[med-svn] [r-cran-vegan] 02/07: Merge tag 'upstream/2.2-0'
Charles Plessy
plessy at moszumanska.debian.org
Mon Jun 1 05:26:39 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository r-cran-vegan.
commit d1753f52a3e92c248295af76935b35b253c6f401
Merge: d09009d 5034510
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jun 1 14:11:43 2015 +0900
Merge tag 'upstream/2.2-0'
Upstream version 2.2-0
# gpg: Signature made Mon 01 Jun 2015 14:11:40 JST using RSA key ID B3443334
# gpg: Good signature from "Charles Plessy <plessy at riken.jp>"
DESCRIPTION | 16 +-
MD5 | 458 +++++-----
NAMESPACE | 151 ++-
R/CCorA.R | 39 +-
R/MDSrotate.R | 56 +-
R/RsquareAdj.R | 13 +
R/SSarrhenius.R | 2 +-
R/add1.cca.R | 15 +-
R/ade2vegancca.R | 7 +-
R/adipart.default.R | 2 +-
R/adonis.R | 70 +-
R/anosim.R | 53 +-
R/anova.cca.R | 109 ++-
R/anova.ccabyaxis.R | 89 --
R/anova.ccabymargin.R | 52 --
R/anova.ccabyterm.R | 233 +++--
R/anova.ccalist.R | 90 ++
R/as.hclust.spantree.R | 158 ++++
R/as.ts.oecosimu.R | 6 +-
R/as.ts.permat.R | 4 +-
R/betadisper.R | 4 +-
R/bioenv.default.R | 97 +-
R/bioenv.formula.R | 7 +-
R/biplot.CCorA.R | 8 +-
R/biplot.rda.R | 4 +-
R/bstick.cca.R | 2 +-
R/cIndexKM.R | 6 +-
R/capscale.R | 12 +-
R/cca.default.R | 20 +-
R/clamtest.R | 254 +++---
R/commsim.R | 24 +
R/commsimulator.R | 100 --
R/confint.MOStest.R | 1 -
R/contribdiv.R | 104 +--
R/decorana.R | 4 +-
R/density.anosim.R | 135 ---
R/density.oecosimu.R | 14 -
R/densityplot.oecosimu.R | 14 -
R/dispweight.R | 59 ++
R/drop1.cca.R | 8 +-
R/envfit.default.R | 26 +-
R/envfit.formula.R | 2 +-
R/estimateR.default.R | 26 +-
R/eventstar.R | 36 +-
R/factorfit.R | 34 +-
R/fitspecaccum.R | 22 +-
R/fitted.radfit.R | 8 +-
R/gdispweight.R | 52 ++
R/getPermuteMatrix.R | 33 +
R/goodness.metaMDS.R | 1 -
R/hiersimu.default.R | 2 +-
R/howHead.R | 51 ++
R/indpower.R | 50 +-
R/make.commsim.R | 436 +++++++++
R/mantel.R | 54 +-
R/mantel.partial.R | 40 +-
R/metaMDSiter.R | 121 ++-
R/mrpp.R | 64 +-
R/mso.R | 31 +-
R/multipart.default.R | 2 +-
R/nestedchecker.R | 1 +
R/nesteddisc.R | 6 +-
R/nestedn0.R | 1 +
R/nestednodf.R | 18 +-
R/nestedtemp.R | 1 +
R/nullmodel.R | 46 +
R/oecosimu.R | 226 +++--
R/ordiR2step.R | 6 +-
R/ordiareatest.R | 69 ++
R/ordiellipse.R | 4 +-
R/ordihull.R | 2 +-
R/ordilabel.R | 10 +-
R/ordiplot3d.R | 92 --
R/ordipointlabel.R | 2 +-
R/ordirgl.R | 57 --
R/ordispider.R | 24 +-
R/ordistep.R | 20 +-
R/ordisurf.R | 15 +-
R/orglpoints.R | 8 -
R/orglsegments.R | 17 -
R/orglspider.R | 34 -
