[med-svn] [r-cran-vegan] branch upstream updated (5094565 -> c054784)
Charles Plessy
plessy at moszumanska.debian.org
Mon Jun 1 05:26:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository r-cran-vegan.
from 5094565 Imported Upstream version 2.0-10
new 5034510 Imported Upstream version 2.2-0
new dbf7661 Imported Upstream version 2.2-1
new c054784 Imported Upstream version 2.3-0
The 3 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 | 16 +-
MD5 | 565 ++++++------
NAMESPACE | 158 +++-
R/CCorA.R | 49 +-
R/MDSrotate.R | 58 +-
R/RsquareAdj.R | 13 +
R/SSarrhenius.R | 2 +-
R/add1.cca.R | 15 +-
R/ade2vegancca.R | 7 +-
R/adipart.default.R | 20 +-
R/adonis.R | 72 +-
R/alias.cca.R | 2 +
R/anosim.R | 56 +-
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 | 160 ++++
R/as.mlm.R | 7 +-
R/as.ts.oecosimu.R | 6 +-
R/as.ts.permat.R | 4 +-
R/betadisper.R | 4 +-
R/betadiver.R | 2 +-
R/bioenv.default.R | 107 ++-
R/bioenv.formula.R | 7 +-
R/biplot.CCorA.R | 8 +-
R/biplot.rda.R | 15 +-
R/bstick.cca.R | 2 +-
R/cIndexKM.R | 6 +-
R/capscale.R | 38 +-
R/cascadeKM.R | 3 -
R/cca.default.R | 61 +-
R/centroids.cca.R | 11 +-
R/clamtest.R | 254 ++---
R/coef.cca.R | 10 +-
R/coef.rda.R | 6 +-
R/commsim.R | 24 +
R/commsimulator.R | 100 --
R/confint.MOStest.R | 1 -
R/contribdiv.R | 104 +--
R/cophenetic.spantree.R | 6 +-
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/estaccumR.R | 38 +-
R/estimateR.default.R | 41 +-
R/eventstar.R | 36 +-
R/factorfit.R | 48 +-
R/fitspecaccum.R | 29 +-
R/fitted.capscale.R | 2 +
R/fitted.cca.R | 2 +
R/fitted.radfit.R | 8 +-
R/fitted.rda.R | 2 +
R/gdispweight.R | 52 ++
R/getPermuteMatrix.R | 33 +
R/goodness.cca.R | 72 +-
R/goodness.metaMDS.R | 1 -
R/goodness.rda.R | 63 --
R/hiersimu.default.R | 2 +-
R/howHead.R | 51 ++
R/indpower.R | 50 +-
R/intersetcor.R | 2 +
R/lines.spantree.R | 7 +-
R/linestack.R | 36 +-
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 | 40 +-
R/nestedchecker.R | 1 +
R/nesteddisc.R | 10 +-
R/nestedn0.R | 1 +
R/nestednodf.R | 18 +-
R/nestedtemp.R | 7 +-
R/nullmodel.R | 46 +
R/oecosimu.R | 226 +++--
R/ordiArrowMul.R | 26 +-
R/ordiArrowTextXY.R | 54 +-
R/ordiGetData.R | 2 +-
R/ordiParseFormula.R | 23 +-
R/ordiR2step.R | 9 +-
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/orditkplot.R | 291 +++---
R/orglpoints.R | 8 -
R/orglsegments.R | 17 -
R/orglspider.R | 34 -
R/orgltext.R | 11 -
R/pcnm.R | 13 +-
R/permatfull.R | 95 +-
R/permatswap.R | 168 +---
R/permustats.R | 272 ++++++
R/permuted.index.R | 1 +
R/permutest.betadisper.R | 157 +++-
R/permutest.cca.R | 138 ++-
R/persp.tsallisaccum.R | 10 +-
R/plot.cca.R | 60 +-
R/plot.clamtest.R | 78 +-
R/plot.contribdiv.R | 44 +-
R/plot.envfit.R | 14 +-
R/plot.meandist.R | 14 +-
R/plot.radfit.frame.R | 6 +-
R/plot.spantree.R | 19 +-
R/plot.specaccum.R | 4 +-
R/points.cca.R | 2 +-
R/poolaccum.R | 20 +-
R/predict.fitspecaccum.R | 16 +
R/predict.specaccum.R | 43 +-
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 | 18 +-
