[med-svn] [r-cran-ape] branch master updated (cc549ad -> d28b0a8)
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sat May 3 14:43:59 UTC 2014
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a change to branch master
in repository r-cran-ape.
from cc549ad Add VCS fields.
new d28b0a8 Imported Upstream version 3.1-1
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
DESCRIPTION | 54 +
MD5 | 337 +++++
NAMESPACE | 142 ++
NEWS | 3005 ++++++++++++++++++++++++++++++++++++++++
R/CADM.global.R | 216 +++
R/CADM.post.R | 276 ++++
R/CDF.birth.death.R | 519 +++++++
R/Cheverud.R | 141 ++
R/DNA.R | 500 +++++++
R/MPR.R | 68 +
R/MoranI.R | 212 +++
R/PGLS.R | 282 ++++
R/SDM.R | 207 +++
R/SlowinskiGuyer.R | 101 ++
R/ace.R | 342 +++++
R/additive.R | 38 +
R/alex.R | 42 +
R/all.equal.phylo.R | 83 ++
R/as.bitsplits.R | 127 ++
R/as.matching.R | 66 +
R/as.phylo.R | 134 ++
R/as.phylo.formula.R | 51 +
R/balance.R | 32 +
R/bind.tree.R | 217 +++
R/biplot.pcoa.R | 49 +
R/birthdeath.R | 150 ++
R/branching.times.R | 31 +
R/cherry.R | 52 +
R/chronoMPL.R | 47 +
R/chronopl.R | 254 ++++
R/chronos.R | 476 +++++++
R/clustal.R | 78 ++
R/coalescent.intervals.R | 56 +
R/collapse.singles.R | 52 +
R/collapsed.intervals.R | 57 +
R/compar.gee.R | 169 +++
R/compar.lynch.R | 74 +
R/compar.ou.R | 79 ++
R/compute.brtime.R | 55 +
R/cophenetic.phylo.R | 32 +
R/cophyloplot.R | 174 +++
R/dbd.R | 117 ++
R/delta.plot.R | 39 +
R/dist.gene.R | 56 +
R/dist.topo.R | 361 +++++
R/diversi.gof.R | 65 +
R/diversi.time.R | 80 ++
R/drop.tip.R | 238 ++++
R/evonet.R | 103 ++
R/ewLasso.R | 28 +
R/extract.popsize.R | 95 ++
R/gammaStat.R | 21 +
R/howmanytrees.R | 44 +
R/identify.phylo.R | 44 +
R/is.binary.tree.R | 26 +
R/is.compatible.R | 36 +
R/is.monophyletic.R | 52 +
R/is.ultrametric.R | 36 +
R/ladderize.R | 41 +
R/lmorigin.R | 163 +++
R/ltt.plot.R | 150 ++
R/makeLabel.R | 117 ++
R/makeNodeLabel.R | 60 +
R/mantel.test.R | 42 +
R/matexpo.R | 18 +
R/mcmc.popsize.R | 440 ++++++
R/me.R | 66 +
R/mrca.R | 89 ++
R/mst.R | 90 ++
R/multi2di.R | 125 ++
R/mvr.R | 52 +
R/nj.R | 24 +
R/njs.R | 48 +
R/nodelabels.R | 296 ++++
R/parafit.R | 160 +++
R/pcoa.R | 170 +++
R/phydataplot.R | 130 ++
R/phymltest.R | 122 ++
R/pic.R | 170 +++
R/plot.phylo.R | 728 ++++++++++
R/plot.popsize.R | 64 +
R/plotPhyloCoor.R | 137 ++
R/print.lmorigin.R | 55 +
R/print.parafit.R | 18 +
R/rTrait.R | 174 +++
R/read.GenBank.R | 53 +
R/read.caic.R | 91 ++
R/read.dna.R | 132 ++
R/read.nexus.R | 253 ++++
R/read.nexus.data.R | 142 ++
R/read.tree.R | 169 +++
R/reorder.phylo.R | 82 ++
R/root.R | 342 +++++
R/rotate.R | 126 ++
R/rtree.R | 213 +++
R/scales.R | 130 ++
R/skyline.R | 149 ++
R/skylineplot.R | 73 +
R/speciesTree.R | 29 +
R/subtreeplot.R | 47 +
R/subtrees.R | 55 +
R/summary.phylo.R | 231 +++
R/treePop.R | 25 +
R/triangMtd.R | 40 +
R/unique.multiPhylo.R | 34 +
R/varcomp.R | 37 +
R/vcv.phylo.R | 72 +
R/which.edge.R | 67 +
R/write.dna.R | 131 ++
R/write.nexus.R | 73 +
R/write.nexus.data.R | 168 +++
R/write.tree.R | 131 ++
R/yule.R | 81 ++
R/yule.time.R | 71 +
R/zoom.R | 37 +
R/zzz.R | 10 +
build/vignette.rds | Bin 0 -> 192 bytes
data/HP.links.rda | Bin 0 -> 412 bytes
