[Vegan-commits] r1983 - in branches/2.0: R inst inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 2 18:52:15 CET 2011
Author: jarioksa
Date: 2011-11-02 18:52:13 +0100 (Wed, 02 Nov 2011)
New Revision: 1983
Modified:
branches/2.0/R/ordispider.R
branches/2.0/inst/ChangeLog
branches/2.0/inst/doc/FAQ-vegan.texi
branches/2.0/man/ordihull.Rd
branches/2.0/man/ordiplot3d.Rd
Log:
merge r1969 (ordiplot3d doc update) r1970 (ordispider returns results) r1974,5,1980,2 (FAQ update)
Modified: branches/2.0/R/ordispider.R
===================================================================
--- branches/2.0/R/ordispider.R 2011-11-02 14:29:50 UTC (rev 1982)
+++ branches/2.0/R/ordispider.R 2011-11-02 17:52:13 UTC (rev 1983)
@@ -1,4 +1,4 @@
-"ordispider" <-
+`ordispider` <-
function (ord, groups, display = "sites", w = weights(ord, display),
show.groups, label = FALSE, ...)
{
@@ -8,9 +8,14 @@
wa <- scores(ord, display = "wa", ...)
ordiArgAbsorber(lc[, 1], lc[, 2], wa[, 1], wa[, 2],
FUN = segments, ...)
- return(invisible())
+ class(lc) <- "ordispider"
+ return(invisible(lc))
}
pts <- scores(ord, display = display, ...)
+ ## spids stores pointwise centroids to be returned invisibly
+ ## (transposed here so that filling is easier, but back-transposed
+ ## when returned).
+ spids <- t(array(NA, dim=dim(pts), dimnames = dimnames(pts)))
## ordihull: draw lines from centre to the points in the hull
if (inherits(ord, "ordihull"))
groups <- attr(pts, "hulls")
@@ -37,6 +42,7 @@
X <- pts[gr, ]
W <- w[gr]
ave <- apply(X, 2, weighted.mean, w = W)
+ spids[,gr] <- ave
ordiArgAbsorber(ave[1], ave[2], X[, 1], X[, 2],
FUN = segments, ...)
if (label) {
@@ -47,5 +53,7 @@
}
if (label)
ordiArgAbsorber(cntrs, label = names, FUN = ordilabel, ...)
- invisible()
+ spids <- t(spids)
+ class(spids) <- "ordispider"
+ invisible(spids)
}
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2011-11-02 14:29:50 UTC (rev 1982)
+++ branches/2.0/inst/ChangeLog 2011-11-02 17:52:13 UTC (rev 1983)
@@ -4,6 +4,9 @@
Version 2.0-2 (opened October 20, 2011)
+ * merge r1974,1975,1980,1982: FAQ update.
+ * merge r1970: ordispider returns invisible plotting structure.
+ * merge r1969: ordiplot3d.Rd tells about xyz.convert().
* merge r1964: clarify stress scaling in iso/monoMDS.
* merge r1961: consinstent 'noshrink' defaults in metaMDSdist()
and metaMDS(..., engine="isoMDS")
Modified: branches/2.0/inst/doc/FAQ-vegan.texi
===================================================================
--- branches/2.0/inst/doc/FAQ-vegan.texi 2011-11-02 14:29:50 UTC (rev 1982)
+++ branches/2.0/inst/doc/FAQ-vegan.texi 2011-11-02 17:52:13 UTC (rev 1983)
@@ -1,7 +1,12 @@
\input texinfo
+
+ at macro pkg {p}
+ at strong{\p\}
+ at end macro
+
@c %**start of header
- at setfilename FAQ-vegan.info
- at settitle vegan FAQ
+ at setfilename FAQ- at pkg{vegan}.info
+ at settitle @pkg{vegan} FAQ
@setchapternewpage on
@set FAQ_YEAR 2011
@afourpaper
@@ -10,14 +15,14 @@
@copying
@ifnottex
This document contains answers to some of the most frequently asked
-questions about R package vegan.
+questions about R package @pkg{vegan}.
