[Vegan-commits] r2101 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 21 09:10:02 CET 2012
Author: jarioksa
Date: 2012-02-21 09:10:02 +0100 (Tue, 21 Feb 2012)
New Revision: 2101
Modified:
pkg/vegan/man/monoMDS.Rd
Log:
Squashed commit of the following:
commit ad85a0cdc48a94ae596a0763b6203466a6dec47d
Author: Jari Oksanen <jari.oksanen at 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 at oulu.fi>
Date: Tue Feb 21 09:47:24 2012 +0200
fix explanation of Kruskal stress
commit 2823a512589d27210fc1ae244db7feb0ae587298
Author: Jari Oksanen <jari.oksanen at 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 at oulu.fi>
Date: Mon Feb 20 20:13:23 2012 +0200
test
commit c3c29c95d2852235b9498b468513c7bd6f664210
Merge: 286ba84 ce8e280
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Feb 19 21:33:55 2012 +0200
Merge branch 'master' into r-forge-svn-local
commit 286ba846449e870acd07f74f0d7433de01dad9b3
Author: jarioksa <jarioksa at 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 at oulu.fi>
Date: Sun Feb 19 21:04:29 2012 +0200
summary.simper(..., ordered=FALSE) failed when permutations = 0
commit a64c253594f747aa76803b5026d8afb207b316cb
Author: jarioksa <jarioksa at 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 at oulu.fi>
Date: Sun Feb 19 18:41:49 2012 +0200
typo
commit 3a33d106a1218a9682b4f45ea7133007caa708df
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Sun Feb 19 18:36:35 2012 +0200
rephrase permutation matrix in simper.Rd
commit 9902e6c87d478992d936d982874fe4ff2ab4b605
Author: Jari Oksanen <jari.oksanen at 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 at oulu.fi>
Date: Sun Feb 19 09:11:32 2012 +0200
simper accepts permutation matrix (like documented)
commit 7dbda9183580d5ced0aad6cae0262d23c9af48c9
Author: jarioksa <jarioksa at 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 at 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 at 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 at 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 at oulu.fi>
Date: Fri Feb 17 09:44:07 2012 +0200
fix description of simper return object
commit 1366393f3e5d2fe38ddfdb30232df4ebe29cf093
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Fri Feb 17 09:35:13 2012 +0200
explain simper output
commit ce4fb23ce91ab674aa7b95b1409e50ce0c1a2551
Author: Jari Oksanen <jari.oksanen at 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 at oulu.fi>
Date: Thu Feb 16 21:40:18 2012 +0200
update examples for simper
commit 78c85d8f7dda7f8db36de6483789508056b7c9c7
Author: jarioksa <jarioksa at 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 at 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 at uni-landau.de>
Date: Thu Feb 16 13:14:17 2012 +0100
typo
commit 5dd3236e2b1240f7f7a462ba7a17dd04cd216061
Author: edisz <szoe8822 at uni-landau.de>
Date: Thu Feb 16 12:02:53 2012 +0100
simper passes now CMD check
commit fe6a9fda1daecdf5627b9f61ca05d31f79b59126
Author: edisz <szoe8822 at uni-landau.de>
Date: Thu Feb 16 11:22:15 2012 +0100
fixed simper.Rd (examples, \alias)
commit 3223c72070f50118ab05a125fdffce1a9eac5634
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 19:08:51 2012 +0100
corrected permutational p-value
commit b38cfc478600cbfbf66abb1f07cea546656e8c68
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 19:04:36 2012 +0100
fixed typo
commit 3d67710d1e18c9feb53132b71ec7b2850b720556
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 18:44:08 2012 +0100
updated documentation
commit 9429d2373e21866e9f0cde9ff102790083128927
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 18:19:59 2012 +0100
updated documentation to changes
commit c3c8814bc6969dd411cf234ba5b1eee3e282fbef
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 17:15:38 2012 +0100
changes make the code noticable faster
commit bc3e13ecc6bd194bf1087821fbff750bc3d3d309
Author: edisz <szoe8822 at 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 at 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 at 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 at uni-landau.de>
Date: Tue Feb 14 12:52:14 2012 +0100
fixed typo
commit 5992276a411361f41239190b0182e57c8e46ffa3
Author: edisz <szoe8822 at 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 at 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 at 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 at uni-landau.de>
Date: Thu Feb 16 13:14:17 2012 +0100
typo
commit 5dd3236e2b1240f7f7a462ba7a17dd04cd216061
Author: edisz <szoe8822 at uni-landau.de>
Date: Thu Feb 16 12:02:53 2012 +0100
simper passes now CMD check
commit fe6a9fda1daecdf5627b9f61ca05d31f79b59126
Author: edisz <szoe8822 at uni-landau.de>
Date: Thu Feb 16 11:22:15 2012 +0100
fixed simper.Rd (examples, \alias)
commit 3223c72070f50118ab05a125fdffce1a9eac5634
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 19:08:51 2012 +0100
corrected permutational p-value
commit b38cfc478600cbfbf66abb1f07cea546656e8c68
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 19:04:36 2012 +0100