data/bird.families.rda | Bin 0 -> 2509 bytes
data/bird.orders.rda | Bin 0 -> 567 bytes
data/carnivora.csv.gz | Bin 0 -> 3544 bytes
data/chiroptera.rda | Bin 0 -> 11971 bytes
data/cynipids.rda | Bin 0 -> 721 bytes
data/gopher.D.rda | Bin 0 -> 1255 bytes
data/hivtree.newick.rda | Bin 0 -> 2189 bytes
data/hivtree.table.txt.gz | Bin 0 -> 1031 bytes
data/landplants.newick.rda | Bin 0 -> 574 bytes
data/lice.D.rda | Bin 0 -> 1544 bytes
data/lmorigin.ex1.rda | Bin 0 -> 979 bytes
data/lmorigin.ex2.rda | Bin 0 -> 455 bytes
data/mat3.RData | Bin 0 -> 714 bytes
data/mat5M3ID.RData | Bin 0 -> 49717 bytes
data/mat5Mrand.RData | Bin 0 -> 49548 bytes
data/opsin.newick.rda | Bin 0 -> 445 bytes
data/woodmouse.rda | Bin 0 -> 1160 bytes
inst/CITATION | 13 +
inst/doc/MoranI.R | 88 ++
inst/doc/MoranI.Rnw | 351 +++++
inst/doc/MoranI.pdf | Bin 0 -> 126448 bytes
man/CADM.global.Rd | 136 ++
man/DNAbin.Rd | 114 ++
man/Initialize.corPhyl.Rd | 24 +
man/LTT.Rd | 74 +
man/MPR.Rd | 69 +
man/MoranI.Rd | 79 ++
man/SDM.Rd | 39 +
man/ace.Rd | 207 +++
man/add.scale.bar.Rd | 51 +
man/additive.Rd | 26 +
man/alex.Rd | 44 +
man/all.equal.phylo.Rd | 67 +
man/ape-internal.Rd | 75 +
man/ape-package.Rd | 38 +
man/as.alignment.Rd | 63 +
man/as.bitsplits.Rd | 61 +
man/as.matching.Rd | 67 +
man/as.phylo.Rd | 110 ++
man/as.phylo.formula.Rd | 30 +
man/axisPhylo.Rd | 34 +
man/balance.Rd | 29 +
man/base.freq.Rd | 62 +
man/bd.ext.Rd | 77 +
man/bd.time.Rd | 87 ++
man/bind.tree.Rd | 115 ++
man/bionj.Rd | 49 +
man/bird.families.Rd | 40 +
man/bird.orders.Rd | 36 +
man/birthdeath.Rd | 66 +
man/boot.phylo.Rd | 155 +++
man/branching.times.Rd | 27 +
man/c.phylo.Rd | 55 +
man/carnivora.Rd | 49 +
man/cherry.Rd | 47 +
man/chiroptera.Rd | 32 +
man/chronoMPL.Rd | 75 +
man/chronopl.Rd | 118 ++
man/chronos.Rd | 137 ++
man/clustal.Rd | 87 ++
man/coalescent.intervals.Rd | 50 +
man/collapse.singles.Rd | 21 +
man/collapsed.intervals.Rd | 74 +
man/compar.cheverud.Rd | 74 +
man/compar.gee.Rd | 123 ++
man/compar.lynch.Rd | 67 +
man/compar.ou.Rd | 102 ++
man/compute.brlen.Rd | 60 +
man/compute.brtime.Rd | 47 +
man/consensus.Rd | 42 +
man/cophenetic.phylo.Rd | 30 +
man/cophyloplot.Rd | 71 +
man/corBlomberg.Rd | 47 +
man/corBrownian.Rd | 55 +
man/corClasses.Rd | 48 +
man/corGrafen.Rd | 53 +
man/corMartins.Rd | 53 +
man/corPagel.Rd | 50 +
man/correlogram.formula.Rd | 58 +
man/cynipids.Rd | 24 +
man/dbd.Rd | 107 ++
man/del.gaps.Rd | 31 +
man/delta.plot.Rd | 54 +
man/dist.dna.Rd | 208 +++
man/dist.gene.Rd | 52 +
man/dist.topo.Rd | 70 +
man/diversi.gof.Rd | 75 +
man/diversi.time.Rd | 58 +
man/diversity.contrast.test.Rd | 97 ++
man/drop.tip.Rd | 96 ++
man/edges.Rd | 50 +
man/evonet.Rd | 70 +
man/ewLasso.Rd | 48 +
man/fastme.Rd | 58 +
man/gammaStat.Rd | 41 +
man/hivtree.Rd | 56 +
man/howmanytrees.Rd | 66 +
man/identify.phylo.Rd | 62 +
man/image.DNAbin.Rd | 66 +
man/is.binary.tree.Rd | 35 +
man/is.compatible.Rd | 25 +
man/is.monophyletic.Rd | 59 +
man/is.ultrametric.Rd | 29 +
man/kronoviz.Rd | 33 +
man/ladderize.Rd | 29 +
man/landplants.Rd | 37 +
man/lmorigin.Rd | 83 ++
man/ltt.plot.Rd | 164 +++
man/makeLabel.Rd | 74 +
man/makeNodeLabel.Rd | 72 +
