fix print.summary.simper

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2100 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit ad85a0cdc48a94ae596a0763b6203466a6dec47d
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Feb 21 09:53:09 2012 +0200

    remove refs to ecodist::nmds (it is not similar to monoMDS)

commit 4a99b47aa88408cdb1e4ecb356799a21fba6a4c5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Feb 21 09:47:24 2012 +0200

    fix explanation of Kruskal stress

commit 2823a512589d27210fc1ae244db7feb0ae587298
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Feb 20 21:04:15 2012 +0200

    print.summary.simper fixes

    Long lists of data frames could be randomly truncated and
    arg 'digits' was not honoured

commit 5ce21029c56a279071c4c6756468712da5807196
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Feb 20 20:13:23 2012 +0200

    test

commit c3c29c95d2852235b9498b468513c7bd6f664210
Merge: 286ba84 ce8e280
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Feb 19 21:33:55 2012 +0200

    Merge branch 'master' into r-forge-svn-local

commit 286ba846449e870acd07f74f0d7433de01dad9b3
Author: jarioksa <jarioksa@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date:   Sun Feb 19 19:19:59 2012 +0000

    merge github fix for summary.simper

    git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2098 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

commit ce8e28066fb6369d51eeb274cb68f1716cec18c5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Feb 19 21:04:29 2012 +0200

    summary.simper(..., ordered=FALSE) failed when permutations = 0

commit a64c253594f747aa76803b5026d8afb207b316cb
Author: jarioksa <jarioksa@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date:   Sun Feb 19 17:50:08 2012 +0000

    merge github updates

    git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2097 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

commit 9b342759506db292c637ce35274f20cfc3e63baf
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Feb 19 18:41:49 2012 +0200

    typo

commit 3a33d106a1218a9682b4f45ea7133007caa708df
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Feb 19 18:36:35 2012 +0200

    rephrase permutation matrix in simper.Rd

commit 9902e6c87d478992d936d982874fe4ff2ab4b605
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Feb 19 18:32:22 2012 +0200

    add print.summary.simper() to get signif.stars

commit ce1b680488a1269e540054943bf9f5a97905d8dd
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Feb 19 09:11:32 2012 +0200

    simper accepts permutation matrix (like documented)

commit 7dbda9183580d5ced0aad6cae0262d23c9af48c9
Author: jarioksa <jarioksa@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date:   Fri Feb 17 13:47:58 2012 +0000

    merge from simper fixes

    git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2092 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

commit 2d5209eec2179c97a12362d984bd6b6f18a4b390
Merge: dd53cd3 92ddaae
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Feb 17 12:48:19 2012 +0200

    Merge branch 'simper' of github.com:jarioksa/vegan into simper

commit dd53cd3c682e63d49e3d2e33e6fe4bb2e657ebb8
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Feb 17 12:33:05 2012 +0200

    use same permutations for all factor pairs

    The permat matrix is generated before the permutation loop so that
    (1) same permutations will be used in all comparisons, (2) permute
    package is used, (3) users can supply their own permutatoin mtrix,
    and (4) as a first step to implement parallel processing. This is
    also marginally faster (ca. 5%).

commit 92ddaae577bab7e8f044b9136611a2a97356be0e
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Feb 17 12:33:05 2012 +0200

    use same permutations for all factor pairs

    The permat matrix is generated before the permutation loop so that
    (1) same permutations will be used in all comparisons, (2) permute
    package is used, and (3) as a first step to implement parallel
    processing. This is also marginally faster (ca. 5%).

commit 4fc0ddd3b29fbaef83079e7557b63694b1e7c85c
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Feb 17 09:44:07 2012 +0200

    fix description of simper return object

commit 1366393f3e5d2fe38ddfdb30232df4ebe29cf093
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Feb 17 09:35:13 2012 +0200

    explain simper output

commit ce4fb23ce91ab674aa7b95b1409e50ce0c1a2551
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Fri Feb 17 07:26:06 2012 +0200

    at least 70% of contribution is shown

    previously stopped so that cumulative contribution was at most 70%,
    but now shows usually one species more so that at least 70% (and
    usually a bit more) of contribution is displayed

commit 602c15325d113efc7e303d36d40c036cf10b0629
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Thu Feb 16 21:40:18 2012 +0200

    update examples for simper

commit 78c85d8f7dda7f8db36de6483789508056b7c9c7
Author: jarioksa <jarioksa@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date:   Thu Feb 16 14:10:36 2012 +0000