This is version of $Date$.
@end ifnottex
@quotation
This work is licensed under the Creative Commons Attribution 3.0
License. To view a copy of this license, visit
- at url{http://creativecommons.org/licenses/by/3.0/} or send a letter to
+ at uref{http://creativecommons.org/licenses/by/3.0/} or send a letter to
Creative Commons, 543 Howard Street, 5th Floor, San Francisco,
California, 94105, USA.
@@ -27,18 +32,18 @@
@dircategory Programming
@direntry
-* R vegan FAQ: (FAQ-vegan). FAQ for R package vegan.
+* R @pkg{vegan} FAQ: (FAQ- at pkg{vegan}). FAQ for R package @pkg{vegan}.
@end direntry
@finalout
@titlepage
- at title vegan @acronym{FAQ}
- at subtitle Frequently Asked Questions on R package vegan
+ at title @pkg{vegan} @acronym{FAQ}
+ at subtitle Frequently Asked Questions on R package @pkg{vegan}
@subtitle Version of $Date$
@author Jari Oksanen
- at vskip 0pt plus 1filll
+ at vskip 0pt plus 1fill
@insertcopying
@end titlepage
@@ -49,7 +54,7 @@
@ifnottex
@node Top, Introduction, (dir), (dir)
- at top vegan FAQ
+ at top @pkg{vegan} FAQ
@insertcopying
@end ifnottex
@@ -66,35 +71,34 @@
@chapter Introduction
@menu
-* What is vegan?::
+* What is @pkg{vegan}?::
* What is R?::
-* How to obtain vegan and R?::
-* What R packages vegan depends on?::
+* 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 vegan?::
-* Is there a Graphical User Interface (GUI) for vegan?::
-* How to cite vegan?::
-* Version numbering in vegan::
-* How to build vegan from sources?::
+* 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?::
-* How to report a bug in vegan?::
+* How to report a bug in @pkg{vegan}?::
* Is it a bug or a feature?::
-* Can I contribute to vegan?::
+* Can I contribute to @pkg{vegan}?::
@end menu
- at node What is vegan?, What is R?, Introduction, Introduction
- at section What is vegan?
+ at node What is @pkg{vegan}?, What is R?, Introduction, Introduction
+ at section What is @pkg{vegan}?
-Vegan is an R package for community ecologists. It contains the most
+ at pkg{Vegan} is an R package for community ecologists. It contains the most
popular methods of multivariate analysis needed in analysing ecological
communities, and tools for diversity analysis, and other potentially
-useful functions. Vegan is not self-contained but it must be run under
+useful functions. @pkg{Vegan} is not self-contained but it must be run under
R statistical environment, and it also depends on many other R
-packages. Vegan is @url{http://www.gnu.org/philosophy/free-sw.html, free
+packages. @pkg{Vegan} is @uref{http://www.gnu.org/philosophy/free-sw.html, free
software} and distributed under
- at url{http://www.gnu.org/licenses/gpl.html, ,GPL2 license}.
+ at uref{http://www.gnu.org/licenses/gpl.html, ,GPL2 license}.
- at node What is R?, How to obtain vegan and R?, What is vegan?, Introduction
+ at node What is R?, How to obtain @pkg{vegan} and R?, What is @pkg{vegan}?, Introduction
@section What is R?
R is a system for statistical computation and graphics. It consists of
@@ -102,77 +106,83 @@
to certain system functions, and the ability to run programs stored in
script files.
-R has a home page at @url{http://www.R-project.org/}. It is
- at url{http://www.gnu.org/philosophy/free-sw.html, free software}
+R has a home page at @uref{http://www.R-project.org/}. It is
+ at uref{http://www.gnu.org/philosophy/free-sw.html, free software}
distributed under a @acronym{GNU}-style
- at url{http://www.gnu.org/copyleft/copyleft.html, copyleft}, and an
-official part of the @url{http://www.gnu.org/, @acronym{GNU}} project
+ at uref{http://www.gnu.org/copyleft/copyleft.html, copyleft}, and an
+official part of the @uref{http://www.gnu.org/, @acronym{GNU}} project
(``@acronym{GNU} S'').
