[med-svn] [r-cran-vegan] 06/07: Merge tag 'upstream/2.3-0'

[Charles Plessy]

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

commit 8f1e0e5bc55c07bf9197af9a573c02f89ef37cb6
Merge: 5cadab9 c054784
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Jun 1 14:12:09 2015 +0900

    Merge tag 'upstream/2.3-0'
    
    Upstream version 2.3-0
    
    # gpg: Signature made Mon 01 Jun 2015 14:12:05 JST using RSA key ID B3443334
    # gpg: Good signature from "Charles Plessy <plessy at riken.jp>"

 DESCRIPTION                   |   8 +-
 MD5                           | 172 +++++++++++++++++++++---------------------
 NAMESPACE                     |  18 +++--
 R/CCorA.R                     |  16 ++--
 R/MDSrotate.R                 |   2 +-
 R/adipart.default.R           |  18 ++---
 R/adonis.R                    |   2 +
 R/anosim.R                    |   2 +
 R/anova.ccabyterm.R           |   2 +-
 R/betadiver.R                 |   2 +-
 R/bioenv.default.R            |   9 +++
 R/capscale.R                  |  26 +++----
 R/cascadeKM.R                 |   3 -
 R/cca.default.R               |  43 ++++++-----
 R/centroids.cca.R             |  11 ++-
 R/estimateR.default.R         |   2 +-
 R/factorfit.R                 |  24 +++---
 R/fitspecaccum.R              |  13 +++-
 R/goodness.cca.R              |  72 ++++++++++++------
 R/goodness.rda.R              |  63 ----------------
 R/make.commsim.R              |  56 +++++++-------
 R/multipart.default.R         |  38 +++++-----
 R/nesteddisc.R                |   4 +-
 R/nestedtemp.R                |   6 +-
 R/ordiArrowMul.R              |  26 +++++--
 R/ordiArrowTextXY.R           |  54 ++++++++++---
 R/ordiGetData.R               |   2 +-
 R/ordiParseFormula.R          |  23 ++++--
 R/ordiR2step.R                |   3 +
 R/orditkplot.R                |  20 ++++-
 R/pcnm.R                      |  13 +++-
 R/permustats.R                |   2 +-
 R/plot.cca.R                  |   2 +-
 R/plot.meandist.R             |  14 ++--
 R/plot.radfit.frame.R         |   6 +-
 R/plot.specaccum.R            |   4 +-
 R/predict.fitspecaccum.R      |  16 ++++
 R/predict.specaccum.R         |  43 +++++++++--
 R/print.oecosimu.R            |   2 +-
 R/print.specaccum.R           |   2 +
 R/print.varpart.R             |   4 +-
 R/print.varpart234.R          |   2 +-
 R/rankindex.R                 |   2 +-
 R/rarecurve.R                 |   2 +-
 R/rarefy.R                    |   5 ++
 R/rareslope.R                 |  42 +++++++++++
 R/rda.default.R               |   7 +-
 R/read.cep.R                  |  10 +--
 R/scores.cca.R                |   4 +-
 R/scores.ordihull.R           |   2 +-
 R/scores.rda.R                |   4 +-
 R/showvarparts.R              |  89 ++++++++++++++++------
 R/specaccum.R                 |   9 ++-
 R/specslope.R                 |  95 +++++++++++++++++++++++
 R/summary.anosim.R            |   6 +-
 R/summary.bioenv.R            |   2 +-
 R/summary.cca.R               |   4 +-
 R/summary.radfit.frame.R      |   4 +-
 R/varpart.R                   |  18 ++---
 R/vegemite.R                  |  50 ++++++------
 build/vignette.rds            | Bin 290 -> 288 bytes
 inst/NEWS.Rd                  | 109 ++++++++++++++++++++++++++
 inst/doc/FAQ-vegan.pdf        | Bin 147419 -> 148353 bytes
 inst/doc/NEWS.html            | 127 +++++++++++++++++++++++++++++++
 inst/doc/decision-vegan.pdf   | Bin 342270 -> 342516 bytes
 inst/doc/diversity-vegan.pdf  | Bin 365631 -> 365737 bytes
 inst/doc/intro-vegan.pdf      | Bin 234860 -> 235169 bytes
 man/cascadeKM.Rd              |  12 +--
 man/cca.Rd                    |   2 +-
 man/diversity.Rd              |  12 ++-
 man/envfit.Rd                 |  19 ++++-
 man/goodness.cca.Rd           |  46 ++++++-----
 man/oecosimu.Rd               |   4 +-
 man/ordiArrowTextXY.Rd        | 109 ++++++++++++++++++++++++++
 man/ordiarrows.Rd             |   8 +-
 man/orditkplot.Rd             |  41 +++++-----
 man/permustats.Rd             |  20 ++---
 man/procrustes.Rd             |   2 +-
 man/sipoo.Rd                  |   4 +-
 man/specaccum.Rd              |  49 ++++++++----
 man/varpart.Rd                |  49 ++++++++----
 man/vegan-internal.Rd         |  22 +-----
 man/vegan-package.Rd          |  11 +--
 vignettes/FAQ-vegan.pdf       | Bin 147419 -> 148353 bytes
 vignettes/FAQ-vegan.texi      |  35 ++++++---
 vignettes/NEWS.html           | 127 +++++++++++++++++++++++++++++++
 vignettes/decision-vegan.tex  |  18 ++---
 vignettes/diversity-vegan.tex |  82 ++++++++++----------
 vignettes/intro-vegan.tex     |  48 ++++++------
 89 files changed, 1506 insertions(+), 655 deletions(-)

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