Merge pull request #23 from mattbarbour34/master

changed >= to > in N.paired.rows and cols calc.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2876 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2877 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2878 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2879 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2880 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2881 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2882 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 33198cba46810c1265f0ba6061225b038272a24f
Merge: 0f86b2b 12aa1f2
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 17:05:15 2014 +0300

    Merge pull request #39 from jarioksa/adapt-print-to-permute-pkg

    Adapt print to permute pkg

commit 12aa1f2555126075ab3fa9fe9ca6a98aa684f73d
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 16:06:49 2014 +0300

    permutest.betadisper also uses howHead() to show permutations

commit 9526decb88cc91ef7db565cafc0adca06989512b
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 21:37:31 2014 +0300

    Document cases when a function returns a "control" item

    Some functions return "control" *attributes* with some of their
    items: this is not (yet?) documented.

commit 61df5998b0695dee2a5784eee79de083b1eba308
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 21:30:02 2014 +0300

    CCorA returns permute  "control" and print uses howHead() to show it

commit 31c401289c14af2790fa733e72ba05cb695f1179
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 21:18:34 2014 +0300

    simper adds "control" attribute for permutations and summary prints it

commit ecce8c723d5e1b68e251e8c16d167af27b0b5a3e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 21:08:34 2014 +0300

    Add empty line between results and permutation details

commit a0333a2640742df2493ae0a75b16b0b17a27b393
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 19:17:20 2014 +0300

    mso adds "control" attribute to the "vario" item and howHead() shows it

commit 711938bd8836a0cdb6210d8c536a8a831986aece
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 18:56:17 2014 +0300

    remove dangling '.' from the output

commit 5ca3ecc14686f89b23902f28c4910d3279c6b968
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 15 18:43:45 2014 +0300

    adonis adds howHead() to the heading of the anova table

    The permutation information is printed similarly as in
    anova.cca.

commit 16dc86254cb8d692511bcc71759f03e1bb2f6ec9
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 14 20:19:00 2014 +0300

    mrpp printing to the new permute API: no more strata

commit 3728b825dda5303788231414c7f3f1e1735c293e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 14 19:37:58 2014 +0300

    mantel printing to the new permute API: no more strata

commit 03f764df31f5528012cd8e55e9bb77d884741e7e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 14 09:10:23 2014 +0300

    adapt envfit printing to the new permute API: no more strata

commit 808cb0c1a0ddafcea99e1f04de16ef4e9b25dfad
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 14 08:40:37 2014 +0300

    print of anosim adapted to the new permute API

    No more stores 'strata', but 'control' and uses howHead() to show
    its result.

    It seems that getPermuteMatrix(..., strata=<name>) does not save the
    name of the 'strata', but howHead() just prints "Blocks: strata".

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2883 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2884 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit e3a3fa09c073ad1a3b9e196a6031b04e4388cf9a
Merge: 793a0c7 b330bbd
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Sep 18 16:49:51 2014 +0300

    Merge pull request #40 from jarioksa/update-docs

    Update docs

commit b330bbd01c877df5c44d48b49191362cc2bf2b71
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Sep 17 21:22:22 2014 +0300

    edit FAQ-vegan

commit 8494bb8c3cf81612c5baa72fdf086253703f9854
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 20:00:09 2014 +0300

    remove svn-specific fields $Date$ and $Id$ from documents

commit 72009ede68c919e31569830dd51fa5c27fe9ca82
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:52:52 2014 +0300

    More fixes for permutation routines in intro-vegan

commit d0b929423a483b32fc8bfa15bab6ced80b21aa0c
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:50:02 2014 +0300

    FAQ-vegan adapted to GitHub

commit ec8fd7e0c27a3f57024fefca3840c19d990c54f5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:34:56 2014 +0300

    FAQ-vegan update to the use of permute package

commit bfb0f79a7a5cb1658c8509e94d8014b01dd24e09
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:20:00 2014 +0300

    update intro-vegan to changes in anova.cca

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2885 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 0d5ef1f29a292811865ff007aa6611b80e533663
Merge: ad80935 8f56476
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 08:33:05 2014 +0300