- at node How to obtain vegan and R?, What R packages vegan depends on?, What is R?, Introduction
- at section How to obtain vegan and R?
+ at node How to obtain @pkg{vegan} and R?, What R packages @pkg{vegan} depends on?, What is R?, Introduction
+ at section How to obtain @pkg{vegan} and R?
-Both R and latest release version of vegan can be obtained through
- at url{http://cran.r-project.org,,CRAN}. Unstable development version of
-vegan can be obtained through
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge}.
+Both R and latest release version of @pkg{vegan} can be obtained through
+ at uref{http://cran.r-project.org,,CRAN}. Unstable development version of
+ at pkg{vegan} can be obtained through
+ at uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge}.
- at node What R packages vegan depends on?, What other packages are available for ecologists?, How to obtain vegan and R?, Introduction
- at section What R packages vegan depends on?
+ at node What R packages @pkg{vegan} depends on?, What other packages are available for ecologists?, How to obtain @pkg{vegan} and R?, Introduction
+ at section What R packages @pkg{vegan} depends on?
-Some vegan functions depend on packages @code{MASS}, @code{mgcv},
- at code{cluster} and @code{lattice}. These all are recommended standard
-R packages that should be available in every R installation. In
-addition, some vegan functions @code{require} non-standard R packages.
-Vegan declares these packages only as suggested ones, and you can install vegan
-and use most of its functions without these packages. The
-non-standard packages needed by some vegan functions are:
+ at 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}.
+
+Some individual @pkg{vegan} functions depend on packages @pkg{MASS},
+ at 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:
@itemize
- at item Package @code{scatterplot3d}
+ at item Package @pkg{scatterplot3d}
is needed by @code{ordiplot3d}
- at item Package @code{rgl}
+ at item Package @pkg{rgl}
is needed by @code{ordirgl}
and @code{rgl.isomap}
@end itemize
- at node What other packages are available for ecologists?, What other documentation is available for vegan?, What R packages vegan depends on?, Introduction
+ at 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?
- at acronym{CRAN} @url{http://cran.r-project.org/src/contrib/Views/,,Task
+ at acronym{CRAN} @uref{http://cran.r-project.org/src/contrib/Views/,,Task
Views} include entries like @code{Environmetrics}, @code{Multivariate}
-and @code{Spatial} that describe several useful packages and
-functions. If you install R package @code{ctv}, you can
-inspect Task Views from your R session, and automatically install sets
-of most important packages.
+and @code{Spatial} that describe several useful packages and functions.
+If you install R package @pkg{ctv}, you can inspect Task Views from your
+R session, and automatically install sets of most important packages.
- at node What other documentation is available for vegan?, Is there a Graphical User Interface (GUI) for vegan?, What other packages are available for ecologists?, Introduction
- at section What other documentation is available for vegan?
+ at node What other documentation is available for @pkg{vegan}?, Is there a Graphical User Interface (GUI) for @pkg{vegan}?, What other packages are available for ecologists?, Introduction
+ at section What other documentation is available for @pkg{vegan}?
-Vegan is a fully documented R package with standard help pages. These
+ at pkg{Vegan} is a fully documented R package with standard help pages. These
are the most authoritative sources of documentation (and as a last
-resource you can use the force and the read the source, as vegan is open
-source). Vegan package ships with other documents which can be read
-with @code{vegandocs} command (documented in the vegan help). The
-documents included in the vegan package are
+resource you can use the force and the read the source, as @pkg{vegan} is open
+source). @pkg{Vegan} package ships with other documents which can be read
+with @code{vegandocs} command (documented in the @pkg{vegan} help). The
+documents included in the @pkg{vegan} package are
@itemize
@item
-Vegan @code{NEWS} (not in the development version: only in CRAN)
+ at pkg{Vegan} @code{NEWS}
@item
-Vegan @code{ChangeLog}.
+ at pkg{Vegan} @code{ChangeLog}.
@item
This document (@code{FAQ-vegan.pdf}).