    Squashed commit of the following:

    commit cf72efd547e0487a62529b382fcc92a3127b8c65
    Merge: 8e08f0c a12a0ec
    Author: jarioksa <jari.oksanen@oulu.fi>
    Date:   Thu Feb 16 05:56:37 2012 -0800

        Merge pull request #2 from EDiLD/master

        simper should be now ready for release

    commit a12a0ecd92d0fde018aa710b3ae3f6f978cd7204
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Thu Feb 16 13:14:17 2012 +0100

        typo

    commit 5dd3236e2b1240f7f7a462ba7a17dd04cd216061
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Thu Feb 16 12:02:53 2012 +0100

        simper passes now CMD check

    commit fe6a9fda1daecdf5627b9f61ca05d31f79b59126
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Thu Feb 16 11:22:15 2012 +0100

        fixed simper.Rd (examples, \alias)

    commit 3223c72070f50118ab05a125fdffce1a9eac5634
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 19:08:51 2012 +0100

        corrected permutational p-value

    commit b38cfc478600cbfbf66abb1f07cea546656e8c68
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 19:04:36 2012 +0100

        fixed typo

    commit 3d67710d1e18c9feb53132b71ec7b2850b720556
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 18:44:08 2012 +0100

        updated documentation

    commit 9429d2373e21866e9f0cde9ff102790083128927
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 18:19:59 2012 +0100

        updated documentation to changes

    commit c3c8814bc6969dd411cf234ba5b1eee3e282fbef
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 17:15:38 2012 +0100

        changes make the code noticable faster

    commit bc3e13ecc6bd194bf1087821fbff750bc3d3d309
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 15:37:31 2012 +0100

        cumsum is also stored in the simper-object
        + style formatting

    commit fbdb8c3f141bc6f1bdc014278c655a047c0e04c9
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 14:54:08 2012 +0100

        embed a permutation test of the average contribution

    commit 31ed428a11c7637b7e4d309079d9280f9edc64d1
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 13:08:01 2012 +0100

        added option to return a summary ordered by cumsum.
        some style formatting

    commit 373913b209357ea0a48d009a338b81239568ca2e
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 12:52:14 2012 +0100

        fixed typo

    commit 5992276a411361f41239190b0182e57c8e46ffa3
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Tue Feb 14 12:44:08 2012 +0100

        restructured output

    git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2091 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

commit fd164f0bc8799b3ff8769f6dcb17f95ea2b2870f
Author: jarioksa <jarioksa@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date:   Thu Feb 16 14:09:15 2012 +0000

    Merge branch 'master' of https://github.com/EDiLD/vegan

    Conflicts:
    	man/simper.Rd

    git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2090 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

commit cf72efd547e0487a62529b382fcc92a3127b8c65
Merge: 8e08f0c a12a0ec
Author: jarioksa <jari.oksanen@oulu.fi>
Date:   Thu Feb 16 05:56:37 2012 -0800

    Merge pull request #2 from EDiLD/master

    simper should be now ready for release

commit a12a0ecd92d0fde018aa710b3ae3f6f978cd7204
Author: edisz <szoe8822@uni-landau.de>
Date:   Thu Feb 16 13:14:17 2012 +0100

    typo

commit 5dd3236e2b1240f7f7a462ba7a17dd04cd216061
Author: edisz <szoe8822@uni-landau.de>
Date:   Thu Feb 16 12:02:53 2012 +0100

    simper passes now CMD check

commit fe6a9fda1daecdf5627b9f61ca05d31f79b59126
Author: edisz <szoe8822@uni-landau.de>
Date:   Thu Feb 16 11:22:15 2012 +0100

    fixed simper.Rd (examples, \alias)

commit 3223c72070f50118ab05a125fdffce1a9eac5634
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 19:08:51 2012 +0100

    corrected permutational p-value

commit b38cfc478600cbfbf66abb1f07cea546656e8c68
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 19:04:36 2012 +0100

    fixed typo

commit 3d67710d1e18c9feb53132b71ec7b2850b720556
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 18:44:08 2012 +0100

    updated documentation

commit 9429d2373e21866e9f0cde9ff102790083128927
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 18:19:59 2012 +0100

    updated documentation to changes

commit c3c8814bc6969dd411cf234ba5b1eee3e282fbef
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 17:15:38 2012 +0100

    changes make the code noticable faster

commit bc3e13ecc6bd194bf1087821fbff750bc3d3d309
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 15:37:31 2012 +0100