R/orgltext.R | 11 -
R/permatfull.R | 95 +-
R/permatswap.R | 168 +---
R/permustats.R | 272 ++++++
R/permuted.index.R | 1 +
R/permutest.betadisper.R | 156 +++-
R/permutest.cca.R | 138 ++-
R/persp.tsallisaccum.R | 10 +-
R/plot.cca.R | 58 +-
R/plot.clamtest.R | 78 +-
R/plot.contribdiv.R | 44 +-
R/plot.envfit.R | 14 +-
R/plot.spantree.R | 2 -
R/points.cca.R | 2 +-
R/poolaccum.R | 6 +-
R/print.CCorA.R | 6 +-
R/print.anosim.R | 8 +-
R/print.bioenv.R | 7 +-
R/print.cca.R | 6 +-
R/print.commsim.R | 11 +
R/print.factorfit.R | 7 +-
R/print.mantel.R | 6 +-
R/print.mantel.correlog.R | 16 +-
R/print.mrpp.R | 11 +-
R/print.mso.R | 4 +-
R/print.nullmodel.R | 14 +
R/print.oecosimu.R | 16 +-
R/print.permat.R | 10 +-
R/print.permutest.betadisper.R | 4 +-
R/print.permutest.cca.R | 9 +-
R/print.protest.R | 10 +-
R/print.simmat.R | 18 +
R/print.specaccum.R | 9 +-
R/print.summary.clamtest.R | 26 +-
R/print.summary.permat.R | 8 +-
R/print.vectorfit.R | 5 +-
R/protest.R | 46 +-
R/radfit.data.frame.R | 6 +
R/rankindex.R | 12 +-
R/rarecurve.R | 14 +-
R/raupcrick.R | 5 +-
R/rda.default.R | 28 +-
R/read.cep.R | 6 +-
R/rgl.isomap.R | 10 -
R/rgl.renyiaccum.R | 31 -
R/scores.default.R | 16 +-
R/scores.lda.R | 1 -
R/simper.R | 95 +-
R/simulate.nullmodel.R | 66 ++
R/simulate.rda.R | 155 +++-
R/specpool.R | 19 +-
R/str.nullmodel.R | 2 +
R/stressplot.R | 12 +-
R/stressplot.wcmdscale.R | 187 ++++
R/summary.clamtest.R | 14 +-
R/summary.dispweight.R | 22 +
R/summary.permat.R | 6 +-
R/tabasco.R | 62 +-
R/text.cca.R | 9 +-
R/tolerance.cca.R | 2 +-
R/treedist.R | 2 +-
R/treedive.R | 8 +-
R/tsallis.R | 88 +-
R/tsallisaccum.R | 96 +-
R/update.nullmodel.R | 40 +
R/vectorfit.R | 32 +-
R/vegan-defunct.R | 10 +-
R/vegan-deprecated.R | 206 ++++-
R/veganCovEllipse.R | 5 +-
R/veganMahatrans.R | 20 +
R/vegdist.R | 5 +-
R/vegemite.R | 1 -
README.md | 7 +
build/vignette.rds | Bin 289 -> 290 bytes
data/BCI.rda | Bin 8093 -> 8503 bytes
data/dune.env.rda | Bin 464 -> 441 bytes
data/dune.phylodis.rda | Bin 0 -> 890 bytes
data/dune.rda | Bin 729 -> 805 bytes
data/dune.taxon.rda | Bin 801 -> 779 bytes
data/varespec.rda | Bin 2102 -> 2187 bytes
inst/ChangeLog | 1978 +++++++++++++++++++++++++++++++++-------
inst/NEWS.Rd | 284 ++++++
inst/doc/FAQ-vegan.pdf | Bin 149064 -> 147419 bytes
inst/doc/NEWS.html | 391 +++++++-
inst/doc/decision-vegan.R | 56 +-
inst/doc/decision-vegan.Rnw | 197 +++-
inst/doc/decision-vegan.pdf | Bin 324746 -> 342552 bytes
inst/doc/diversity-vegan.R | 12 +-
