[Vegan-commits] r2885 - pkg/vegan/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 18 15:57:33 CEST 2014
Author: jarioksa
Date: 2014-09-18 15:57:33 +0200 (Thu, 18 Sep 2014)
New Revision: 2885
Modified:
pkg/vegan/vignettes/FAQ-vegan.texi
pkg/vegan/vignettes/decision-vegan.Rnw
pkg/vegan/vignettes/diversity-vegan.Rnw
pkg/vegan/vignettes/intro-vegan.Rnw
Log:
Squashed commit of the following:
commit e3a3fa09c073ad1a3b9e196a6031b04e4388cf9a
Merge: 793a0c7 b330bbd
Author: Jari Oksanen <jari.oksanen at 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 at oulu.fi>
Date: Wed Sep 17 21:22:22 2014 +0300
edit FAQ-vegan
commit 8494bb8c3cf81612c5baa72fdf086253703f9854
Author: Jari Oksanen <jari.oksanen at 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 at 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 at oulu.fi>
Date: Tue Sep 16 19:50:02 2014 +0300
FAQ-vegan adapted to GitHub
commit ec8fd7e0c27a3f57024fefca3840c19d990c54f5
Author: Jari Oksanen <jari.oksanen at 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 at oulu.fi>
Date: Tue Sep 16 19:20:00 2014 +0300
update intro-vegan to changes in anova.cca
Modified: pkg/vegan/vignettes/FAQ-vegan.texi
===================================================================
--- pkg/vegan/vignettes/FAQ-vegan.texi 2014-09-17 11:29:19 UTC (rev 2884)
+++ pkg/vegan/vignettes/FAQ-vegan.texi 2014-09-18 13:57:33 UTC (rev 2885)
@@ -8,7 +8,7 @@
@setfilename FAQ- at pkg{vegan}.info
@settitle @pkg{vegan} FAQ
@setchapternewpage on
- at set FAQ_YEAR 2013
+ at set FAQ_YEAR 2014
@afourpaper
@c %**end of header
@@ -16,7 +16,6 @@
@ifnottex
This document contains answers to some of the most frequently asked
questions about R package @pkg{vegan}.
-This is version of $Date$.
@end ifnottex
@quotation
@@ -40,7 +39,6 @@
@titlepage
@title @pkg{vegan} @acronym{FAQ}
@subtitle Frequently Asked Questions on R package @pkg{vegan}
- at subtitle Version of $Date$
@author Jari Oksanen
@vskip 0pt plus 1fill
@@ -62,30 +60,29 @@
@menu
-* Introduction::
-* Ordination::
-* Other analysis methods ::
+* Introduction::
+* Ordination::
+* Other analysis methods ::
@end menu
@node Introduction, Ordination, Top, Top
@chapter Introduction
@menu
-* What is @pkg{vegan}?::
-* What is R?::
-* How to obtain @pkg{vegan} and R?::
-* What R packages @pkg{vegan} depends on?::
-* What other packages are available for ecologists?::
-* What other documentation is available for @pkg{vegan}?::
-* Is there a Graphical User Interface (GUI) for @pkg{vegan}?::
-* How to cite @pkg{vegan}?::
-* How to build @pkg{vegan} from sources?::
-* Are there binaries for devel versions?::
-* Can I use @pkg{vegan} in Mac?::
-* How to report a bug in @pkg{vegan}?::
-* Is it a bug or a feature?::
-* Can I contribute to @pkg{vegan}?::
-* Can I have write access to @pkg{vegan} repository?::
+* What is @pkg{vegan}?::
+* What is R?::
+* How to obtain @pkg{vegan} and R?::
+* What R packages @pkg{vegan} depends on?::
+* What other packages are available for ecologists?::
+* What other documentation is available for @pkg{vegan}?::
+* Is there a Graphical User Interface (GUI) for @pkg{vegan}?::
+* How to cite @pkg{vegan}?::
+* How to build @pkg{vegan} from sources?::
+* Are there binaries for devel versions?::
+* Can I use @pkg{vegan} in Mac?::
+* How to report a bug in @pkg{vegan}?::
+* Is it a bug or a feature?::
+* Can I contribute to @pkg{vegan}?::
@end menu
@node What is @pkg{vegan}?, What is R?, Introduction, Introduction
@@ -121,38 +118,31 @@
Both R and latest release version of @pkg{vegan} can be obtained through
@uref{http://cran.r-project.org,,CRAN}. Unstable development version of
@pkg{vegan} can be obtained through
- at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}.