@item
-Short introduction to basic ordination methods in vegan
+Short introduction to basic ordination methods in @pkg{vegan}
(@code{intro-vegan.pdf}).
@item
-Introduction to diversity methods in vegan (@code{diversity-vegan.pdf}).
+Introduction to diversity methods in @pkg{vegan} (@code{diversity-vegan.pdf}).
@item
-Discussion on design decisions in vegan (@code{decision-vegan.pdf}).
+Discussion on design decisions in @pkg{vegan} (@code{decision-vegan.pdf}).
@item
Description of variance partition procedures in function
@code{varpart} (@code{partitioning.pdf}).
@@ -183,61 +193,47 @@
@itemize
@item
- at url{http://vegan.r-forge.r-project.org/}: vegan homepage.
+ at uref{http://vegan.r-forge.r-project.org/}: @pkg{vegan} homepage.
@item
- at url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}: vegan
+ at uref{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf}: @pkg{vegan}
tutorial.
@end itemize
- at node Is there a Graphical User Interface (GUI) for vegan?, How to cite vegan?, What other documentation is available for vegan?, Introduction
- at section Is there a Graphical User Interface (GUI) for vegan?
+ at node Is there a Graphical User Interface (GUI) for @pkg{vegan}?, How to cite @pkg{vegan}?, What other documentation is available for @pkg{vegan}?, Introduction
+ at section Is there a Graphical User Interface (GUI) for @pkg{vegan}?
-Roeland Kindt has made package @code{BiodiversityR} which provides a
-GUI for vegan. The package is available at
- at url{http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN}.
-It is not a mere GUI for vegan, but adds some new functions and
-complements vegan functions in order to provide a
-workbench for biodiversity analysis. You can install @code{BiodiversityR} using
+Roeland Kindt has made package @pkg{BiodiversityR} which provides a
+GUI for @pkg{vegan}. The package is available at
+ at uref{http://cran.r-project.org/src/contrib/Descriptions/BiodiversityR.html,,CRAN}.
+It is not a mere GUI for @pkg{vegan}, but adds some new functions and
+complements @pkg{vegan} functions in order to provide a
+workbench for biodiversity analysis. You can install @pkg{BiodiversityR} using
@code{install.packages("BiodiversityR")} or graphical package
management menu in R. The GUI works on Windows, MacOS X and Linux.
- at node How to cite vegan?, Version numbering in vegan, Is there a Graphical User Interface (GUI) for vegan?, Introduction
- at section How to cite vegan?
+ at node How to cite @pkg{vegan}?, How to build @pkg{vegan} from sources?, Is there a Graphical User Interface (GUI) for @pkg{vegan}?, Introduction
+ at section How to cite @pkg{vegan}?
Use command @code{citation("vegan")} in R to see the recommended
citation to be used in publications.
- at node Version numbering in vegan, How to build vegan from sources?, How to cite vegan?, Introduction
- at section Version numbering in vegan
+ at node How to build @pkg{vegan} from sources?, Are there binaries for devel versions?, How to cite @pkg{vegan}?, Introduction
+ at section How to build @pkg{vegan} from sources?
-From version 1.10-0, vegan is developed at
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge} and there
-is a general progression of version numbers mixed with stable (at
- at url{http://cran.r-project.org,,CRAN}) and devel versions (at
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge}).
-
-Vegan version numbers are of type x.y-z, where number y is odd for
-stable release versions at @url{http://cran.r-project.org,,CRAN} and
-even for unstable release versions at
- at url{http://r-forge.r-project.org/projects/vegan,,F-Forge}.
-
- at node How to build vegan from sources?, Are there binaries for devel versions?, Version numbering in vegan, Introduction
- at section How to build vegan from sources?
-
-In general, you do not need to build vegan from sources, but binary
+In general, you do not need to build @pkg{vegan} from sources, but binary
builds of release versions are available through
- at url{http://cran.r-project.org/,,CRAN} for Windows and MacOS X. If you
+ at uref{http://cran.r-project.org/,,CRAN} for Windows and MacOS X. If you
use some other operating systems, you may have to use source packages.