man/mantel.test.Rd | 68 +
man/mat3.Rd | 23 +
man/mat5M3ID.Rd | 19 +
man/mat5Mrand.Rd | 19 +
man/matexpo.Rd | 26 +
man/mcconwaysims.test.Rd | 56 +
man/mcmc.popsize.Rd | 116 ++
man/mixedFontLabel.Rd | 64 +
man/mrca.Rd | 36 +
man/mst.Rd | 76 +
man/multi2di.Rd | 47 +
man/multiphylo.Rd | 69 +
man/mvr.Rd | 45 +
man/nj.Rd | 49 +
man/njs.Rd | 45 +
man/node.depth.Rd | 46 +
man/nodelabels.Rd | 162 +++
man/opsin.Rd | 35 +
man/parafit.Rd | 77 +
man/pcoa.Rd | 119 ++
man/phydataplot.Rd | 116 ++
man/phymltest.Rd | 149 ++
man/pic.Rd | 71 +
man/pic.ortho.Rd | 59 +
man/plot.correlogram.Rd | 55 +
man/plot.phylo.Rd | 249 ++++
man/plot.varcomp.Rd | 22 +
man/print.phylo.Rd | 40 +
man/rTraitCont.Rd | 100 ++
man/rTraitDisc.Rd | 102 ++
man/rTraitMult.Rd | 60 +
man/read.GenBank.Rd | 70 +
man/read.caic.Rd | 43 +
man/read.dna.Rd | 146 ++
man/read.nexus.Rd | 56 +
man/read.nexus.data.Rd | 112 ++
man/read.tree.Rd | 116 ++
man/reorder.phylo.Rd | 59 +
man/richness.yule.test.Rd | 37 +
man/rlineage.Rd | 75 +
man/root.Rd | 81 ++
man/rotate.Rd | 108 ++
man/rtree.Rd | 68 +
man/seg.sites.Rd | 40 +
man/skyline.Rd | 150 ++
man/skylineplot.Rd | 93 ++
man/slowinskiguyer.test.Rd | 64 +
man/speciesTree.Rd | 57 +
man/stree.Rd | 45 +
man/subtreeplot.Rd | 41 +
man/subtrees.Rd | 41 +
man/summary.phylo.Rd | 53 +
man/treePop.Rd | 19 +
man/trex.Rd | 69 +
man/triangMtd.Rd | 32 +
man/unique.multiPhylo.Rd | 38 +
man/varCompPhylip.Rd | 68 +
man/varcomp.Rd | 35 +
man/vcv.phylo.Rd | 56 +
man/weight.taxo.Rd | 34 +
man/where.Rd | 35 +
man/which.edge.Rd | 31 +
man/woodmouse.Rd | 31 +
man/write.dna.Rd | 93 ++
man/write.nexus.Rd | 43 +
man/write.nexus.data.Rd | 78 ++
man/write.tree.Rd | 57 +
man/yule.Rd | 49 +
man/yule.cov.Rd | 99 ++
man/yule.time.Rd | 86 ++
man/zoom.Rd | 55 +
src/BIONJ.c | 341 +++++
src/Makevars | 1 +
src/NNI.c | 387 ++++++
src/SPR.c | 420 ++++++
src/TBR.c | 454 ++++++
src/additive.c | 66 +
src/ape.c | 139 ++
src/ape.h | 28 +
src/bNNI.c | 329 +++++
src/bionjs.c | 403 ++++++
src/bipartition.c | 213 +++
src/bitsplits.c | 268 ++++
src/delta_plot.c | 49 +
src/dist_dna.c | 1166 ++++++++++++++++
src/dist_nodes.c | 41 +
src/ewLasso.c | 239 ++++
src/heap.c | 112 ++
src/mat_expo.c | 61 +
src/me.c | 502 +++++++
src/me.h | 141 ++
src/me_balanced.c | 444 ++++++
src/me_ols.c | 641 +++++++++
src/mvr.c | 188 +++
src/mvrs.c | 399 ++++++
src/nj.c | 151 ++
src/njs.c | 681 +++++++++
src/pic.c | 37 +
src/plot_phylo.c | 105 ++
src/rTrait.c | 39 +
src/read_dna.c | 150 ++
src/reorder_phylo.c | 152 ++
src/treePop.c | 242 ++++
src/tree_build.c | 198 +++
src/tree_phylo.c | 79 ++
src/triangMtd.c | 357 +++++
src/triangMtds.c | 223 +++
src/ultrametric.c | 61 +
vignettes/MoranI.Rnw | 351 +++++
vignettes/ape.bib | 51 +
338 files changed, 38610 insertions(+)
create mode 100644 DESCRIPTION
create mode 100644 MD5
create mode 100644 NAMESPACE
create mode 100644 NEWS
create mode 100644 R/CADM.global.R
create mode 100644 R/CADM.post.R
create mode 100644 R/CDF.birth.death.R
create mode 100644 R/Cheverud.R
create mode 100644 R/DNA.R
create mode 100644 R/MPR.R
create mode 100644 R/MoranI.R
create mode 100644 R/PGLS.R
create mode 100644 R/SDM.R