+ at uref{https://github.com/vegandevs/vegan,,GitHub}. Formerly @pkg{vegan}
+was developed in
+ at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge},
+but after moving to @uref{https://github.com/vegandevs/vegan,,GitHub}
+the R-Forge repository may be out of date.
-
-
@node What R packages @pkg{vegan} depends on?, What other packages are available for ecologists?, How to obtain @pkg{vegan} and R?, Introduction
@section What R packages @pkg{vegan} depends on?
@pkg{Vegan} depends on the @pkg{permute} package which will provide
-advanced and flexible permutation routines for vegan (but currently only
-a small part of functions use @pkg{permute}). The @pkg{permute} package
-is developed together with @pkg{vegan} in
- at uref{http://vegan.r-forge.r-project.org/,,R-Forge}.
+advanced and flexible permutation routines for @pkg{vegan}. The
+ at pkg{permute} package is developed together with @pkg{vegan} in
+ at uref{https://github.com/gavinsimpson/permute,,GitHub}.
Some individual @pkg{vegan} functions depend on packages @pkg{MASS},
@pkg{mgcv}, @pkg{cluster}, @pkg{lattice} and @pkg{tcltk}. These all are
base or recommended R packages that should be available in every R
-installation. In addition, some @pkg{vegan} functions @code{require}
-non-standard R packages. @pkg{Vegan} declares these packages only as
-suggested ones, and you can install @pkg{vegan} and use most of its
-functions without these packages. The non-standard packages needed by
-some @pkg{vegan} functions are:
- at itemize
+installation. @pkg{Vegan} declares these as suggested or imported
+packages, and you can install @pkg{vegan} and use most of its functions
+without these packages.
- at item Package @pkg{scatterplot3d}
-is needed by @code{ordiplot3d}
+ at pkg{Vegan} is accompanied with a supporting package @pkg{vegan3d} for
+three-dimensional and dynamic plotting. The @pkg{vegan3d} package needs
+non-standard packages @pkg{rgl} and @pkg{scatterplot3d}.
- at item Package @pkg{rgl}
-is needed by @code{ordirgl}
-and @code{rgl.isomap}
-
- at end itemize
-
@node What other packages are available for ecologists?, What other documentation is available for @pkg{vegan}?, What R packages @pkg{vegan} depends on?, Introduction
@section What other packages are available for ecologists?
@@ -195,7 +185,7 @@
@itemize
@item
- at uref{http://vegan.r-forge.r-project.org/}: @pkg{vegan} homepage.
+ at uref{https://github.com/vegandevs/vegan}: @pkg{vegan} homepage.
@item
@uref{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}: @pkg{vegan}
tutorial.
@@ -237,7 +227,9 @@
@uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge} runs daily
tests on the devel package, and if passed, it builds source package
-together with Windows and MacOS X binaries. You can install those
+together with Windows binaries. However, the R-Forge may be out of date,
+because @pkg{vegan} is mainly developed in
+ at uref{https://github.com/vegandevs/vegan,,GitHub}. You can install R-Forge
packages within R with command
@code{install.packages("vegan", repos="http://r-forge.r-project.org/")}.
If you use GUI menu entry, you must select or define the R-Forge
@@ -251,16 +243,16 @@
need to install extra tools packages available in
@uref{http://cran.r-project.org/bin/macosx/tools/,,MacOS tools} pages:
If you use function such as @code{orditkplot} that need @code{Tcl/Tk}
-you may need to install @code{tcltk} package. If you use @pkg{vegan}
-binaries from other places than from
- at uref{http://cran.r-project.org,,CRAN}, you may also need to install
- at code{gfortran} package.
+you may need to install @code{tcltk} package. No Mac binaries of
+development versions are available in any repository we know.
@node How to report a bug in @pkg{vegan}?, Is it a bug or a feature?, Can I use @pkg{vegan} in Mac?, Introduction
@section How to report a bug in @pkg{vegan}?