-Vegan is a standard R package, and can be built like instructed in R
-documentation. Vegan contains source files in C and @acronym{FORTRAN},
+ at pkg{Vegan} is a standard R package, and can be built like instructed in R
+documentation. @pkg{Vegan} contains source files in C and @acronym{FORTRAN},
and you need appropriate compilers (which may need more work in Windows
and MacOS X).
- at node Are there binaries for devel versions?, How to report a bug in vegan?, How to build vegan from sources?, Introduction
+ at node Are there binaries for devel versions?, How to report a bug in @pkg{vegan}?, How to build @pkg{vegan} from sources?, Introduction
@section Are there binaries for devel versions?
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge} runs daily
+ at 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
packages within R with command
@@ -245,27 +241,27 @@
If you use GUI menu entry, you must select or define the R-Forge
repository.
- at node How to report a bug in vegan?, Is it a bug or a feature?, Are there binaries for devel versions?, Introduction
- at section How to report a bug in vegan?
+ at node How to report a bug in @pkg{vegan}?, Is it a bug or a feature?, Are there binaries for devel versions?, Introduction
+ at section How to report a bug in @pkg{vegan}?
-If you think you have found a bug in vegan, you should report it to
-vegan maintainers or developers. The bug report should be so detailed
+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
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
should paste the output or error message in your message. You also
-should specify which version of vegan you used.
+should specify which version of @pkg{vegan} you used.
-Bug reports are welcome: they are the only way to make vegan non-buggy.
+Bug reports are welcome: they are the only way to make @pkg{vegan} non-buggy.
Please note that you shall not send bug reports to R mailing lists,
-since vegan is not a standard R package.
+since @pkg{vegan} is not a standard R package.
There also is a bug reporting tool at
- at url{http://r-forge.r-project.org/projects/vegan/,,R-Forge}, but you
+ 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).
- at node Is it a bug or a feature?, Can I contribute to vegan?, How to report a bug in vegan?, Introduction
+ at 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?
It is not necessarily a bug if some function gives different
@@ -277,11 +273,11 @@
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 vegan?, , Is it a bug or a feature?, Introduction
- at section Can I contribute to vegan?
+ at node Can I contribute to @pkg{vegan}?, , Is it a bug or a feature?, Introduction
+ at section Can I contribute to @pkg{vegan}?
-Vegan is dependent on user contribution. All feedback is welcome. If
-you have problem with vegan, it may be as simple as incomplete
+ at 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.
Feature requests also are welcome, but they are not necessarily
@@ -290,95 +286,126 @@
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 vegan. We also audit the code, and
-typically we edit the code in vegan style for easier maintenance. All
+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.
@node Ordination, Other analysis methods , Introduction, Top
@chapter Ordination
@menu
-* I have only numeric and positive data but vegan still complaints::
+* I have only numeric and positive data but @pkg{vegan} still complaints::
* Can you analyse binary or cover class data?::
-* Why dissimilarities in vegan differ from other sources?::
+* Why dissimilarities in @pkg{vegan} differ from other sources?::
+* Why NMDS stress is sometimes 0.1 and sometimes 10?::
* Zero dissimilarities in isoMDS::
+* How the RDA results are scaled?::
* cca fails with ``data.frame expected'' or ``"site.env" missing''::
* Variance explained by ordination axes::
* 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 vegan::
+* 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?::
@end menu
- at node I have only numeric and positive data but vegan still complaints, Can you analyse binary or cover class data?, Ordination, Ordination
+ at node I have only numeric and positive data but @pkg{vegan} still complaints, Can you analyse binary or cover class data?, Ordination, Ordination
@comment node-name, next, previous, up
- at section I have only numeric and positive data but vegan still complaints
+ at section I have only numeric and positive data but @pkg{vegan} still complaints
You are wrong! Computers are painfully pedantic, and if they find
non-numeric or negative data entries, you really have them. Check your
data. Most common reasons for non-numeric data are that row names were
read as a non-numeric variable instead of being used as row names (check
argument @code{row.names} in reading the data), or that the column names
-were interpted as data (check argument @code{header = TRUE} in reading
+were interpreted as data (check argument @code{header = TRUE} in reading
the data). Another common reason is that you had empty cells in your
-input data, and these were interprted as missing values.