create mode 100644 R/SlowinskiGuyer.R
create mode 100644 R/ace.R
create mode 100644 R/additive.R
create mode 100644 R/alex.R
create mode 100644 R/all.equal.phylo.R
create mode 100644 R/as.bitsplits.R
create mode 100644 R/as.matching.R
create mode 100644 R/as.phylo.R
create mode 100644 R/as.phylo.formula.R
create mode 100644 R/balance.R
create mode 100644 R/bind.tree.R
create mode 100644 R/biplot.pcoa.R
create mode 100644 R/birthdeath.R
create mode 100644 R/branching.times.R
create mode 100644 R/cherry.R
create mode 100644 R/chronoMPL.R
create mode 100644 R/chronopl.R
create mode 100644 R/chronos.R
create mode 100644 R/clustal.R
create mode 100644 R/coalescent.intervals.R
create mode 100644 R/collapse.singles.R
create mode 100644 R/collapsed.intervals.R
create mode 100644 R/compar.gee.R
create mode 100644 R/compar.lynch.R
create mode 100644 R/compar.ou.R
create mode 100644 R/compute.brtime.R
create mode 100644 R/cophenetic.phylo.R
create mode 100644 R/cophyloplot.R
create mode 100644 R/dbd.R
create mode 100644 R/delta.plot.R
create mode 100644 R/dist.gene.R
create mode 100644 R/dist.topo.R
create mode 100644 R/diversi.gof.R
create mode 100644 R/diversi.time.R
create mode 100644 R/drop.tip.R
create mode 100644 R/evonet.R
create mode 100644 R/ewLasso.R
create mode 100644 R/extract.popsize.R
create mode 100644 R/gammaStat.R
create mode 100644 R/howmanytrees.R
create mode 100644 R/identify.phylo.R
create mode 100644 R/is.binary.tree.R
create mode 100644 R/is.compatible.R
create mode 100644 R/is.monophyletic.R
create mode 100644 R/is.ultrametric.R
create mode 100644 R/ladderize.R
create mode 100644 R/lmorigin.R
create mode 100644 R/ltt.plot.R
create mode 100644 R/makeLabel.R
create mode 100644 R/makeNodeLabel.R
create mode 100644 R/mantel.test.R
create mode 100644 R/matexpo.R
create mode 100644 R/mcmc.popsize.R
create mode 100644 R/me.R
create mode 100644 R/mrca.R
create mode 100644 R/mst.R
create mode 100644 R/multi2di.R
create mode 100644 R/mvr.R
create mode 100644 R/nj.R
create mode 100644 R/njs.R
create mode 100644 R/nodelabels.R
create mode 100644 R/parafit.R
create mode 100644 R/pcoa.R
create mode 100644 R/phydataplot.R
create mode 100644 R/phymltest.R
create mode 100644 R/pic.R
create mode 100644 R/plot.phylo.R
create mode 100644 R/plot.popsize.R
create mode 100644 R/plotPhyloCoor.R
create mode 100644 R/print.lmorigin.R
create mode 100644 R/print.parafit.R
create mode 100644 R/rTrait.R
create mode 100644 R/read.GenBank.R
create mode 100644 R/read.caic.R
create mode 100644 R/read.dna.R
create mode 100644 R/read.nexus.R
create mode 100644 R/read.nexus.data.R
create mode 100644 R/read.tree.R
create mode 100644 R/reorder.phylo.R
create mode 100644 R/root.R
create mode 100644 R/rotate.R
create mode 100644 R/rtree.R
create mode 100644 R/scales.R
create mode 100644 R/skyline.R
create mode 100644 R/skylineplot.R
create mode 100644 R/speciesTree.R
create mode 100644 R/subtreeplot.R
create mode 100644 R/subtrees.R
create mode 100644 R/summary.phylo.R
create mode 100644 R/treePop.R
create mode 100644 R/triangMtd.R
create mode 100644 R/unique.multiPhylo.R