inst/doc/diversity-vegan.Rnw | 55 +-
inst/doc/diversity-vegan.pdf | Bin 357896 -> 360242 bytes
inst/doc/intro-vegan.R | 25 +-
inst/doc/intro-vegan.Rnw | 34 +-
inst/doc/intro-vegan.pdf | Bin 260455 -> 234792 bytes
man/BCI.Rd | 31 +-
man/CCorA.Rd | 14 +-
man/MDSrotate.Rd | 30 +-
man/add1.cca.Rd | 13 +-
man/adipart.Rd | 14 +-
man/adonis.Rd | 23 +-
man/anosim.Rd | 19 +-
man/anova.cca.Rd | 218 +++--
man/betadisper.Rd | 13 +-
man/bioenv.Rd | 67 +-
man/cca.object.Rd | 29 +-
man/clamtest.Rd | 301 +++---
man/commsim.Rd | 413 +++++++++
man/decostand.Rd | 5 +-
man/density.adonis.Rd | 114 ---
man/dispweight.Rd | 120 +++
man/diversity.Rd | 8 +-
man/dune.Rd | 15 +-
man/dune.taxon.Rd | 48 +-
man/envfit.Rd | 17 +-
man/eventstar.Rd | 248 ++---
man/goodness.cca.Rd | 6 +-
man/goodness.metaMDS.Rd | 8 +-
man/humpfit.Rd | 2 +
man/isomap.Rd | 17 +-
man/mantel.Rd | 20 +-
man/mantel.correlog.Rd | 344 +++----
man/metaMDS.Rd | 11 +-
man/monoMDS.Rd | 4 +-
man/mrpp.Rd | 21 +-
man/mso.Rd | 13 +-
man/multipart.Rd | 8 +-
man/nestedtemp.Rd | 23 +-
man/nullmodel.Rd | 168 ++++
man/oecosimu.Rd | 360 ++++----
man/ordihull.Rd | 33 +-
man/ordiplot3d.Rd | 228 -----
man/ordistep.Rd | 16 +-
man/ordisurf.Rd | 30 +-
man/orditkplot.Rd | 2 +-
man/pcnm.Rd | 228 ++---
man/permatfull.Rd | 574 ++++++------
man/permustats.Rd | 144 +++
man/permutations.Rd | 255 ++++--
man/permutest.betadisper.Rd | 20 +-
man/prc.Rd | 13 +-
man/procrustes.Rd | 23 +-
man/rankindex.Rd | 35 +-
man/raupcrick.Rd | 4 +-
man/renyi.Rd | 19 +-
man/reorder.hclust.Rd | 115 +++
man/simper.Rd | 24 +-
man/simulate.rda.Rd | 86 +-
man/spantree.Rd | 13 +
man/specaccum.Rd | 42 +-
man/specpool.Rd | 88 +-
man/stressplot.wcmdscale.Rd | 94 ++
man/treedive.Rd | 64 +-
man/tsallis.Rd | 268 +++---
man/vegan-defunct.Rd | 36 +-
man/vegan-deprecated.Rd | 189 +++-
man/vegan-internal.Rd | 32 +-
man/vegandocs.Rd | 10 +-
man/vegdist.Rd | 20 +-
man/vegemite.Rd | 12 +-
man/wcmdscale.Rd | 4 +-
src/nestedness.c | 214 +++--
src/vegdist.c | 6 +-
vignettes/FAQ-vegan.pdf | Bin 149064 -> 147419 bytes
vignettes/FAQ-vegan.texi | 252 +++--
vignettes/NEWS.html | 391 +++++++-
vignettes/decision-vegan.Rnw | 197 +++-
vignettes/decision-vegan.tex | 249 ++++-
vignettes/diversity-vegan.Rnw | 55 +-
vignettes/diversity-vegan.tex | 137 +--
vignettes/intro-vegan.Rnw | 34 +-
vignettes/intro-vegan.tex | 174 ++--
vignettes/vegan.bib | 10 +
252 files changed, 11713 insertions(+), 5386 deletions(-)
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