    cumsum is also stored in the simper-object
    + style formatting

commit fbdb8c3f141bc6f1bdc014278c655a047c0e04c9
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 14:54:08 2012 +0100

    embed a permutation test of the average contribution

commit 31ed428a11c7637b7e4d309079d9280f9edc64d1
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 13:08:01 2012 +0100

    added option to return a summary ordered by cumsum.
    some style formatting

commit 373913b209357ea0a48d009a338b81239568ca2e
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 12:52:14 2012 +0100

    fixed typo

commit 5992276a411361f41239190b0182e57c8e46ffa3
Author: edisz <szoe8822@uni-landau.de>
Date:   Tue Feb 14 12:44:08 2012 +0100

    restructured output

commit 8e08f0cbfccd4263c89d3935656a8476640a6066
Merge: 318e43a 1667511
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Feb 14 10:13:54 2012 +0200

    Merge branch 'r-forge-svn-local'

commit 1667511652ceee8fb883801d0f6c32261873739c
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Feb 14 10:02:02 2012 +0200

    Squashed commit of the following:

    commit 318e43a9a66743141759de429387858c1420a64a
    Merge: bd99fef 1d3e3ad
    Author: Jari Oksanen <jari.oksanen@oulu.fi>
    Date:   Mon Feb 13 15:26:21 2012 +0200

        Merge branch 'master' of https://github.com/EDiLD/vegan

        Conflicts:
        	man/simper.Rd

    commit 1d3e3ad660fb5d9310337886a7612b1213190d7a
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Mon Feb 13 13:11:03 2012 +0100

        removed roxygen, since the link to the rd is broken

    commit 9bab8e59ebb3da2ce3f177073a6a2a9a50133fa8
    Merge: 96a6f23 2a4ad28
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Mon Feb 13 12:54:58 2012 +0100

        test

        Merge branch 'master' of github.com:EDiLD/vegan

        Conflicts:
        	man/simper.Rd

    commit 96a6f230295bfe70262143576c30bdf0c23de042
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Mon Feb 13 12:45:24 2012 +0100

        changed Argument description

    commit 2a4ad280ec97e6c5971b0e6aff837080de0b69bd
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Mon Feb 13 12:45:24 2012 +0100

        changed Argument description

    commit 41b12727a684637b0a3aa0e0b25f145e3b403e6a
    Author: edisz <szoe8822@uni-landau.de>
    Date:   Mon Feb 13 12:41:28 2012 +0100

        colMeans is faster than apply

commit 318e43a9a66743141759de429387858c1420a64a
Merge: bd99fef 1d3e3ad
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Mon Feb 13 15:26:21 2012 +0200

    Merge branch 'master' of https://github.com/EDiLD/vegan

    Conflicts:
    	man/simper.Rd

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2101 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 15b43b26bb65248bb07339233646943e8a9d0703
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Tue Feb 21 10:30:45 2012 +0200

    update tests for print.summary.simper

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2102 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
fix bug in permutation p-values in simper

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2103 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
merge Cao index (CYd) in vegdist

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2104 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Merge branch 'up' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2105 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
doc updates for scores and vegdist from github.com

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    scores.monoMDS did not know 'choices'

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2107 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
names were dropped if a 2-class factor was the only constraint

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2110 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
tweak simper.Rd formatting

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Merge simper updates from pull request #6 at github.com

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2115 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
CRAN release vegan_2.0-3

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Tell about location/dispersion mix-up in anosim, mrpp & simper

References to a new paper by Warton et al (MEE 3, 89-101; 2012)
to support previous warnings on the same issue in help pages.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2121 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
ChangeLog entry on location/dispersion mixupin adonis, mrpp, simper

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Merge branch 'master' into r-forge-svn-local

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2123 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
update NEWS.Rd to the the latest CRAN release (2.0-3)

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missing quote (reported by Emili Garcia-Berthou)

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2125 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@2127 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 636a35f0c513b5688b119c16967d97c74eff0ba5
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Wed Apr 11 11:08:46 2012 +0300

    anova(<prc-object>, by = ...) failed due to NAMESPACE issues

    Reported as issue #7 by Eduard Scöcz in github.com

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2128 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Squashed commit of the following:

commit 511d3642fb58717c78f4f17e5059aa26732f652d
Author: Jari Oksanen <jari.oksanen@oulu.fi>
Date:   Sun Apr 15 08:32:20 2012 +0300

    envfit()/factorfit() failed factors had unused levels

    Reported as issue #8 in github.com by Eduard Szöcz and fixed
    in centroids.cca()

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