[med-svn] [r-cran-vegan] 04/07: Merge tag 'upstream/2.2-1'

[Charles Plessy]

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

commit 5cadab97c13e69714b489ad10c28aaf448c0cf64
Merge: d1753f5 dbf7661
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Jun 1 14:11:55 2015 +0900

    Merge tag 'upstream/2.2-1'
    
    Upstream version 2.2-1
    
    # gpg: Signature made Mon 01 Jun 2015 14:11:51 JST using RSA key ID B3443334
    # gpg: Good signature from "Charles Plessy <plessy at riken.jp>"

 DESCRIPTION                   |   8 +-
 MD5                           | 137 +++++++++---------
 NAMESPACE                     |   7 +-
 R/adonis.R                    |   2 +-
 R/alias.cca.R                 |   2 +
 R/anosim.R                    |   9 +-
 R/as.hclust.spantree.R        |   4 +-
 R/as.mlm.R                    |   7 +-
 R/bioenv.default.R            |   3 +-
 R/biplot.rda.R                |  11 +-
 R/coef.cca.R                  |  10 +-
 R/coef.rda.R                  |   6 +-
 R/cophenetic.spantree.R       |   6 +-
 R/estaccumR.R                 |  38 +++--
 R/estimateR.default.R         |  31 ++--
 R/fitted.capscale.R           |   2 +
 R/fitted.cca.R                |   2 +
 R/fitted.rda.R                |   2 +
 R/intersetcor.R               |   2 +
 R/lines.spantree.R            |   7 +-
 R/linestack.R                 |  36 +++--
 R/mantel.R                    |   2 +-
 R/mantel.partial.R            |   2 +-
 R/metaMDSiter.R               |   2 +-
 R/mrpp.R                      |   2 +-
 R/oecosimu.R                  |   2 +-
 R/ordiareatest.R              |   2 +-
 R/orditkplot.R                | 275 ++++++++++++++++++------------------
 R/permutest.betadisper.R      |   5 +-
 R/permutest.cca.R             |   2 +-
 R/plot.spantree.R             |  17 ++-
 R/poolaccum.R                 |  14 +-
 R/print.mantel.correlog.R     |   2 +-
 R/renyiaccum.R                |   6 +-
 R/simper.R                    |  44 +++---
 R/spantree.R                  |   4 +-
 R/specaccum.R                 |  12 +-
 R/specpool.R                  |   2 +-
 R/tolerance.cca.R             |   6 +-
 R/tsallisaccum.R              |  10 +-
 R/vegandocs.R                 |   2 +-
 R/vif.cca.R                   |   2 +
 README.md                     |   7 -
 inst/ChangeLog                |  11 ++
 inst/NEWS.Rd                  |  66 +++++++++
 inst/doc/FAQ-vegan.pdf        | Bin 147419 -> 147419 bytes
 inst/doc/NEWS.html            |  82 +++++++++++
 inst/doc/decision-vegan.pdf   | Bin 342552 -> 342270 bytes
 inst/doc/diversity-vegan.R    |  50 +++----
 inst/doc/diversity-vegan.Rnw  | 245 ++++++++++++++++++++------------
 inst/doc/diversity-vegan.pdf  | Bin 360242 -> 365631 bytes
 inst/doc/intro-vegan.pdf      | Bin 234792 -> 234860 bytes
 man/betadisper.Rd             |   8 +-
 man/isomap.Rd                 |  19 +--
 man/kendall.global.Rd         |   2 +-
 man/linestack.Rd              |  31 +++-
 man/monoMDS.Rd                |   2 +-
 man/pcnm.Rd                   |   2 +-
 man/renyi.Rd                  |   6 +-
 man/specaccum.Rd              |   7 +-
 man/specpool.Rd               |  11 +-
 man/tsallis.Rd                |   8 +-
 man/vegandocs.Rd              |   5 +-
 vignettes/FAQ-vegan.pdf       | Bin 147419 -> 147419 bytes
 vignettes/NEWS.html           |  82 +++++++++++
 vignettes/decision-vegan.tex  |  18 +--
 vignettes/diversity-vegan.Rnw | 245 ++++++++++++++++++++------------
 vignettes/diversity-vegan.tex | 321 +++++++++++++++++++++++++-----------------
 vignettes/intro-vegan.tex     |  57 ++++----
 vignettes/vegan.bib           |  20 ++-
 70 files changed, 1302 insertions(+), 750 deletions(-)

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