R/print.mrpp.R | 11 +-
R/print.mso.R | 4 +-
R/print.nullmodel.R | 14 +
R/print.oecosimu.R | 18 +-
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 | 11 +-
R/print.summary.clamtest.R | 26 +-
R/print.summary.permat.R | 8 +-
R/print.varpart.R | 4 +-
R/print.varpart234.R | 2 +-
R/print.vectorfit.R | 5 +-
R/protest.R | 46 +-
R/radfit.data.frame.R | 6 +
R/rankindex.R | 14 +-
R/rarecurve.R | 14 +-
R/rarefy.R | 5 +
R/rareslope.R | 42 +
R/raupcrick.R | 5 +-
R/rda.default.R | 35 +-
R/read.cep.R | 16 +-
R/renyiaccum.R | 6 +-
R/rgl.isomap.R | 10 -
R/rgl.renyiaccum.R | 31 -
R/scores.cca.R | 4 +-
R/scores.default.R | 16 +-
R/scores.lda.R | 1 -
R/scores.ordihull.R | 2 +-
R/scores.rda.R | 4 +-
R/showvarparts.R | 89 +-
R/simper.R | 113 ++-
R/simulate.nullmodel.R | 66 ++
R/simulate.rda.R | 155 +++-
R/spantree.R | 4 +-
R/specaccum.R | 19 +-
R/specpool.R | 19 +-
R/specslope.R | 95 ++
R/str.nullmodel.R | 2 +
R/stressplot.R | 12 +-
R/stressplot.wcmdscale.R | 187 ++++
R/summary.anosim.R | 6 +-
R/summary.bioenv.R | 2 +-
R/summary.cca.R | 4 +-
R/summary.clamtest.R | 14 +-
R/summary.dispweight.R | 22 +
R/summary.permat.R | 6 +-
R/summary.radfit.frame.R | 4 +-
R/tabasco.R | 62 +-
R/text.cca.R | 9 +-
R/tolerance.cca.R | 8 +-
R/treedist.R | 2 +-
R/treedive.R | 8 +-
R/tsallis.R | 88 +-
R/tsallisaccum.R | 98 +-
R/update.nullmodel.R | 40 +
R/varpart.R | 18 +-
R/vectorfit.R | 32 +-
R/vegan-defunct.R | 10 +-
R/vegan-deprecated.R | 206 ++++-
R/veganCovEllipse.R | 5 +-
R/veganMahatrans.R | 20 +
R/vegandocs.R | 2 +-
R/vegdist.R | 5 +-
R/vegemite.R | 51 +-
R/vif.cca.R | 2 +
build/vignette.rds | Bin 289 -> 288 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 | 1989 +++++++++++++++++++++++++++++++++-------
inst/NEWS.Rd | 459 ++++++++++
inst/doc/FAQ-vegan.pdf | Bin 149064 -> 148353 bytes
inst/doc/NEWS.html | 600 +++++++++++-
inst/doc/decision-vegan.R | 56 +-
inst/doc/decision-vegan.Rnw | 197 +++-
inst/doc/decision-vegan.pdf | Bin 324746 -> 342516 bytes
inst/doc/diversity-vegan.R | 50 +-
inst/doc/diversity-vegan.Rnw | 232 +++--
inst/doc/diversity-vegan.pdf | Bin 357896 -> 365737 bytes
inst/doc/intro-vegan.R | 25 +-
inst/doc/intro-vegan.Rnw | 34 +-
inst/doc/intro-vegan.pdf | Bin 260455 -> 235169 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 | 21 +-
man/bioenv.Rd | 67 +-
man/cascadeKM.Rd | 12 +-
man/cca.Rd | 2 +-
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 | 20 +-
man/dune.Rd | 15 +-
man/dune.taxon.Rd | 48 +-
man/envfit.Rd | 36 +-
man/eventstar.Rd | 248 ++---
man/goodness.cca.Rd | 50 +-
man/goodness.metaMDS.Rd | 8 +-
man/humpfit.Rd | 2 +
man/isomap.Rd | 36 +-
man/kendall.global.Rd | 2 +-
man/linestack.Rd | 31 +-
man/mantel.Rd | 20 +-
man/mantel.correlog.Rd | 344 +++----
man/metaMDS.Rd | 11 +-
man/monoMDS.Rd | 6 +-
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/ordiArrowTextXY.Rd | 109 +++
man/ordiarrows.Rd | 8 +-
man/ordihull.Rd | 33 +-
man/ordiplot3d.Rd | 228 -----
