[Vegan-commits] r2391 - in branches/2.0: inst inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 28 09:15:37 CET 2013
Author: jarioksa
Date: 2013-01-28 09:15:37 +0100 (Mon, 28 Jan 2013)
New Revision: 2391
Modified:
branches/2.0/inst/ChangeLog
branches/2.0/inst/doc/FAQ-vegan.texi
branches/2.0/man/orditorp.Rd
branches/2.0/man/wcmdscale.Rd
Log:
merge r2382,3 (tweak Rd) and 2384 (new FAQ entries)
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2013-01-25 13:09:27 UTC (rev 2390)
+++ branches/2.0/inst/ChangeLog 2013-01-28 08:15:37 UTC (rev 2391)
@@ -4,7 +4,9 @@
Version 2.0-6 (opened October 8, 2012)
- * merge 2374,6,7: orditorp gains argument select
+ * merge 2384: new FAQ entries.
+ * merge 2383: remove alias to print.wcmdscale.
+ * merge 2374,2376,2378,2382: orditorp gains argument select
* merge 2372: ordilabel uses ordiArgAbsorber when plotting
* merge 2369: clamtest fix and border cases.
* merge 2367: rectify mantel, summary.anosim print.
Modified: branches/2.0/inst/doc/FAQ-vegan.texi
===================================================================
--- branches/2.0/inst/doc/FAQ-vegan.texi 2013-01-25 13:09:27 UTC (rev 2390)
+++ branches/2.0/inst/doc/FAQ-vegan.texi 2013-01-28 08:15:37 UTC (rev 2391)
@@ -81,6 +81,7 @@
* 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}?::
@@ -231,7 +232,7 @@
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 @pkg{vegan}?, How to build @pkg{vegan} from sources?, Introduction
+ at node Are there binaries for devel versions?, Can I use @pkg{vegan} in Mac?, How to build @pkg{vegan} from sources?, Introduction
@section Are there binaries for devel versions?
@uref{http://r-forge.r-project.org/projects/vegan/,,R-Forge} runs daily
@@ -242,7 +243,20 @@
If you use GUI menu entry, you must select or define the R-Forge
repository.
- 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 node Can I use @pkg{vegan} in Mac?, How to report a bug in @pkg{vegan}?, Are there binaries for devel versions?, Introduction
+ at section Can I use @pkg{vegan} in Mac?
+
+Yes, you can, and @pkg{vegan} binaries are available for Mac through
+ at uref{http://cran.r-project.org,,CRAN}. However, in some cases you may
+need to install extra tools packages available in
+ at 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.
+
+ at 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
@@ -317,6 +331,7 @@
* 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''::
* Variance explained by ordination axes::
@@ -423,7 +438,7 @@
the kluge (or work harder with your data). Usually it is better to use
@code{monoMDS}.
- 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 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
Claims like this have indeed been at large in the Internet, but they are
@@ -437,9 +452,22 @@
are strictly Euclidean, it is correct to use @pkg{vegan} functions
@code{envfit} and @code{ordisurf} with @acronym{NMDS} results.
+ at node Where can I find numerical scores of ordination axes?, How the RDA results are scaled?, I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores, Ordination
+ at section Where can I find numerical scores of ordination axes?
+Normally you can use function @code{scores} to extract ordination scores
+for any ordination method. The @code{scores} function can also find
+ordination scores for many non- at pkg{vegan} functions such as for
+ at code{prcomp} and @code{princomp} and for some @pkg{ade4} functions.
- 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
+In some cases the ordination result object stores raw scores, and
+the axes are also scaled appropriate when you access them with
+ at code{scores}. For instance, in @code{cca} and @code{rda} the
+ordination object has only so-called normalized scores, and they are
+scaled for ordination plots or for other use when they are accessed with
+ at code{scores}.
+
+ at node How the RDA results are scaled?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Where can I find numerical scores of ordination axes?, Ordination
@section How the @acronym{RDA} results are scaled?
The scaling or @acronym{RDA} results indeed differ from most other
Modified: branches/2.0/man/orditorp.Rd
===================================================================
--- branches/2.0/man/orditorp.Rd 2013-01-25 13:09:27 UTC (rev 2390)
+++ branches/2.0/man/orditorp.Rd 2013-01-28 08:15:37 UTC (rev 2391)
@@ -84,6 +84,10 @@
stems <- colSums(BCI)
orditorp(mod, "sp", label = cnam, priority=stems, select = take,
pch="+", pcol="grey")
+\dontshow{
+## example(orditorp) should not set random seed in the user session
+rm(.Random.seed)
}
+}
\keyword{ aplot }
\keyword{ hplot }
Modified: branches/2.0/man/wcmdscale.Rd
===================================================================
--- branches/2.0/man/wcmdscale.Rd 2013-01-25 13:09:27 UTC (rev 2390)
+++ branches/2.0/man/wcmdscale.Rd 2013-01-28 08:15:37 UTC (rev 2391)
@@ -6,7 +6,6 @@
\name{wcmdscale}
\alias{wcmdscale}
-\alias{print.wcmdscale}
\alias{scores.wcmdscale}
\alias{plot.wcmdscale}
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