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
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
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
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
update examples for simper
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
explain simper output
fix description of simper return object
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%).
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%).
Merge branch 'simper' of github.com:jarioksa/vegan into simper
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
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
simper accepts permutation matrix (like documented)
add print.summary.simper() to get signif.stars
rephrase permutation matrix in simper.Rd
typo
merge github updates

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

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/vegan/pkg/vegan@2097 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
summary.simper(..., ordered=FALSE) failed when permutations = 0