If you think you have found a bug in @pkg{vegan}, you should report it to
- at pkg{vegan} maintainers or developers. The bug report should be so detailed
+ at pkg{vegan} maintainers or developers. The preferred forum to report
+bugs is @uref{https://github.com/vegandevs/vegan/issues,,GitHub}. The
+bug report should be so detailed
that the bug can be replicated and corrected. Preferably, you should
send an example that causes a bug. If it needs a data set that is not
available in R, you should send a minimal data set as well. You also
@@ -272,10 +264,6 @@
Please note that you shall not send bug reports to R mailing lists,
since @pkg{vegan} is not a standard R package.
-There also is a bug reporting tool at
- at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}, but you
-need to register as a site user to report bugs (this is site policy).
-
@node Is it a bug or a feature?, Can I contribute to @pkg{vegan}?, How to report a bug in @pkg{vegan}?, Introduction
@section Is it a bug or a feature?
@@ -288,66 +276,48 @@
indices (when this is possible). If you expect it to calculate a
binary index, you should use argument @code{binary = TRUE}.
- at node Can I contribute to @pkg{vegan}?, Can I have write access to @pkg{vegan} repository?, Is it a bug or a feature?, Introduction
+ at node Can I contribute to @pkg{vegan}?, , Is it a bug or a feature?, Introduction
@section Can I contribute to @pkg{vegan}?
@pkg{Vegan} is dependent on user contribution. All feedback is welcome. If
-you have problem with @pkg{vegan}, it may be as simple as incomplete
-documentation, and we'll do our best to improve the documents.
+you have problems with @pkg{vegan}, it may be as simple as incomplete
+documentation, and we shall do our best to improve the documents.
Feature requests also are welcome, but they are not necessarily
fulfilled. A new feature will be added if it is easy to do and it looks
-useful to me or in general, or if you submit code.
+useful, or if you submit code.
-Contributed code and functions are welcome and more certain to be
-included than mere requests. However, not all functions will be added,
-but I they must be suitable for @pkg{vegan}. We also audit the code, and
-typically we edit the code in @pkg{vegan} style for easier maintenance. All
-included contributions will be credited.
+If you can write code yourself, the best forum to contribute to vegan is
+ at uref{https://github.com/vegandevs/vegan,,GitHub}.
- at node Can I have write access to @pkg{vegan} repository?, , Can I contribute to @pkg{vegan}?, Introduction
- at section Can I have write access to @pkg{vegan} repository?
-
-The @pkg{vegan} development happens mainly in
- at uref{http://r-forge.r-project.org/,,R-Forge} which uses subversion for
-version control. Subversion is a centralized version control system,
-and only @pkg{vegan} developers can have write access to the central
-repository. However, the @uref{http://r-forge.r-project.org/,,R-Forge}
-is mirrored in
- at uref{https://github.com/jarioksa/vegan.git,,GitHub}. This is a
-distributed version control system and freely accessible for anybody. We
-suggest you develop your own ideas in
- at uref{https://github.com/jarioksa/vegan.git,,GitHub} and send a pull
-request to us for incorporating your changes in @pkg{vegan} releases.