+input data, and these were interpreted as missing values.
- at node Can you analyse binary or cover class data?, Why dissimilarities in vegan differ from other sources?, I have only numeric and positive data but vegan still complaints, Ordination
+ at node Can you analyse binary or cover class data?, Why dissimilarities in @pkg{vegan} differ from other sources?, I have only numeric and positive data but @pkg{vegan} still complaints, Ordination
@section Can you analyse binary or cover class data?
-Yes. Most vegan methods can handle binary data or cover abundance data.
+Yes. Most @pkg{vegan} methods can handle binary data or cover abundance data.
Most statistical tests are based on permutation, and do not make
distributional assumptions. There are some methods (mainly in diversity
analysis) that need count data. These methods check that input data are
integers, but they may be fooled by cover class data.
- at node Why dissimilarities in vegan differ from other sources?, Zero dissimilarities in isoMDS, Can you analyse binary or cover class data?, Ordination
- at section Why dissimilarities in vegan differ from other sources?
+ at node Why dissimilarities in @pkg{vegan} differ from other sources?, Why NMDS stress is sometimes 0.1 and sometimes 10?, Can you analyse binary or cover class data?, Ordination
+ at section Why dissimilarities in @pkg{vegan} differ from other sources?
Most commonly the reason is that other software use presence--absence
-data whereas vegan used quantitative data. Usually vegan indices are
+data whereas @pkg{vegan} used quantitative data. Usually @pkg{vegan} indices are
quantitative, but you can use argument @code{binary = TRUE} to make them
presence--absence. However, the index name is the same in both cases,
although different names usually occur in literature. For instance,
-Jaccard index actually refers to the binary index, but vegan uses
+Jaccard index actually refers to the binary index, but @pkg{vegan} uses
name @code{"jaccard"} for the quantitative index, too.
Another reason may be that indices indeed are defined differently,
because people use same names for different indices.
- at node Zero dissimilarities in isoMDS, cca fails with ``data.frame expected'' or ``"site.env" missing'', Why dissimilarities in vegan differ from other sources?, Ordination
+ at node Why NMDS stress is sometimes 0.1 and sometimes 10?, Zero dissimilarities in isoMDS, Why dissimilarities in @pkg{vegan} differ from other sources?, Ordination
+ at section Why @acronym{NMDS} stress is sometimes 0.1 and sometimes 10?
+
+Stress is a proportional measure of badness of fit. The proportions can
+be expressed either as parts of one or as percents. Function
+ at code{isoMDS} (@pkg{MASS} package) uses percents, and function @code{monoMDS}
+(@pkg{vegan} package) uses proportions, and therefore the same stress is 100
+times higher in @code{isoMDS}. The results of @code{goodness} function
+also depend on the definition of stress, and the same @code{goodness} is
+100 times higher in @code{isoMDS} than in @code{monoMDS}. Both of these
+conventions are equally correct.
+
+ at node Zero dissimilarities in isoMDS, How the RDA results are scaled?, Why NMDS stress is sometimes 0.1 and sometimes 10?, Ordination
@section Zero dissimilarities in isoMDS
-You can use argument @code{zerodist = "add"} in @code{metaMDS} or
- at code{metaMDSdist} to handle zero dissimilarities. With this argument,
-zero dissimilarities are replace 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).
+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}.
- at node cca fails with ``data.frame expected'' or ``"site.env" missing'', Variance explained by ordination axes, Zero dissimilarities in isoMDS, Ordination
+ at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Zero dissimilarities in isoMDS, Ordination
+ at section How the @acronym{RDA} results are scaled?
+
+The scaling or @acronym{RDA} results indeed differ from most other
+software packages. The scaling of @acronym{RDA} is such a complicated
+issue that it cannot be explained in this @acronym{FAQ}, but it is
+explained in a separate @acronym{pdf} document on ``Design decision and
+implementation details in vegan'' that you can read with @pkg{vegan}
+command @code{vegandocs("decision")}.