    Merge remote-tracking branch 'upstream/master'

commit ad809359a6ffd9b4497503a02360602a4f8f7874
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Sep 21 15:39:49 2014 -0600

    fix a typo

commit f25f30c479d1fec51cccd48b0a2b8941703744da
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Aug 31 20:18:42 2014 +0300

    Delete ccanova* in favour of anova.cca*

    When anova.cca* switched to parallel processing, the old code was
    backed up as ccanova* functions. Now these functions were removed
    and only the new anova.cca* functions remain

commit 8f56476067432f58a1d8c739f017ddf69c8755e1
Merge: 272e918 413dcb6
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Sep 21 19:00:36 2014 -0600

    Merge pull request #41 from jarioksa/parallel

    Delete ccanova* in favour of anova.cca*

commit 272e918baaa57b35c2bcd5f50e4406e41cde00d9
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Sun Sep 21 15:39:49 2014 -0600

    fix a typo

commit e3a3fa09c073ad1a3b9e196a6031b04e4388cf9a
Merge: 793a0c7 b330bbd
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Sep 18 16:49:51 2014 +0300

    Merge pull request #40 from jarioksa/update-docs

    Update docs

commit b330bbd01c877df5c44d48b49191362cc2bf2b71
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Sep 17 21:22:22 2014 +0300

    edit FAQ-vegan

commit 8494bb8c3cf81612c5baa72fdf086253703f9854
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 20:00:09 2014 +0300

    remove svn-specific fields $Date$ and $Id$ from documents

commit 72009ede68c919e31569830dd51fa5c27fe9ca82
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:52:52 2014 +0300

    More fixes for permutation routines in intro-vegan

commit d0b929423a483b32fc8bfa15bab6ced80b21aa0c
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:50:02 2014 +0300

    FAQ-vegan adapted to GitHub

commit ec8fd7e0c27a3f57024fefca3840c19d990c54f5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:34:56 2014 +0300

    FAQ-vegan update to the use of permute package

commit bfb0f79a7a5cb1658c8509e94d8014b01dd24e09
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 16 19:20:00 2014 +0300

    update intro-vegan to changes in anova.cca

commit 413dcb6b5853755c1b8a2c6f90e8c201a31d492d
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Aug 31 20:18:42 2014 +0300

    Delete ccanova* in favour of anova.cca*

    When anova.cca* switched to parallel processing, the old code was
    backed up as ccanova* functions. Now these functions were removed
    and only the new anova.cca* functions remain

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2886 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2887 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit b0dde2c6e4e9d415a56e3fa62740a036a515bd7f
Merge: abb5b0b 1391a30
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Sep 24 11:42:01 2014 +0300

    Merge pull request #43 from jarioksa/veganify-dispweight

    Veganify dispweight

commit 1391a306e31808f4a901d3078764aeadc1eb3461
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Sep 24 10:10:27 2014 +0300

    more detailed authors information for [g]dispweight

commit d688532098d63fbc1faaed66905a13a1eb1230e6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Sep 24 10:09:58 2014 +0300

    tweak formatting of dispweight summary

commit 3d8b06a476222e8b13ff46a26fad9d5234c6fc8c
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Sep 24 09:57:34 2014 +0300

    edit man/dispweight.Rd

commit 6ce39e51e152f8d3397eb785a446c56ccbf3aaa5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 23 17:11:05 2014 +0300

    gdispweight cannot handle missing values and fails informatively

    dispweight already fails informatively from nullmodel

commit 6a9d84eb91ab157fc4d430d9d4d54b4a570d51b6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Sep 23 07:23:26 2014 +0300

    print.summary.dispweight passes ... to printCoefmat

commit 6d5eea1d530fb2131bfb13ea7ff3f1a841e4933a
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 21:39:40 2014 +0300

    avoid using anonymous functions in sapply() within gdispweight

commit 704d4c2f3879fd2ffa77cc8ea70df01d331a68ee
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 16:42:05 2014 +0300

    add summary.dispweight to extract and print simulation results

commit 00a68c93498e53b0a6bfe967744ecbf90f1dd372
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 16:15:44 2014 +0300

    dispweight returns the name of the nullmodel

commit c9b929181efe901d0483e3ed9b07d0e9830d3d1e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 12:47:54 2014 +0300

    dot expansion of terms works in gdispweight(comm ~ ., data=<data>)

commit 02f947d8ac0dadcfafb422e42e2747d5eebede70
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 11:07:41 2014 +0300