-
@node Ordination, Other analysis methods , Introduction, Top
@chapter Ordination
@menu
-* I have only numeric and positive data but @pkg{vegan} still complains::
-* Can I analyse binary or cover class data?::
-* Why dissimilarities in @pkg{vegan} differ from other sources?::
-* Why NMDS stress is sometimes 0.1 and sometimes 10?::
-* I get zero stress but no convergent solutions in @code{metaMDS}::
-* Zero dissimilarities in isoMDS::
-* I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores::
-* Where can I find numerical scores of ordination axes?::
-* How the RDA results are scaled?::
-* cca fails with ``data.frame expected'' or ``"site.env" missing''::
-* Ordination fails with ``Error in La.svd''::
-* Variance explained by ordination axes::
-* Can I have random effects in constrained ordination or in @code{adonis}?::
-* Is it possible to have passive points in ordination?::
-* Class variables and dummies::
-* How are environmental arrows scaled?::
-* I want to use Helmert or sum contrasts::
-* What are aliased variables and how to see them?::
-* Plotting aliased variables::
-* Constrained permutations in @pkg{vegan}::
-* How to use different plotting symbols in ordination graphics?::
-* How to avoid cluttered ordination graphs?::
-* Can I flip an axis in ordination diagram?::
-* Can I zoom into an ordination plot?::
+* I have only numeric and positive data but @pkg{vegan} still complains::
+* Can I analyse binary or cover class data?::
+* Why dissimilarities in @pkg{vegan} differ from other sources?::
+* Why NMDS stress is sometimes 0.1 and sometimes 10?::
+* I get zero stress but no convergent solutions in @code{metaMDS}::
+* Zero dissimilarities in isoMDS::
+* I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores::
+* Where can I find numerical scores of ordination axes?::
+* How the RDA results are scaled?::
+* cca fails with ``data.frame expected'' or ``"site.env" missing''::
+* Ordination fails with ``Error in La.svd''::
+* Variance explained by ordination axes::
+* Can I have random effects in constrained ordination or in @code{adonis}?::
+* Is it possible to have passive points in ordination?::
+* Class variables and dummies::
+* How are environmental arrows scaled?::
+* I want to use Helmert or sum contrasts::
+* What are aliased variables and how to see them?::
+* Plotting aliased variables::
+* Restricted permutations in @pkg{vegan}::
+* How to use different plotting symbols in ordination graphics?::
+* How to avoid cluttered ordination graphs?::
+* Can I flip an axis in ordination diagram?::
+* Can I zoom into an ordination plot?::
@end menu
@node I have only numeric and positive data but @pkg{vegan} still complains, Can I analyse binary or cover class data?, Ordination, Ordination
@@ -427,18 +397,17 @@
Function @code{metaMDS} uses function @code{monoMDS} as its default
method for @acronym{NMDS}, and this function can handle zero
-dissimilarities. The alternative function @code{isoMDS} was the only
-choice before @pkg{vegan} 2.0-0, and it cannot handle zero dissimilarities. If
-you want to use @code{isoMDS}, you can use argument @code{zerodist =
-"add"} in @code{metaMDS} to handle zero dissimilarities. With this
-argument, zero dissimilarities are replaced with a small above zero
-value, and they can be handled in @code{isoMDS}. This is a kluge, and
-some people do not like this. A more principal solution is to remove
-duplicate sites using R command @code{unique}. However, after some
-standardizations or with some dissimilarity indices, originally
-non-unique sites can have zero dissimilarity, and you have to resort to
-the kluge (or work harder with your data). Usually it is better to use
- at code{monoMDS}.
+dissimilarities. Alternative function @code{isoMDS} cannot handle zero
+dissimilarities. If you want to use @code{isoMDS}, you can use argument
+ at code{zerodist = "add"} in @code{metaMDS} to handle zero
+dissimilarities. With this argument, zero dissimilarities are replaced
+with a small positive value, and they can be handled in @code{isoMDS}.
+This is a kluge, and some people do not like this. A more principal
+solution is to remove duplicate sites using R command @code{unique}.
+However, after some standardizations or with some dissimilarity indices,
+originally non-unique sites can have zero dissimilarity, and you have to
+resort to the kluge (or work harder with your data). Usually it is
+better to use @code{monoMDS}.
@node I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Where can I find numerical scores of ordination axes?, Zero dissimilarities in isoMDS, Ordination
@section I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores
@@ -596,11 +565,10 @@
random effects, although they are fitted in the same way as all other
terms, and strictly speaking they are fixed terms.
-The permutation tests can usually have a @code{strata} argument which
-restricts the permutations within levels of a factor given in the
-argument. This can be used to restrict the permutations within levels of
-factor regarded as a random term. More structured permutations are
-available with the @pkg{permute} package.
+All permutation tests in @pkg{vegan} are based on the @pkg{permute}
+package that allows constructing various restricted permutation
+schemes. For instance, you can set levels of @code{plots} or
+ at code{blocks} for a factor regarded as a random term.
A major reason why real random effects models are impossible in most
@pkg{vegan} functions is that their tests are based on the permutation
@@ -701,7 +669,7 @@
variables. If you only want to see the names of aliased variables or
levels in solution @code{sol}, use @code{alias(sol, names.only=TRUE)}.