man/ordistep.Rd | 16 +-
man/ordisurf.Rd | 30 +-
man/orditkplot.Rd | 43 +-
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 | 25 +-
man/rankindex.Rd | 35 +-
man/raupcrick.Rd | 4 +-
man/renyi.Rd | 25 +-
man/reorder.hclust.Rd | 115 +++
man/simper.Rd | 24 +-
man/simulate.rda.Rd | 86 +-
man/sipoo.Rd | 4 +-
man/spantree.Rd | 13 +
man/specaccum.Rd | 98 +-
man/specpool.Rd | 99 +-
man/stressplot.wcmdscale.Rd | 94 ++
man/treedive.Rd | 64 +-
man/tsallis.Rd | 270 +++---
man/varpart.Rd | 49 +-
man/vegan-defunct.Rd | 36 +-
man/vegan-deprecated.Rd | 189 +++-
man/vegan-internal.Rd | 54 +-
man/vegan-package.Rd | 11 +-
man/vegandocs.Rd | 15 +-
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 -> 148353 bytes
vignettes/FAQ-vegan.texi | 285 +++---
vignettes/NEWS.html | 600 +++++++++++-
vignettes/decision-vegan.Rnw | 197 +++-
vignettes/decision-vegan.tex | 249 ++++-
vignettes/diversity-vegan.Rnw | 232 +++--
vignettes/diversity-vegan.tex | 308 ++++---
vignettes/intro-vegan.Rnw | 34 +-
vignettes/intro-vegan.tex | 175 ++--
vignettes/vegan.bib | 30 +-
307 files changed, 14029 insertions(+), 6299 deletions(-)
delete mode 100644 R/anova.ccabyaxis.R
delete mode 100644 R/anova.ccabymargin.R
create mode 100644 R/anova.ccalist.R
create mode 100644 R/as.hclust.spantree.R
create mode 100644 R/commsim.R
delete mode 100644 R/commsimulator.R
delete mode 100644 R/density.anosim.R
delete mode 100644 R/density.oecosimu.R
delete mode 100644 R/densityplot.oecosimu.R
create mode 100644 R/dispweight.R
create mode 100644 R/gdispweight.R
create mode 100644 R/getPermuteMatrix.R
delete mode 100644 R/goodness.rda.R
create mode 100644 R/howHead.R
create mode 100644 R/make.commsim.R
create mode 100644 R/nullmodel.R
create mode 100644 R/ordiareatest.R
delete mode 100644 R/ordiplot3d.R
delete mode 100644 R/ordirgl.R
delete mode 100644 R/orglpoints.R
delete mode 100644 R/orglsegments.R
delete mode 100644 R/orglspider.R
delete mode 100644 R/orgltext.R
create mode 100644 R/permustats.R
create mode 100644 R/print.commsim.R
create mode 100644 R/print.nullmodel.R
create mode 100644 R/print.simmat.R
create mode 100644 R/rareslope.R
delete mode 100644 R/rgl.isomap.R
delete mode 100644 R/rgl.renyiaccum.R
create mode 100644 R/simulate.nullmodel.R
create mode 100644 R/specslope.R
create mode 100644 R/str.nullmodel.R
create mode 100644 R/stressplot.wcmdscale.R
create mode 100644 R/summary.dispweight.R
create mode 100644 R/update.nullmodel.R
create mode 100644 R/veganMahatrans.R
create mode 100644 data/dune.phylodis.rda
create mode 100644 man/commsim.Rd
delete mode 100644 man/density.adonis.Rd
create mode 100644 man/dispweight.Rd
create mode 100644 man/nullmodel.Rd
create mode 100644 man/ordiArrowTextXY.Rd
delete mode 100644 man/ordiplot3d.Rd
create mode 100644 man/permustats.Rd
create mode 100644 man/reorder.hclust.Rd
create mode 100644 man/stressplot.wcmdscale.Rd
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