:40 +0000)]
fixing nj() with many 0 distances
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@82
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 7 Jul 2009 06:35:45 +0000 (06:35 +0000)]
several bug fixes while in JKT
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@81
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 23 Jun 2009 13:39:20 +0000 (13:39 +0000)]
fixes for ape 2.3-1
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@80
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 23 Jun 2009 13:10:19 +0000 (13:10 +0000)]
fix a bug in drop.tip + add new option 'rooted'
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@79
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 19 Jun 2009 13:59:08 +0000 (13:59 +0000)]
new is.monophyletic() + various changes/fixes
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@78
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 12 Jun 2009 09:36:38 +0000 (09:36 +0000)]
removed klastorin()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@77
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 10 Jun 2009 09:49:21 +0000 (09:49 +0000)]
improved ace()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@76
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 9 Jun 2009 06:51:23 +0000 (06:51 +0000)]
fixed null model in yule.cov + various things
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@75
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 19 May 2009 13:10:25 +0000 (13:10 +0000)]
new c.DNAbin()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@74
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 14 May 2009 08:19:05 +0000 (08:19 +0000)]
faster rcoal... at last!
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@73
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 12 May 2009 13:54:52 +0000 (13:54 +0000)]
many changes.......
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@72
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 27 Apr 2009 07:00:32 +0000 (07:00 +0000)]
fixed a small bug in read.tree
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@71
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 1 Apr 2009 07:35:31 +0000 (07:35 +0000)]
fix on dist.gene + a few man pages corrections
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@70
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 30 Mar 2009 07:26:50 +0000 (07:26 +0000)]
various changes for ape 2.3
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@69
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 27 Mar 2009 10:20:14 +0000 (10:20 +0000)]
added edge.lty to plot.phylo
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@68
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 23 Mar 2009 12:48:07 +0000 (12:48 +0000)]
adding contribs by Daniel Lawson
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@67
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 23 Mar 2009 07:49:41 +0000 (07:49 +0000)]
change nlm to nlminb in ace() + new makeNodeLabel + fixed drop.tip
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@66
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 10 Mar 2009 10:53:04 +0000 (10:53 +0000)]
various fixes + del xenarthra
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@65
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 4 Mar 2009 08:38:20 +0000 (08:38 +0000)]
correcting bug in drop.tip
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@64
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 20 Feb 2009 10:28:02 +0000 (10:28 +0000)]
added the contribution of PL on CDAM
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@63
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 20 Feb 2009 09:45:11 +0000 (09:45 +0000)]
new yule.time + several corrections in man pages
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@62
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 20 Jan 2009 09:16:20 +0000 (09:16 +0000)]
fix to avoid uncessary warning in ace(method = "GLS")
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@61
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 19 Jan 2009 09:48:04 +0000 (09:48 +0000)]
bug fix in read.nexus + new ?ape man page
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@60
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 13 Jan 2009 09:02:52 +0000 (09:02 +0000)]
correcting errors in Rd files
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@59
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 12 Jan 2009 14:36:11 +0000 (14:36 +0000)]
updates for ape 2.2-3
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@58
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 8 Jan 2009 08:48:22 +0000 (08:48 +0000)]
various updates + adding SPR+TBR in fastme.bal()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@57
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Sat, 20 Dec 2008 16:45:04 +0000 (16:45 +0000)]
bug fixed in ltt.plot.R
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@56
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 24 Nov 2008 08:30:45 +0000 (08:30 +0000)]
fix bug in read.nexus()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@55
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 4 Nov 2008 20:11:38 +0000 (20:11 +0000)]
fixing bug in chronopl(, CV = TRUE)
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@54
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 9 Oct 2008 08:39:56 +0000 (08:39 +0000)]
improved cbind.DNAbin for ape 2.2-2
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@53
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 8 Oct 2008 14:42:35 +0000 (14:42 +0000)]
updated phymltest() for PhyML 3.0 + changed rbind.DNAbin()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@52
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 2 Oct 2008 15:40:07 +0000 (15:40 +0000)]
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
paradis [Thu, 25 Sep 2008 08:53:06 +0000 (08:53 +0000)]
correcting ref in mcmc.popsize.Rd (from Gramlitz)
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@50
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 18 Sep 2008 14:37:04 +0000 (14:37 +0000)]
fix a few bugs + correct some the man page of sh.test()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@49
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 28 Jul 2008 14:58:38 +0000 (14:58 +0000)]
changed some data sets (made lighter) + clarified man page for rcoal()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@48
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 21 Jul 2008 09:37:25 +0000 (09:37 +0000)]
adding tree_build.c
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@47
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 18 Jul 2008 17:28:17 +0000 (17:28 +0000)]
correcting 2 bugs in new dist.gene()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@46
