[med-svn] [r-cran-vegan] 02/05: Merge tag 'upstream/2.4-0'
Andreas Tille
tille at debian.org
Mon Aug 8 08:35:05 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-vegan.
commit fc150fb25784862dc86f9aa3c7b5be39bb6805d2
Merge: 70344d5 d118e5b
Author: Andreas Tille <tille at debian.org>
Date: Mon Aug 8 09:05:59 2016 +0200
Merge tag 'upstream/2.4-0'
Upstream version 2.4-0
DESCRIPTION | 17 +--
MD5 | 293 ++++++++++++++++++++++---------------------
NAMESPACE | 31 +++--
R/GowerDblcen.R | 48 +++++++
R/MDSrotate.R | 13 ++
R/RsquareAdj.R | 22 +---
R/adipart.default.R | 9 +-
R/adipart.formula.R | 11 +-
R/adonis2.R | 109 ++++++++++++++++
R/anova.cca.R | 2 +-
R/anova.ccabyterm.R | 36 +++++-
R/anova.ccalist.R | 2 +-
R/anova.ccanull.R | 2 +-
R/as.fisher.R | 4 +-
R/as.mcmc.oecosimu.R | 40 +++++-
R/as.ts.oecosimu.R | 5 +-
R/betadisper.R | 19 ++-
R/betadiver.R | 2 +-
R/calibrate.cca.R | 7 ++
R/capscale.R | 64 +++++++---
R/contribdiv.R | 2 +
R/dbrda.R | 252 +++++++++++++++++++++++++++++++++++++
R/decorana.R | 6 +-
R/designdist.R | 13 +-
R/deviance.rda.R | 2 +-
R/eigenvals.R | 22 +++-
R/eventstar.R | 6 +-
R/extractAIC.cca.R | 6 +-
R/fitted.capscale.R | 18 ++-
R/fitted.dbrda.R | 54 ++++++++
R/goodness.cca.R | 118 ++++++++---------
R/hiersimu.default.R | 9 +-
R/hiersimu.formula.R | 10 +-
R/inertcomp.R | 60 +++++----
R/intersetcor.R | 3 +-
R/lines.spantree.R | 8 +-
R/make.commsim.R | 86 ++++++++++---
R/metaMDS.R | 16 ++-
R/metaMDSdist.R | 5 +-
R/metaMDSiter.R | 37 ++++--
R/monoMDS.R | 6 +-
R/mso.R | 4 +-
R/multipart.default.R | 7 +-
R/multipart.formula.R | 10 +-
R/nesteddisc.R | 28 ++---
R/nobs.R | 4 +-
R/oecosimu.R | 17 ++-
R/oldCapscale.R | 30 +++++
R/ordiGetData.R | 2 +-
R/ordiR2step.R | 20 ++-
R/ordiareatest.R | 8 +-
R/ordiarrows.R | 18 ++-
R/ordibar.R | 80 ++++++++++++
R/ordicluster.R | 19 ++-
R/ordiellipse.R | 91 +++++++++++---
R/ordihull.R | 77 +++++++++---
R/ordisegments.R | 11 +-
R/ordispider.R | 20 ++-
R/pcnm.R | 14 +--
R/permustats.R | 86 +++++++++++--
R/permutest.cca.R | 43 +++++--
R/plot.betadisper.R | 87 ++++++++++---
R/plot.isomap.R | 6 +
R/plot.spantree.R | 16 ++-
R/plot.specaccum.R | 6 +-
R/points.orditkplot.R | 7 +-
R/postMDS.R | 7 +-
R/predict.rda.R | 58 ++++++---
R/print.capscale.R | 9 --
R/print.cca.R | 47 ++++---
R/print.simmat.R | 10 +-
R/print.varpart.R | 6 +-
R/print.varpart234.R | 10 +-
R/print.wcmdscale.R | 2 +
R/rarecurve.R | 2 +
R/renyi.R | 12 +-
R/scores.betadisper.R | 4 +-
R/scores.rda.R | 16 ++-
R/simpleRDA2.R | 19 ++-
R/simulate.nullmodel.R | 18 +--
R/simulate.rda.R | 11 ++