create mode 100644 R/varcomp.R
create mode 100644 R/vcv.phylo.R
create mode 100644 R/which.edge.R
create mode 100644 R/write.dna.R
create mode 100644 R/write.nexus.R
create mode 100644 R/write.nexus.data.R
create mode 100644 R/write.tree.R
create mode 100644 R/yule.R
create mode 100644 R/yule.time.R
create mode 100644 R/zoom.R
create mode 100644 R/zzz.R
create mode 100644 build/vignette.rds
create mode 100644 data/HP.links.rda
create mode 100644 data/bird.families.rda
create mode 100644 data/bird.orders.rda
create mode 100644 data/carnivora.csv.gz
create mode 100644 data/chiroptera.rda
create mode 100644 data/cynipids.rda
create mode 100644 data/gopher.D.rda
create mode 100644 data/hivtree.newick.rda
create mode 100644 data/hivtree.table.txt.gz
create mode 100644 data/landplants.newick.rda
create mode 100644 data/lice.D.rda
create mode 100644 data/lmorigin.ex1.rda
create mode 100644 data/lmorigin.ex2.rda
create mode 100644 data/mat3.RData
create mode 100644 data/mat5M3ID.RData
create mode 100644 data/mat5Mrand.RData
create mode 100644 data/opsin.newick.rda
create mode 100644 data/woodmouse.rda
create mode 100644 inst/CITATION
create mode 100644 inst/doc/MoranI.R
create mode 100644 inst/doc/MoranI.Rnw
create mode 100644 inst/doc/MoranI.pdf
create mode 100644 man/CADM.global.Rd
create mode 100644 man/DNAbin.Rd
create mode 100644 man/Initialize.corPhyl.Rd
create mode 100644 man/LTT.Rd
create mode 100644 man/MPR.Rd
create mode 100644 man/MoranI.Rd
create mode 100644 man/SDM.Rd
create mode 100644 man/ace.Rd
create mode 100644 man/add.scale.bar.Rd
create mode 100644 man/additive.Rd
create mode 100644 man/alex.Rd
create mode 100644 man/all.equal.phylo.Rd
create mode 100644 man/ape-internal.Rd
create mode 100644 man/ape-package.Rd
create mode 100644 man/as.alignment.Rd
create mode 100644 man/as.bitsplits.Rd
create mode 100644 man/as.matching.Rd
create mode 100644 man/as.phylo.Rd
create mode 100644 man/as.phylo.formula.Rd
create mode 100644 man/axisPhylo.Rd
create mode 100644 man/balance.Rd
create mode 100644 man/base.freq.Rd
create mode 100644 man/bd.ext.Rd
create mode 100644 man/bd.time.Rd
create mode 100644 man/bind.tree.Rd
create mode 100644 man/bionj.Rd
create mode 100644 man/bird.families.Rd
create mode 100644 man/bird.orders.Rd
create mode 100644 man/birthdeath.Rd
create mode 100644 man/boot.phylo.Rd
create mode 100644 man/branching.times.Rd
create mode 100644 man/c.phylo.Rd
create mode 100644 man/carnivora.Rd
create mode 100644 man/cherry.Rd
create mode 100644 man/chiroptera.Rd
create mode 100644 man/chronoMPL.Rd
create mode 100644 man/chronopl.Rd
create mode 100644 man/chronos.Rd
create mode 100644 man/clustal.Rd
create mode 100644 man/coalescent.intervals.Rd
create mode 100644 man/collapse.singles.Rd
create mode 100644 man/collapsed.intervals.Rd
create mode 100644 man/compar.cheverud.Rd
create mode 100644 man/compar.gee.Rd
create mode 100644 man/compar.lynch.Rd
create mode 100644 man/compar.ou.Rd
create mode 100644 man/compute.brlen.Rd
create mode 100644 man/compute.brtime.Rd
create mode 100644 man/consensus.Rd
create mode 100644 man/cophenetic.phylo.Rd
create mode 100644 man/cophyloplot.Rd
