[Vegan-commits] r2346 - in branches/2.0: R inst inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 7 12:42:37 CET 2013
Author: jarioksa
Date: 2013-01-07 12:42:36 +0100 (Mon, 07 Jan 2013)
New Revision: 2346
Modified:
branches/2.0/R/envfit.default.R
branches/2.0/R/factorfit.R
branches/2.0/inst/ChangeLog
branches/2.0/inst/doc/FAQ-vegan.texi
branches/2.0/inst/doc/diversity-vegan.Rnw
branches/2.0/inst/doc/intro-vegan.Rnw
Log:
merge r2342 (unused factor levels in envit),
r2341 (doc edits) rand r2345 (new FAQs)
Modified: branches/2.0/R/envfit.default.R
===================================================================
--- branches/2.0/R/envfit.default.R 2013-01-07 10:58:43 UTC (rev 2345)
+++ branches/2.0/R/envfit.default.R 2013-01-07 11:42:36 UTC (rev 2346)
@@ -13,7 +13,7 @@
if (!na.rm)
stop("missing values in data: consider na.rm = TRUE")
X <- X[keep,, drop=FALSE]
- env <- env[keep,, drop=FALSE]
+ env <- droplevels(env[keep,, drop=FALSE]) ## drop any lost levels
na.action <- structure(seq_along(keep)[!keep], class="omit")
}
if (is.data.frame(env)) {
Modified: branches/2.0/R/factorfit.R
===================================================================
--- branches/2.0/R/factorfit.R 2013-01-07 10:58:43 UTC (rev 2345)
+++ branches/2.0/R/factorfit.R 2013-01-07 11:42:36 UTC (rev 2346)
@@ -2,6 +2,7 @@
function (X, P, permutations = 0, strata, w, ...)
{
P <- as.data.frame(P)
+ P <- droplevels(P) ## make sure only the used levels are present
if (any(!sapply(P, is.factor)))
stop("All fitted variables must be factors")
NR <- nrow(X)
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2013-01-07 10:58:43 UTC (rev 2345)
+++ branches/2.0/inst/ChangeLog 2013-01-07 11:42:36 UTC (rev 2346)
@@ -4,6 +4,9 @@
Version 2.0-6 (opened October 8, 2012)
+ * merge 2345: FAQ update (github, metric NMDS space).
+ * merge 2342: unused factor levels in envfit/factorfit.
+ * merge 2341 (partial): visible space in pdf of Rnw files.
* merge 2336: stricter monoMDS convergence criteria.
* merge 2334,5: scores.monoMDS,metaMDS updates.
* merge 2332: add plot.nestednodf().
Modified: branches/2.0/inst/doc/FAQ-vegan.texi
===================================================================
--- branches/2.0/inst/doc/FAQ-vegan.texi 2013-01-07 10:58:43 UTC (rev 2345)
+++ branches/2.0/inst/doc/FAQ-vegan.texi 2013-01-07 11:42:36 UTC (rev 2346)
@@ -84,6 +84,7 @@
* 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?::
@end menu
@node What is @pkg{vegan}?, What is R?, Introduction, Introduction
@@ -273,7 +274,7 @@
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}?, , Is it a bug or a feature?, Introduction
+ 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
@section Can I contribute to @pkg{vegan}?
@pkg{Vegan} is dependent on user contribution. All feedback is welcome. If
@@ -288,8 +289,23 @@
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.
+included contributions will be credited.
+ 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
@@ -300,6 +316,7 @@
* 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::
* How the RDA results are scaled?::
* cca fails with ``data.frame expected'' or ``"site.env" missing''::
* Variance explained by ordination axes::
@@ -388,7 +405,7 @@
with @code{monoMDS} and in principal coordinates analysis
(@code{cmdscale} in @pkg{stats}, @code{wcmdscale} in @pkg{vegan}).
- at node Zero dissimilarities in isoMDS, How the RDA results are scaled?, I get zero stress but no convergent solutions in @code{metaMDS}, Ordination
+ at node Zero dissimilarities in isoMDS, I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, I get zero stress but no convergent solutions in @code{metaMDS}, Ordination
@section Zero dissimilarities in isoMDS
Function @code{metaMDS} uses function @code{monoMDS} as its default
@@ -406,7 +423,23 @@
the kluge (or work harder with your data). Usually it is better to use
@code{monoMDS}.
- at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Zero dissimilarities in isoMDS, Ordination
+ at node I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, How the RDA results are scaled?, Zero dissimilarities in isoMDS, Ordination
+ at section I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores
+
+Claims like this have indeed been at large in the Internet, but they are
+based on grave misunderstanding and are plainly wrong. @acronym{NMDS}
+ordination results are strictly metric, and in @pkg{vegan}
+ at code{metaMDS} and @code{monoMDS} they are even strictly Euclidean. The
+method is called ``non-metric'' because the Euclidean distances in
+ordination space have a non-metric rank-order relationship to community
+dissimilarities. You can inspect this non-linear step curve using
+function @code{stressplot} in @pkg{vegan}. Because the ordination scores
+are strictly Euclidean, it is correct to use @pkg{vegan} functions
+ at code{envfit} and @code{ordisurf} with @acronym{NMDS} results.
+
+
+
+ at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Ordination
@section How the @acronym{RDA} results are scaled?
The scaling or @acronym{RDA} results indeed differ from most other
Modified: branches/2.0/inst/doc/diversity-vegan.Rnw
===================================================================
--- branches/2.0/inst/doc/diversity-vegan.Rnw 2013-01-07 10:58:43 UTC (rev 2345)
+++ branches/2.0/inst/doc/diversity-vegan.Rnw 2013-01-07 11:42:36 UTC (rev 2346)
@@ -49,7 +49,7 @@
\tableofcontents
- ~\\[2ex]
+
\noindent The \pkg{vegan} package has two major components:
multivariate analysis (mainly ordination), and methods for diversity
analysis of ecological communities. This document gives an
Modified: branches/2.0/inst/doc/intro-vegan.Rnw
===================================================================
--- branches/2.0/inst/doc/intro-vegan.Rnw 2013-01-07 10:58:43 UTC (rev 2345)
+++ branches/2.0/inst/doc/intro-vegan.Rnw 2013-01-07 11:42:36 UTC (rev 2346)
@@ -55,7 +55,7 @@
\tableofcontents
-~\\[2ex]
+\vspace{3ex}
\noindent \pkg{Vegan} is a package for community ecologists. This
documents explains how the commonly used ordination methods can be
performed in \pkg{vegan}. The document only is a very basic
More information about the Vegan-commits
mailing list