R/smbind.R | 170 +++++++++++++++++++++++++
R/spenvcor.R | 4 +-
R/stressplot.wcmdscale.R | 113 +++++++++++++++--
R/summary.ordiellipse.R | 4 +-
R/summary.ordihull.R | 2 +-
R/text.orditkplot.R | 11 +-
R/update.nullmodel.R | 1 +
R/varpart.R | 58 +++++++--
R/varpart2.R | 15 ++-
R/varpart3.R | 15 ++-
R/varpart4.R | 15 ++-
R/vegan-defunct.R | 74 ++++++++++-
R/vegan-deprecated.R | 188 +--------------------------
R/wascores.R | 6 +-
R/wcmdscale.R | 22 +++-
R/weights.rda.R | 4 +-
build/partial.rdb | Bin 0 -> 21794 bytes
data/BCI.env.rda | Bin 337 -> 705 bytes
data/BCI.rda | Bin 8503 -> 8759 bytes
inst/NEWS.Rd | 216 +++++++++++++++++++++++++++++++
inst/doc/decision-vegan.R | 30 ++---
inst/doc/decision-vegan.Rnw | 141 +++++++++------------
inst/doc/decision-vegan.pdf | Bin 342272 -> 340954 bytes
inst/doc/diversity-vegan.pdf | Bin 365179 -> 365970 bytes
inst/doc/intro-vegan.R | 42 ++++---
inst/doc/intro-vegan.Rnw | 16 +--
inst/doc/intro-vegan.pdf | Bin 234604 -> 238817 bytes
inst/doc/partitioning.pdf | Bin 137301 -> 137524 bytes
man/BCI.Rd | 76 ++++++++---
man/MDSrotate.Rd | 28 ++++-
man/RsquareAdj.Rd | 17 ++-
man/adipart.Rd | 32 +++--
man/adonis.Rd | 198 +++++++++++++----------------
man/anosim.Rd | 4 +-
man/betadisper.Rd | 49 +++++++-
man/betadiver.Rd | 21 ++--
man/capscale.Rd | 204 +++++++++++++++---------------
man/cca.object.Rd | 65 +++++++++-
man/commsim.Rd | 157 +++++++++++++----------
man/decorana.Rd | 14 +--
man/designdist.Rd | 38 ++++--
man/envfit.Rd | 2 +-
man/isomap.Rd | 12 +-
man/linestack.Rd | 2 +-
man/metaMDS.Rd | 71 ++++++++---
man/monoMDS.Rd | 37 ++++++
man/mrpp.Rd | 4 +-
man/multipart.Rd | 101 +++++++++------
man/nullmodel.Rd | 126 ++++++++++++++++---
man/ordiarrows.Rd | 18 ++-
man/ordihull.Rd | 118 +++++++++++------
man/ordipointlabel.Rd | 8 +-
man/ordistep.Rd | 39 +++---
man/ordisurf.Rd | 2 +-
man/orditkplot.Rd | 20 +--
man/ordixyplot.Rd | 2 +-
man/permustats.Rd | 63 +++++++---
man/permutest.betadisper.Rd | 4 +-
man/plot.cca.Rd | 2 +-
man/predict.cca.Rd | 3 +-
man/spantree.Rd | 15 ++-
man/specaccum.Rd | 6 +-
man/stressplot.wcmdscale.Rd | 14 ++-
man/varpart.Rd | 144 ++++++++++++++-------
man/vegan-defunct.Rd | 38 ++++--
man/vegan-deprecated.Rd | 72 +----------
man/vegan-internal.Rd | 18 +++
man/wcmdscale.Rd | 36 ++++--
src/nestedness.c | 138 ++++++++++++++++----
vignettes/decision-vegan.Rnw | 141 +++++++++------------
vignettes/intro-vegan.Rnw | 16 +--
152 files changed, 3965 insertions(+), 1774 deletions(-)
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