    [g]dispweight returns attribute on degrees of freedom used ("df")

    gdispweight finds d.f. directly from glm() and this is normally
    constant for all species, but dispweight discards factor levels where
    species does not occur, and degrees of freedom is non-constant for
    species. The d.f. is used to divide the Pearson Chi-square to get
    the overdispersion, and because d.f. is reduced for some species in
    dispweight, these will get higher overdispersion and hence lower
    weight in dispweight than in gdispweight. With this commit, the
    same original Pearson Chi-square will be found for both dispweight
    and gdispweight object:

    attr(object, "D") * attr(object, "df")

commit 99f9a6bc2e2849bb7319157839e69866968b3bd6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Sep 22 10:53:06 2014 +0300

    export gdispweight from the NAMESPACE

commit 94a0d4349256b423c2a7e9066a73d4216f44e656
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 20:41:51 2014 +0300

    Update author information for dispweight + gdispweight

    I think that email address of Eduard Szöcs also was out of date.

commit 87391813102ed27cadd0986fd8b78ed72d3293fd
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 20:32:00 2014 +0300

    Introduce generalized (parametric) dispersion weighting

    This is a new unpublished method. Original method uses Pearson
    Chi-square for a Poisson model with one factor and assesses the
    significance using multinomial simulation ("c0_ind" nullmodel).
    The new method estimates the same Pearson Chi-square for any glm
    model and evaluates the significance parametrically. Otherwise the
    models are identical except that the original method ignores
    completely the factor levels where species in assessing the number
    of degrees of freedom, but the generalized method defines the
    degrees of freedom in a standard way (number of observations minus
    number of model coefficients). As the degrees of freedom is used as
    divisor for weights, this will influence the strength of downweighting.

commit 37f5261e2f2933c90c6521f6c258c1a850a3426b
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 08:50:24 2014 +0300

    Relax data requirements in dispweight: reject only binary models

    The test of data properties was moved to checking properties of
    defined nullmodel, and only binary null models are rejected (these
    would all have p=1). We now accept also non-integer quantitative
    data. I don't know if these make sense, but that is none of my
    business -- users decide.

commit f4d1394fd7216effef1b3670974b44627b2fc08c
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 08:38:45 2014 +0300

    dispweight handles 1-level 'groups': analysis wrt community mean

commit 9092774c0f46c177a6ca4ce254478e4a348141fb
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 08:28:21 2014 +0300

    Expose nullmodel and plimit as user arguments in dispweight

commit 21e0362b1f7ee3ae101684466921b59919008b89
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 08:24:11 2014 +0300

    adapt docs to 999 simulations of commit 67adb96

commit 67adb967a5d13bc439cfa52844dc4fb9f10cd0c9
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 08:17:05 2014 +0300

    default to 999 simulations in dispweight

commit 7ba5092c9bbbd6519fdba2c1e590e9f4f5000e64
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Sep 21 08:08:22 2014 +0300

    major rewrite of dispweight: rethink, streamline & use vegan::nullmodel

    The function was completely rewritten to use vegan::nullmodel
    "c0_ind" which is equal to the simulation used in the original
    function. The original function looped over species, but  now we
    perform simulation for all species simultaneously using nullmodel,
    and loop over levels of 'groups'. All code that could be moved
    out of this loop was moved, and calculation of 'dhat' statistics
    was refactored and streamlined -- and done outside the loop.

    There are not many unchanged lines, but the results are equal provided
    the 'p' values are on the same side of the fixed critical level.