- at node Plotting aliased variables, Constrained permutations in @pkg{vegan}, What are aliased variables and how to see them?, Ordination
+ at node Plotting aliased variables, Restricted permutations in @pkg{vegan}, What are aliased variables and how to see them?, Ordination
@section Plotting aliased variables
You can fit vectors or class centroids for aliased variables using
@@ -709,22 +677,17 @@
fitting, and the fitted vectors are identical to the vectors in
correspondence analysis.
- at node Constrained permutations in @pkg{vegan}, How to use different plotting symbols in ordination graphics?, Plotting aliased variables, Ordination
- at section Constrained permutations in @pkg{vegan}
+ at node Restricted permutations in @pkg{vegan}, How to use different plotting symbols in ordination graphics?, Plotting aliased variables, Ordination
+ at section Restricted permutations in @pkg{vegan}
-You can constrain your permutations within @code{strata} or levels of
-factors. You can use stratified permutations in all @pkg{vegan}
-functions that use permutation, such as @code{adonis}, @code{anosim},
- at code{anova.cca}, @code{mantel}, @code{mrpp}, @code{envfit} and
- at code{protest}.
+ at pkg{Vegan} uses @pkg{permute} package in all its permutation tests.
+The @pkg{permute} package will allow restricted permutation designs for
+time series, line transects, spatial grids and blocking factors. The
+construction of restricted permutation schemes is explained in the
+manual page @code{permutations} in @pkg{vegan} and in the documentation
+of the @pkg{permute} package.
- at pkg{Vegan} will move to use @pkg{permute} package in all its
-permutation tests, but currently this package is only used in
- at code{permutest.betadisper}. The @pkg{permute} package will allow
-restricted permutation designs for time series, line transects, spatial
-grids and blocking factors.
-
- at node How to use different plotting symbols in ordination graphics?, How to avoid cluttered ordination graphs?, Constrained permutations in @pkg{vegan}, Ordination
+ at node How to use different plotting symbols in ordination graphics?, How to avoid cluttered ordination graphs?, Restricted permutations in @pkg{vegan}, Ordination
@section How to use different plotting symbols in ordination graphics?
The default ordination @code{plot} function is intended for fast
@@ -817,12 +780,12 @@
@chapter Other analysis methods
@menu
-* Is there TWINSPAN?::
-* Why strata do not influence adonis results?::
-* How is deviance calculated?::
+* Is there TWINSPAN?::
+* Why restricted permutation does not influence adonis results?::
+* How is deviance calculated?::
@end menu
- at node Is there TWINSPAN?, Why strata do not influence adonis results?, Other analysis methods , Other analysis methods
+ at node Is there TWINSPAN?, Why restricted permutation does not influence adonis results?, Other analysis methods , Other analysis methods
@section Is there TWINSPAN?
No. It may be possible to port @acronym{TWINSPAN} to @pkg{vegan}, but it is
@@ -830,16 +793,15 @@
will be happy to help. @acronym{TWINSPAN} has a very permissive
license, and it would be completely legal to port the function into R.
- at node Why strata do not influence adonis results?, How is deviance calculated?, Is there TWINSPAN?, Other analysis methods
+ at node Why restricted permutation does not influence adonis results?, How is deviance calculated?, Is there TWINSPAN?, Other analysis methods
@comment node-name, next, previous, up
- at section Why strata do not influence adonis results?
-Permutation happens only within @code{strata} and this influences the
-permutation distribution of the statistics and probably the significance
-levels, but @code{strata} do not influence the calculation of the
-statistics.
+ at section Why restricted permutation does not influence adonis results?
+The permutation scheme influences the permutation distribution of the
+statistics and probably the significance levels, but does not influence
+the calculation of the statistics.
- at node How is deviance calculated?, , Why strata do not influence adonis results?, Other analysis methods
+ at node How is deviance calculated?, , Why restricted permutation does not influence adonis results?, Other analysis methods
@section How is deviance calculated?