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 18 Jul 2008 13:03:53 +0000 (13:03 +0000)]
fixed prop.part()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@45
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 18 Jul 2008 11:39:37 +0000 (11:39 +0000)]
new dist.gene() + corrected mlphylo()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@44
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 11 Jul 2008 15:44:44 +0000 (15:44 +0000)]
fixed sh.test() for ape 2.2-1
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@43
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 11 Jul 2008 15:12:16 +0000 (15:12 +0000)]
final fix in read.nexus() for ape 2.2-1
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@42
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 9 Jul 2008 07:36:08 +0000 (07:36 +0000)]
bug fix in read.nexus()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@41
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 8 Jul 2008 04:03:24 +0000 (04:03 +0000)]
various corrections
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@40
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 3 Jul 2008 15:13:42 +0000 (15:13 +0000)]
new makeLabel() + modifs in read.dna() & write.dna()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@39
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Sat, 28 Jun 2008 05:52:48 +0000 (05:52 +0000)]
changed check.labels = TRUE in dist.topo() and consensus()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@38
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 24 Jun 2008 09:51:36 +0000 (09:51 +0000)]
bug fix in read.nexus()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@37
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 19 Jun 2008 10:24:37 +0000 (10:24 +0000)]
bug fix in collapsed.singles()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@36
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 18 Jun 2008 05:42:34 +0000 (05:42 +0000)]
bugs fixing in mlphylo()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@35
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 12 Jun 2008 07:37:31 +0000 (07:37 +0000)]
bug fix in root()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@34
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 9 Jun 2008 23:55:32 +0000 (23:55 +0000)]
improved unique.multiPhylo()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@33
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Sun, 8 Jun 2008 06:46:38 +0000 (06:46 +0000)]
adding del.gaps()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@32
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 8 May 2008 05:18:09 +0000 (05:18 +0000)]
doc for corBlomberg
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@31
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 8 May 2008 05:14:48 +0000 (05:14 +0000)]
final wrap of ape 2.2
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@30
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 6 May 2008 13:40:20 +0000 (13:40 +0000)]
cosmetic modif on rtree() + last (?) changes to Damien's functions
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@29
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 24 Apr 2008 19:25:35 +0000 (19:25 +0000)]
fix bug in seg.sites + improved Damien's man pages
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@28
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 18 Apr 2008 10:02:18 +0000 (10:02 +0000)]
added corPagel + gave version # 2.2
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@27
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 17 Apr 2008 19:51:15 +0000 (19:51 +0000)]
fix on drop.tip()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@26
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 17 Apr 2008 12:46:51 +0000 (12:46 +0000)]
new files by Damien + a few bug fixes
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@25
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 10 Apr 2008 18:30:02 +0000 (18:30 +0000)]
removed the print(node.labels)
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@24
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 31 Mar 2008 13:06:28 +0000 (13:06 +0000)]
improved chronopl
bug fixes in read.dna & plot.phylo
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@23
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 17 Mar 2008 07:43:39 +0000 (07:43 +0000)]
fixed bugs in multi2di and di2multi + code and doc clean-up
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@22
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 11 Mar 2008 12:54:40 +0000 (12:54 +0000)]
code clean-up in DNA.R
fixed ace() with GLS
added some links in the man pages
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@21
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 3 Mar 2008 17:29:31 +0000 (17:29 +0000)]
update for ape 2.1-2
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@20
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 27 Feb 2008 16:07:52 +0000 (16:07 +0000)]
fixing a few bugs...
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@19
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Wed, 13 Feb 2008 16:32:14 +0000 (16:32 +0000)]
improved root()
changed plot.phylo so that last_plot.phylo is now
in a proper environment, no in .GlobalEnv
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@18
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 8 Feb 2008 14:12:44 +0000 (14:12 +0000)]
added "DUP=FALSE, NAOK=TRUE" to .C in DNA.R
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@17
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Thu, 7 Feb 2008 12:42:57 +0000 (12:42 +0000)]
various updates...[21~
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@16
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 21 Jan 2008 13:58:58 +0000 (13:58 +0000)]
fix a bug in nuc.div()
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@15
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 14 Jan 2008 13:34:37 +0000 (13:34 +0000)]
conversion tree -> phylo
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@14
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Mon, 14 Jan 2008 13:33:26 +0000 (13:33 +0000)]
stabler and faster C code for ME and BIONJ
package loading now silent and/or when needed
fix small bug in identify.phylo
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@13
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Tue, 8 Jan 2008 11:57:26 +0000 (11:57 +0000)]
new function rmtree
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@12
6e262413-ae40-0410-9e79-
b911bd7a66b7
paradis [Fri, 4 Jan 2008 18:15:23 +0000 (18:15 +0000)]
current 2.1 release
git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@11
6e262413-ae40-0410-9e79-
b911bd7a66b7
projects / ape.git / log