    In my laptop, this is also about 3x faster than the original.

commit 824de6ca248a29faa0290b4f4fda8b7ef9aa3994
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sat Sep 20 08:54:09 2014 +0300

    remove empty levels from "groups" or dispweight fails cryptically

    Error in if (any(means == 0)) { : missing value where TRUE/FALSE needed

commit 70277611eacc86153d56cac101f076d547bf3666
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sat Sep 20 08:45:20 2014 +0300

    dispweight used arg 'group', but other vegan functions use 'groups'

commit ae6c6af97b7a033e85931ba9801d5cf8db8c074f
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Sep 19 08:45:15 2014 +0300

    dispweight doc says that it is 'nsimul' (not 'nperm')

commit cd129e362142ba2b4b08d70a2da1a4710c9e6c85
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Sep 19 08:40:57 2014 +0300

    document that dispweight returns transformed data

commit 8087340689d133b6dd5b34aae136452687a99984
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Aug 6 17:37:36 2013 +0300

    check that input are integers, fix docs

commit bff23ee508a7338503f9ac2eb7280bf0217e0432
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Aug 6 16:53:46 2013 +0300

    dispweight does simulations, not permutations

commit 7d5a6ed8828ead61c81b6b4f9ebe9d651253f8c7
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Aug 5 08:55:18 2013 +0300

    all dispweights return transformed data (with attributes)

commit 6b6a47b9dd16bc0421103a0900f659f15d7f8bc8
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Aug 4 09:04:39 2013 +0300

    dispweights work without 'group' argument

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2888 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'master' into r-forge-svn-local

Add permustats() function and their support with replace and
enhance old density and densityplot methods for permutation
and simulation results.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2889 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 951be045be7286ce35160f36562b795b2bec7f96
Merge: 1ca9538 47f3482
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Tue Sep 30 10:22:12 2014 -0600

    Merge pull request #49 from gavinsimpson/master

    fix a bug in calculation of p value in group pairwise permutation test

commit 47f348283bff6c9d8939b2780b62fcde15e1ed84
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Tue Sep 30 10:01:53 2014 -0600

    fix a bug in calculation of p value in group pairwise permutation test introduced in c6b76f1

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2890 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit c36a60df653b55f05f218b47a714f236a8734cfd
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 2 08:21:53 2014 +0300

    update tests/Examples

commit 51db4dab9329ca8fd26dfe8476b4cad15c5a6ec2
Merge: 2ac73ea f6ad372
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Wed Oct 1 15:53:29 2014 -0600

    Merge pull request #50 from jarioksa/revert-scoverage

    remove scoverage()

commit f6ad3723b084ab0abdad89132c524c6457f1a3bd
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 1 23:11:24 2014 +0300

    remove scoverage()

    If this function is resurrected, it should be documented independently
    and not with the decostand.

commit 2ac73ea242b5388ba935dd9efe5bc904ed8af509
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 1 15:02:53 2014 +0300

    simulate.[rda,cca,capscale] only work with constrained ordination

    Earlier they gave results, but these were wrong because fitted
    component did not exist, and wrong component was used for them.
    Now check and stop informatively.

commit 087a7250d12ee08e543696cfa84ebe84bbcd5ea5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 1 12:01:32 2014 +0300

    Update tests/Examples

commit fddbfc7c683d6a8f58e4838c20b07c2ddb22bde7
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 1 11:56:41 2014 +0300

    nestedness indices return named statistics

commit 951be045be7286ce35160f36562b795b2bec7f96
Merge: 1ca9538 47f3482
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Tue Sep 30 10:22:12 2014 -0600

    Merge pull request #49 from gavinsimpson/master

    fix a bug in calculation of p value in group pairwise permutation test

commit 47f348283bff6c9d8939b2780b62fcde15e1ed84
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Tue Sep 30 10:01:53 2014 -0600

    fix a bug in calculation of p value in group pairwise permutation test introduced in c6b76f1

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2891 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit fba9b24cc98f984254544db5cd87cdb224098588
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Thu Oct 2 23:16:46 2014 -0600

    Update test example output

commit 8d70932789980c484b108c14f7166f0bac24f3ff
Merge: 8086446 a439b75
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Thu Oct 2 22:43:57 2014 -0600

    Merge pull request #45 from jarioksa/fix-no-of-permutations-in-permutest.beadisper

    @jarioksa has convinced me of the benefits of treating permutations following Phipson, B. & Smyth, G. K. Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Stat. Appl. Genet. Mol. Biol. 9, Article39 (2010). permutest.betadisper: no. of permutations counted without observed stat

commit 8086446245adb253f6cf8bbd749c21195dff2dc8
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Oct 2 16:34:17 2014 +0300

    update tests/Examples

commit a439b751ed64b32c1234a6993c726153f8f8f6cf
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Sep 26 12:00:39 2014 +0300

    permutest.betadisper: no. of permutations counted without observed stat

    Although we put the observed value among permutations, the number
    of permutations should be given without that observed statistic
    (like done in all other vegan functions).