fixed typo
commit 3d67710d1e18c9feb53132b71ec7b2850b720556
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 18:44:08 2012 +0100
updated documentation
commit 9429d2373e21866e9f0cde9ff102790083128927
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 18:19:59 2012 +0100
updated documentation to changes
commit c3c8814bc6969dd411cf234ba5b1eee3e282fbef
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 17:15:38 2012 +0100
changes make the code noticable faster
commit bc3e13ecc6bd194bf1087821fbff750bc3d3d309
Author: edisz <szoe8822 at 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 at 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 at 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 at uni-landau.de>
Date: Tue Feb 14 12:52:14 2012 +0100
fixed typo
commit 5992276a411361f41239190b0182e57c8e46ffa3
Author: edisz <szoe8822 at uni-landau.de>
Date: Tue Feb 14 12:44:08 2012 +0100
restructured output
commit 8e08f0cbfccd4263c89d3935656a8476640a6066
Merge: 318e43a 1667511
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Tue Feb 14 10:13:54 2012 +0200
Merge branch 'r-forge-svn-local'
commit 1667511652ceee8fb883801d0f6c32261873739c
Author: Jari Oksanen <jari.oksanen at 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 at 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 at 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 at 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 at uni-landau.de>
Date: Mon Feb 13 12:45:24 2012 +0100
changed Argument description
commit 2a4ad280ec97e6c5971b0e6aff837080de0b69bd
Author: edisz <szoe8822 at uni-landau.de>
Date: Mon Feb 13 12:45:24 2012 +0100
changed Argument description
commit 41b12727a684637b0a3aa0e0b25f145e3b403e6a
Author: edisz <szoe8822 at 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 at oulu.fi>
Date: Mon Feb 13 15:26:21 2012 +0200
Merge branch 'master' of https://github.com/EDiLD/vegan
Conflicts:
man/simper.Rd
Modified: pkg/vegan/man/monoMDS.Rd
===================================================================
--- pkg/vegan/man/monoMDS.Rd 2012-02-20 19:18:39 UTC (rev 2100)
+++ pkg/vegan/man/monoMDS.Rd 2012-02-21 08:10:02 UTC (rev 2101)
@@ -77,9 +77,8 @@
species and dissimilarities are tied to their maximum value of
one. Breaking ties allows these points to be at different
distances and can help in recovering very long coenoclines
- (gradients). Functions \code{\link[smacof]{smacofSym}}
- (\pkg{smacof} package) and \code{\link[ecodist]{nmds}}
- (\pkg{ecodist} package) also have adequate tie treatment.
+ (gradients). Function \code{\link[smacof]{smacofSym}}
+ (\pkg{smacof} package) also has adequate tie treatment.
\item Handles missing values in a meaningful way.
@@ -99,22 +98,21 @@
\deqn{s^2 = \frac{\sum (d - \hat d)^2}{\sum(d - d_0)^2}}{stress^2 = sum (d-dhat)^2/ sum (d-dnull)^2}
- where \eqn{d} are the observed dissimilarities, \eqn{\hat d}{dhat}
- are the fitted ordination distances, and \eqn{d_0}{dnull} are the
- ordination distances under null model. For \dQuote{stress 1}
- \eqn{d_0 = 0}{dnull = 0}, and for \dQuote{stress 2} \eqn{d_0 =
- \bar{d}}{dnull = dbar} or mean dissimilarities. \dQuote{Stress 2}
- can be expressed as \eqn{s^2 = 1 - R^2}{stress^2 = 1 - R2}, where
- \eqn{R^2}{R2} is squared correlation between fitted values and
+ where \eqn{d} are distances among points in ordination configuration,
+ \eqn{\hat d}{dhat} are the fitted ordination distances, and
+ \eqn{d_0}{dnull} are the ordination distances under null model. For
+ \dQuote{stress 1} \eqn{d_0 = 0}{dnull = 0}, and for \dQuote{stress 2}
+ \eqn{d_0 = \bar{d}}{dnull = dbar} or mean distances. \dQuote{Stress 2}
+ can be expressed as \eqn{s^2 = 1 - R^2}{stress^2 = 1 - R2},
+ where\eqn{R^2}{R2} is squared correlation between fitted values and
ordination distances, and so related to the \dQuote{linear fit} of
\code{\link{stressplot}}.
Function \code{monoMDS} can fit several alternative NMDS variants
that can be selected with argument \code{model}. The default
\code{model = "global"} fits global NMDS, or Kruskal's (1964a,b)
- original NMDS similar to \code{\link[MASS]{isoMDS}} (\pkg{MASS}),
- \code{\link[smacof]{smacofSym}} (\pkg{smacof}) or
- \code{\link[ecodist]{nmds}} (\pkg{ecodist}). Alternative
+ original NMDS similar to \code{\link[MASS]{isoMDS}} (\pkg{MASS})
+ or \code{\link[smacof]{smacofSym}} (\pkg{smacof}). Alternative
\code{model = "local"} fits local NMDS where independent monotone
regression is used for each point (Sibson 1972). Alternative
\code{model = "linear"} fits a linear MDS. This fits a linear
@@ -183,9 +181,9 @@
}
\seealso{ \code{\link[vegan]{metaMDS}} for the \pkg{vegan} way of
- running NMDS, and \code{\link[MASS]{isoMDS}},
- \code{\link[smacof]{smacofSym}}, \code{\link[ecodist]{nmds}} for
- some alternative implementations of NMDS. }
+ running NMDS, and \code{\link[MASS]{isoMDS}} and
+ \code{\link[smacof]{smacofSym}} for some alternative implementations
+ of NMDS. }
\examples{
data(dune)
More information about the Vegan-commits
mailing list