+
+ at node cca fails with ``data.frame expected'' or ``"site.env" missing'', Variance explained by ordination axes, How the RDA results are scaled?, Ordination
@section cca fails with ``data.frame expected'' or ``"site.env" missing''
-This is not a vegan error message, but it comes from the @code{cca}
-function in the ade4 package. There is an unfortunate name clash, and if
-you have loaded ade4 after vegan, the ade4 version of @code{cca} will
-mask the vegan version. You can use the vegan version using command
- at code{vegan:cca()}. If you do not need package ade4, you can detach it
-with command @code{detach(package:ade4)}.
+This is not a @pkg{vegan} error message, but it comes from the
+ at code{cca} function in the @pkg{ade4} package. There is an unfortunate
+name clash, and if you have loaded @pkg{ade4} after @pkg{vegan}, the
+ at pkg{ade4} version of @code{cca} will mask the @pkg{vegan} version. You
+can use the @pkg{vegan} version using command @code{vegan::cca()}. If
+you do not need package @pkg{ade4}, you can detach it with command
+ at code{detach(package:ade4)}.
@node Variance explained by ordination axes, Is it possible to have passive points in ordination?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Ordination
@section Variance explained by ordination axes.
-In general, vegan does not directly give any statistics on the
+In general, @pkg{vegan} does not directly give any statistics on the
``variance explained'' by ordination axes or by the constrained axes.
This is a design decision: I think this information is normally useless
and often misleading. In community ordination, the goal typically is
@@ -395,7 +422,7 @@
typically are much more useful for the whole community. Correspondence
analysis uses another measure of variation (which is not variance), and
again it typically explains a ``smaller proportion'' than principal
-componentsm but with a better result. Detrended correspondence analysis
+components but with a better result. Detrended correspondence analysis
and nonmetric multidimensional scaling even do not try to ``explain''
the variation, but use other criteria. All methods are incommensurable,
and it is impossible to compare methods using ``explanation of
@@ -437,13 +464,13 @@
@node Is it possible to have passive points in ordination?, Class variables and dummies, Variance explained by ordination axes, Ordination
@section Is it possible to have passive points in ordination?
-Vegan does not have a concept of passive points, or a point that should
+ at pkg{Vegan} does not have a concept of passive points, or a point that should
only little influence the ordination results. However, you can add
points to eigenvector methods using @code{predict} functions with
@code{newdata}. You can first perform an ordination without some
species or sites, and then you can find scores for all points using your
complete data as @code{newdata}. The @code{predict} functions are
-available for basic eigenvector methods in vegan (@code{cca},
+available for basic eigenvector methods in @pkg{vegan} (@code{cca},
@code{rda}, @code{decorana}, for an up-to-date list, use command
@code{methods("predict")}). You also can simulate the passive points in
R by using low weights to row and columns (this is the method used in
@@ -451,29 +478,56 @@
row 3 ``passive'': @code{dune[3,] <- 0.001*dune[3,]}.
- at node Class variables and dummies, I want to use Helmert or sum contrasts, Is it possible to have passive points in ordination?, Ordination
+ at node Class variables and dummies, How are environmental arrows scaled?, Is it possible to have passive points in ordination?, Ordination
@section Class variables and dummies
-You should define a class variable as an R @code{factor}, and vegan will
+You should define a class variable as an R @code{factor}, and @pkg{vegan} will
automatically handle them with formula interface. You also can define
constrained ordination without formula interface, but then you must
code your class variables by hand.
-R (and vegan) knows both unordered and ordered factors. Unordered
+R (and @pkg{vegan}) knows both unordered and ordered factors. Unordered
factors are internally coded as dummy variables, but one redundant
level is removed or aliased. With default contrasts, the removed
level is the first one. Ordered factors are expressed as polynomial
contrasts. Both of these contrasts explained in standard R
documentation.
-You should never make your own dummy variables, but you should use
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1983
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