create mode 100644 man/corBlomberg.Rd
create mode 100644 man/corBrownian.Rd
create mode 100644 man/corClasses.Rd
create mode 100644 man/corGrafen.Rd
create mode 100644 man/corMartins.Rd
create mode 100644 man/corPagel.Rd
create mode 100644 man/correlogram.formula.Rd
create mode 100644 man/cynipids.Rd
create mode 100644 man/dbd.Rd
create mode 100644 man/del.gaps.Rd
create mode 100644 man/delta.plot.Rd
create mode 100644 man/dist.dna.Rd
create mode 100644 man/dist.gene.Rd
create mode 100644 man/dist.topo.Rd
create mode 100644 man/diversi.gof.Rd
create mode 100644 man/diversi.time.Rd
create mode 100644 man/diversity.contrast.test.Rd
create mode 100644 man/drop.tip.Rd
create mode 100644 man/edges.Rd
create mode 100644 man/evonet.Rd
create mode 100644 man/ewLasso.Rd
create mode 100644 man/fastme.Rd
create mode 100644 man/gammaStat.Rd
create mode 100644 man/hivtree.Rd
create mode 100644 man/howmanytrees.Rd
create mode 100644 man/identify.phylo.Rd
create mode 100644 man/image.DNAbin.Rd
create mode 100644 man/is.binary.tree.Rd
create mode 100644 man/is.compatible.Rd
create mode 100644 man/is.monophyletic.Rd
create mode 100644 man/is.ultrametric.Rd
create mode 100644 man/kronoviz.Rd
create mode 100644 man/ladderize.Rd
create mode 100644 man/landplants.Rd
create mode 100644 man/lmorigin.Rd
create mode 100644 man/ltt.plot.Rd
create mode 100644 man/makeLabel.Rd
create mode 100644 man/makeNodeLabel.Rd
create mode 100644 man/mantel.test.Rd
create mode 100644 man/mat3.Rd
create mode 100644 man/mat5M3ID.Rd
create mode 100644 man/mat5Mrand.Rd
create mode 100644 man/matexpo.Rd
create mode 100644 man/mcconwaysims.test.Rd
create mode 100644 man/mcmc.popsize.Rd
create mode 100644 man/mixedFontLabel.Rd
create mode 100644 man/mrca.Rd
create mode 100644 man/mst.Rd
create mode 100644 man/multi2di.Rd
create mode 100644 man/multiphylo.Rd
create mode 100644 man/mvr.Rd
create mode 100644 man/nj.Rd
create mode 100644 man/njs.Rd
create mode 100644 man/node.depth.Rd
create mode 100644 man/nodelabels.Rd
create mode 100644 man/opsin.Rd
create mode 100644 man/parafit.Rd
create mode 100644 man/pcoa.Rd
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create mode 100644 man/read.GenBank.Rd
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create mode 100644 man/read.dna.Rd
create mode 100644 man/read.nexus.Rd
create mode 100644 man/read.nexus.data.Rd
create mode 100644 man/read.tree.Rd
create mode 100644 man/reorder.phylo.Rd
create mode 100644 man/richness.yule.test.Rd
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create mode 100644 man/skylineplot.Rd
create mode 100644 man/slowinskiguyer.test.Rd
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create mode 100644 man/varCompPhylip.Rd
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create mode 100644 man/yule.Rd
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create mode 100644 src/BIONJ.c
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create mode 100644 src/ultrametric.c
create mode 100644 vignettes/MoranI.Rnw
create mode 100644 vignettes/ape.bib
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