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2892 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit ea6dcea6a34dc8b52624bb17b08a43de5bb82af7
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Oct 7 10:48:27 2014 +0300

    Do not yet warn on commsimulator deprecation

    We do not yet warn on commsimulator deprecation in vegan 2.2-0
    but only in the next release to give other packages time to
    adapt. There were thousands of warnings in CRAN packages
    bipartite and metacom.

commit dde0dd6c726f0781b8ffabe8cdc402e939546bb8
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Oct 6 14:50:11 2014 +0300

    allow missing 'strata' in permutations

    getPermuteMatrix used 'strata=NULL' to define there are no
    strata. Vegan functions were adopted to this, but this broke
    CRAN packages cocorresp and mpmcorrelogram. The fix was so simple
    and obvious that it is almost annoying.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2893 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 16d74e39dd745c445cb862aae860ddbc83d25a57
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Oct 7 21:06:02 2014 +0300

    skeleton of NEWS about vegan 2.2-0

commit 70e5542754fbf3c67cf55bc19db42b61708ec0b8
Merge: ea6dcea 54aa57f
Author: Gavin Simpson <ucfagls@gmail.com>
Date:   Tue Oct 7 08:37:56 2014 -0600

    Merge pull request #51 from jarioksa/remove-u.eig-etc

    Remove u.eig etc

commit 54aa57fa08c06424a8d0ad7aa4575f5de52352e0
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 5 20:15:40 2014 +0300

    man/cca.object tells about imaginary.u.eig scores in capscale

commit 971a7f602364109e13cfb21e21216c067c6f8cf8
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 5 08:44:48 2014 +0300

    man/cca.object.Rd updated to new cca object without .eig scores

    There is a note about changes which here are suggested to be
    effective in vegan 2.2-0.

commit c4ab85b43a13d0ac1a61aae7ac9c63e60b494368
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 5 08:43:46 2014 +0300

    neither ade2vegancca returns u.eig, v.eig, wa.eig

commit 5f33e5be3092f5102d4e7b33d11990a66fa3b8e6
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 5 08:39:38 2014 +0300

    remove v.eig item from capscale result

    wa.eig and u.eig already disappeared with rda changes.

    The result still has CA$imaginary.u.eig (scaled scores for
    imaginary axes). These are the only scores returned for
    imaginary axes.

commit 96d8bdf0695ac0254b8233fb48f585a764130251
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 5 08:14:13 2014 +0300

    remove u.eig etc from rda

commit 761afcb0a6895a530b74334f0ffa0c727483b425
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Oct 5 07:56:11 2014 +0300

    remove u.eig, v.eig and wa.eig items from cca.default

    The cca.object was documented in vegan 1.6-10 (Sep 26, 2005), and
    in that document we warn that there is "no guarantee" that these
    itmems will be kept in future release. In commit bddfea39 (Mar 5, 2013)
    we use harsher tone and said that the "item will be removed". However,
    that harsher text has not been in any release version so that this
    may be an abrupt change.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2895 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 53c612015bd1acbb54f189800c62f48c48744ca7
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 8 14:27:22 2014 +0300

    ChangeLog heading to the github time

commit af070de7f5246f53e732d6ca86c9137aa2cc77be
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 8 14:19:08 2014 +0300

    compile ChangeLog from git logs, long afterwards

    I am not sure if we need to keep ChangeLog. This needs a bit care,
    because ChangeLog is essentially linear and git is a web. However,
    I collected major changes from git logs to still have a ChangeLog
    of major events.

commit a143de91c4d840952bdcb638119bfb9245b148f1
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Oct 8 11:05:18 2014 +0300

    more NEWS picked from the ChangeLog

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2896 edb9625f-4e0d-4859-8d74-9fd3b1da38cb