[med-svn] [r-cran-vegan] branch upstream updated (ea8b48f -> d118e5b)
Andreas Tille
tille at debian.org
Mon Aug 8 08:35:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-cran-vegan.
from ea8b48f Imported Upstream version 2.3-5
new d118e5b Imported Upstream version 2.4-0
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 | 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(-)
create mode 100644 R/GowerDblcen.R
create mode 100644 R/adonis2.R
create mode 100644 R/dbrda.R
create mode 100644 R/fitted.dbrda.R
create mode 100644 R/oldCapscale.R
create mode 100644 R/ordibar.R
delete mode 100644 R/print.capscale.R
create mode 100644 R/smbind.R
create mode 100644 build/partial.rdb
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