Some @pkg{vegan} functions, such as @code{radfit} use base R facility of
Modified: pkg/vegan/vignettes/decision-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/decision-vegan.Rnw 2014-09-17 11:29:19 UTC (rev 2884)
+++ pkg/vegan/vignettes/decision-vegan.Rnw 2014-09-18 13:57:33 UTC (rev 2885)
@@ -7,7 +7,7 @@
\author{Jari Oksanen}
\title{Design decisions and implementation details in vegan}
-\date{\footnotesize{$ $Id$ $
+\date{\footnotesize{
processed with vegan
\Sexpr{packageDescription("vegan", field="Version")}
in \Sexpr{R.version.string} on \today}}
Modified: pkg/vegan/vignettes/diversity-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/diversity-vegan.Rnw 2014-09-17 11:29:19 UTC (rev 2884)
+++ pkg/vegan/vignettes/diversity-vegan.Rnw 2014-09-18 13:57:33 UTC (rev 2885)
@@ -9,7 +9,7 @@
\title{Vegan: ecological diversity} \author{Jari Oksanen}
-\date{\footnotesize{$ $Id$ $
+\date{\footnotesize{
processed with vegan \Sexpr{packageDescription("vegan", field="Version")}
in \Sexpr{R.version.string} on \today}}
Modified: pkg/vegan/vignettes/intro-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/intro-vegan.Rnw 2014-09-17 11:29:19 UTC (rev 2884)
+++ pkg/vegan/vignettes/intro-vegan.Rnw 2014-09-18 13:57:33 UTC (rev 2885)
@@ -6,7 +6,7 @@
\title{Vegan: an introduction to ordination}
\author{Jari Oksanen}
-\date{\footnotesize{$ $Id$ $
+\date{\footnotesize{
processed with vegan
\Sexpr{packageDescription("vegan", field="Version")}
in \Sexpr{R.version.string} on \today}}
@@ -246,7 +246,7 @@
interface, and it optionally can assess the ``significance'' of the
variables using permutation tests:
<<>>=
-ord.fit <- envfit(ord ~ A1 + Management, data=dune.env, perm=1000)
+ord.fit <- envfit(ord ~ A1 + Management, data=dune.env, perm=999)
ord.fit
@
The result can be drawn directly or added to an ordination diagram
@@ -330,33 +330,21 @@
correct \code{anova} variant for the result of constrained
ordination.
-The \code{anova.cca} function tries to be clever and lazy: it
-automatically stops if the observed permutation significance probably
-differs from the targeted critical value ($0.05$ as default), but it
-will continue long in uncertain cases. You must set \code{step} and
-\code{perm.max} to same values to override this behaviour.
-
It is also possible to analyse terms separately:
<<>>=
-anova(ord, by="term", permu=200)
+anova(ord, by="term", permutations=199)
@
-In this case, the function is unable to automatically select the
-number of iterations. This test is sequential: the terms are analysed
+This test is sequential: the terms are analysed
in the order they happen to be in the model. You can also analyse
significances of marginal effects (``Type III effects''):
<<>>=
-anova(ord, by="mar")
+anova(ord, by="mar", permutations=199)
@
Moreover, it is possible to analyse significance of each axis:
<<a>>=
-anova(ord, by="axis", perm=500)
+anova(ord, by="axis", permutations=499)
@
-Now the automatic selection works, but typically some of your axes
-will be very close to the critical value, and it may be useful to set
-a lower \code{perm.max} than the default $10000$ (typically you use
-higher limits than in these examples: we used lower limits to save
-time when this document is automatically generated with this package).
\subsection{Conditioned or partial ordination}
@@ -370,13 +358,17 @@
effects of \code{A1} and \code{Management}. This also influences
the significances of the terms:
<<>>=
-anova(ord, by="term", perm=500)
+anova(ord, by="term", permutations=499)
@
If we had a designed experiment, we may wish to restrict the
permutations so that the observations only are permuted within levels
-of \code{strata}:
+of \code{Moisture}. Restricted permutation is based on the powerful
+\pkg{permute} package. Function \code{how()} can be used to define
+permutation schemes. In the following, we set the levels with
+\code{plots} argument:
<<>>=
-anova(ord, by="term", perm=500, strata=Moisture)
+how <- how(nperm=499, plots = Plots(strata=dune.env$Moisture))
+anova(ord, by="term", permutations = how)
@
%%%%%%%%%%%%%%%%%%%
More information about the Vegan-commits
mailing list