[med-svn] [r-cran-vegan] 02/05: Merge tag 'upstream/2.3-1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-cran-vegan.

commit 89ad2673ea01ce63bf3032993efbd6b5bdcaa806
Merge: ecc38fe 8fe98ea
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 10 21:08:57 2015 +0100

    Merge tag 'upstream/2.3-1'
    
    Upstream version 2.3-1

 DESCRIPTION                     |  10 +--
 MD5                             | 135 ++++++++++++++++++++--------------------
 NAMESPACE                       |   4 +-
 R/adonis.R                      |   6 +-
 R/alias.cca.R                   |   4 +-
 R/anosim.R                      |   3 +-
 R/anova.cca.R                   |  16 +++--
 R/anova.ccabyterm.R             |  70 ++++++++++++++-------
 R/anova.ccalist.R               |  30 +++++----
 R/anova.ccanull.R               |  21 ++++---
 R/biplot.rda.R                  |   7 ++-
 R/centroids.cca.R               |   2 +-
 R/factorfit.R                   |   3 +-
 R/mantel.R                      |   3 +-
 R/mantel.partial.R              |   3 +-
 R/metaMDS.R                     |  21 ++++---
 R/metaMDSdist.R                 |   1 +
 R/monoMDS.R                     |   2 +-
 R/mrpp.R                        |   3 +-
 R/mso.R                         |   4 +-
 R/oecosimu.R                    |  11 +++-
 R/ordiR2step.R                  |   5 ++
 R/ordiareatest.R                |   3 +-
 R/permustats.R                  |  37 +++++++----
 R/permutest.betadisper.R        |  10 +--
 R/permutest.cca.R               |   4 --
 R/plot.cca.R                    |  10 +--
 R/plot.prc.R                    |   9 +--
 R/points.cca.R                  |   9 +--
 R/predict.cca.R                 |  11 ++--
 R/predict.rda.R                 |  11 ++--
 R/print.cca.R                   |   2 +-
 R/print.permutest.cca.R         |   3 +-
 R/protest.R                     |   3 +-
 R/rarecurve.R                   |  10 +++
 R/scalingUtils.R                |  27 ++++++++
 R/scores.cca.R                  |  22 ++++---
 R/scores.rda.R                  |   6 +-
 R/simper.R                      |   3 +-
 R/summary.cca.R                 |  14 +++--
 R/summary.prc.R                 |   7 +--
 R/text.cca.R                    |   9 +--
 R/tolerance.cca.R               |   9 ++-
 R/vectorfit.R                   |   3 +-
 data/BCI.env.rda                | Bin 0 -> 337 bytes
 inst/NEWS.Rd                    |  79 +++++++++++++++++++++++
 inst/doc/FAQ-vegan.pdf          | Bin 148353 -> 148353 bytes
 inst/doc/NEWS.html              |  92 +++++++++++++++++++++++++++
 inst/doc/decision-vegan.pdf     | Bin 342516 -> 342248 bytes
 inst/doc/diversity-vegan.pdf    | Bin 365737 -> 365321 bytes
 inst/doc/intro-vegan.pdf        | Bin 235169 -> 234771 bytes
 man/BCI.Rd                      |  42 +++++++++----
 man/adipart.Rd                  |   6 +-
 man/anova.cca.Rd                |   5 +-
 man/biplot.rda.Rd               |  22 +++++--
 man/cca.Rd                      |   4 +-
 man/diversity.Rd                | 107 +++++--------------------------
 man/monoMDS.Rd                  |   2 +-
 man/permustats.Rd               |  12 ++--
 man/plot.cca.Rd                 |  75 ++++++++++++++--------
 man/prc.Rd                      |  23 +++++--
 man/predict.cca.Rd              |  16 +++--
 man/{diversity.Rd => rarefy.Rd} |  95 ++++------------------------
 man/specaccum.Rd                |  77 +++++++++++------------
 man/tolerance.Rd                |   8 ++-
 vignettes/FAQ-vegan.pdf         | Bin 148353 -> 148353 bytes
 vignettes/NEWS.html             |  92 +++++++++++++++++++++++++++
 vignettes/decision-vegan.tex    |  20 +++---
 vignettes/diversity-vegan.tex   |  80 ++++++++++++------------
 vignettes/intro-vegan.tex       |  50 +++++++--------
 70 files changed, 915 insertions(+), 578 deletions(-)

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