Squashed commit of the following:

commit 73619424238a9fe15a6297bdd715a2204f6c9075
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Nov 6 11:08:31 2014 +0200

    Update examples (see comments below for: commsim swhs_samp)

    * CHECK THIS: commsim models seem to have changed with
      allowing double in swsh_samp methods
    * Changes in avoiding dollar for with, and with for data
    * Chao changes, in particular the small sample correction

commit 1f038ef610efc1fc7a317a9aaf87474ed36cbdf9
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Nov 6 10:59:42 2014 +0200

    Bad \usage lines found in documentation object 'specpool'

commit c20e2f330776f260bce1c218ba451bfc1851a26b
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Nov 6 10:51:58 2014 +0200

    Proof read NEWS (and dune.taxon man page accordingly)

commit 9e8329093b8077d7164086bb1f8b899f6a54688f
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Nov 6 10:25:37 2014 +0200

    NEWS about changes in Chao extrapolated richness

commit e92c6af0f46e197c170166104bd69746ea79c48f
Merge: f238aa9 b77c88d
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Wed Nov 5 07:37:01 2014 -0700

    Merge pull request #64 from jarioksa/ordiareatests

    Add ordiareatests for ordihull and ordiellipse

commit f238aa9c5a20936f0b4df0cfa721643fdc47417c
Merge: 6c108fa 01af54f
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Wed Nov 5 07:26:32 2014 -0700

    Merge pull request #67 from jarioksa/chao

    Chao equations

commit 01af54fbc842dec7f90879296276485d742d7ab2
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Nov 5 10:11:31 2014 +0200

    sync poolaccum with Chao changes in specpool

    * switch to bias-corrected Chao when a2==0
    * use small-sample correction in Chao (hard-wired)

commit 69c971df80cb088e933d8927e304ac1979aa60e6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Nov 5 09:56:58 2014 +0200

    estimateR will not use small sample correction

    In addition, clarify man/ page for estimateR

commit 2e2df0e15eb45170519554a16aedd6902fa8d292
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Nov 4 13:41:02 2014 +0200

    Make small sample correction optional in specpool

commit 3af5f26640f18f000911fb908f348f39a77a8b4e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Nov 4 11:41:59 2014 +0200

    Update diversity vignette for the current state of Chao estimates

commit b5b8b8e19bc2fc0869690cd6120a8e7b39e38ec6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Nov 4 11:39:02 2014 +0200

    fix small sample correction of var(Chao) when there are no doubletons

    I reconstructed the variance formula (3b) of Chiu et al. 2014 using
    the procedure described in their online appendix. I could get the same
    formula except for the small-sample correction: it seems that EstimateS
    web page got this correctly, but Chiu et al. ignore the small-sample
    correction for all but the first term.

commit 562a531935df234fd204f917a813602ac5e9d3a2
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Nov 3 11:08:03 2014 +0200

    Use EstimateS formula (eq6) for the variance

    The EstimateS web page eq6 formula is actually incorrect: it is
    derived on the partial derivatives of classic Chao, but the terms
    of the final result are replaced with the terms of bias-corrected
    Chao. However, numerically the error is only about 1% of the correct
    form and therefore we resent to use this widespread approximation.

commit 6c108fa55254aa06c0286f8b4e4bdecf4260eae0
Merge: 6819b9d feaf74e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Nov 2 16:41:57 2014 +0200

    Merge pull request #68 from gavinsimpson/text-cca-labels-and-centroids

    Text cca labels and centroids

commit feaf74e1ac5001831946a2fe8649d2e8d25963f7
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sat Nov 1 20:09:48 2014 -0600

    document change to text.cca with centroids and user-supplied labels

commit c439fae28d932500e1992cad2a4b5689c61c2382
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sat Nov 1 20:08:10 2014 -0600

    fix testing if centroids in biplot scores when user-supplied labels are given

commit 1768ac0d0eea8171b05791a3ea5e958cab1f5b65
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Oct 31 10:00:27 2014 +0200

    Forgot to take the sd of variance in estimateR

commit cdbaa810c18a6b7924f65aeacf61155a41223f53
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 30 19:28:46 2014 +0200

    Proof-read equations in updated Chao documentation

commit b128c28d8c5c2913d8714236d08c0cffea4736f7
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 30 19:23:29 2014 +0200

    proof-read and format man/specpool.Rd

commit 7ae52d63725e684723a6259193d760d16ccb170b
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 30 18:42:55 2014 +0200

    update man/ pages for upgraded Chao richness

commit 38f01e08de3a3413cc6e96a170b6dbaaee17b223
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 30 18:17:09 2014 +0200

    Use always bias-corrected form in Chao1 of estimateR

commit 0502202e501f878adc38cc5c1a869980c11b3374
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 30 16:49:51 2014 +0200

    Update vignettes to the update Chao richness estimators

commit 4e056265951a001aac8b1b41f3f53c1c80e3bc4a
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 30 16:08:31 2014 +0200

    Finally complete eq. for variance of extrapolated bootstrap richness

commit a34f01f7fdc9a2903fba9517cac2bac6c1e7ef88
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 29 21:00:30 2014 +0200

    Chao index in specpool got small-sample correction and bias-correction

commit a0a2b1fd664214aded5b902eee83e420f47742ae
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 29 20:20:37 2014 +0200

    Chao1 got small-sample correction and bias-corrected variance

    estimateR upgrade following Chun et al., Biometrics 70, 671-682
    (2014). Now the behaviour should be similar as in EstimateS, but
    the variance formulae differ (our based on the cited publication).

commit 016b37945d8ddcd57756cb7ef51c940702e4a3c6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 29 19:55:56 2014 +0200

    esttimateR: use bias-corrected Chao1 only when doubletons = 0

    Previously we always used bias-corrected form of Chao1, but
    it seems that the normal biased form should normally be used, and
    only when it cannot be estimated (because we divide by the number
    of doubletons).

    The sd of bias-corrected form is made NA in this commit: fixed in
    the next one.

commit b77c88d91e57e08b47a9646947095c2d0d8fa3ab
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Oct 27 11:30:06 2014 +0200

    NEWS about ordiareatests

commit 8117a128d867501b5e1c6dfd5d7811c39e3cff4d
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 26 20:00:08 2014 +0200

    permutations need be transposed in permustats of ordiareatest

commit ffa3878e89fcf67a02e1bc487dde99ab098a3dab
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 26 19:41:53 2014 +0200

    Add permustats.ordiareatest

commit 04eb066c03e5c2262c299944f5dcc82cc5cbf75f
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 26 19:41:07 2014 +0200

    Document and export ordiareatest: passes R CMD check

commit d96189be2f931bd2b017dc404e20e875ffe0c09b
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 26 18:52:09 2014 +0200

    Add print.ordiareatest

commit 86a385a44011dead168f902f343b172aeb83354e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 26 18:28:55 2014 +0200

    Add ordiareatest for the areas of convex hulls or ellipses in ordination

    The function is bases on ordihull and ordiellipse and performs permutation
    tests on the sizes of fitted convex hulls or ellipses. The tests are
    one-sided and the alternative hypothesis is that the areas covered by
    convex hulls or ellipses are smaller than random expectations.

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/vegan@2906 edb9625f-4e0d-4859-8d74-9fd3b1da38cb