(CCA) model after using the
function goodness.cca in vegan. In his explanation of the diagnostic
tools for CCA
(http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/goodness.cca.html),
Jari Oksanen states that It is a common practise to use goodness
statistics to remove
species from ordination
if
you are serious), dig up the late 2008 issue of the Ecology with the
Legendre mates vs. Tuomisto discussion -- somewhere around pages 3230 to
3256 of vol 89).
That's for the starter.
Cheers, Jari Oksanen
I've been exploring using this approach for a similar problem. I'd be
curious to know
for mixed models in any other vegan function.
Cheers, Jari Oksanen
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On 3/12/09 23:54 PM, gabriel singer gabriel.sin...@univie.ac.at wrote:
Hi everybody,
Anybody has used capscale() in package vegan to compute a PCoA-CDA as
suggested by Anderson and Willis 2003 (Ecology 84: 511 ff) using one or
more factors as predictors?
Then I wonder about:
*) How to
print.wcmdscale!)
NMDS is really intended for nonlinear mapping onto *low* number of
dimensions.
Cheers, Jari Oksanen
NMS.trial
Call:
metaMDS(comm = sqrtABCD, distance = bray, k = 23, trymax = 100,
autotransform = F)
Nonmetric Multidimensional Scaling using isoMDS (MASS package)
Data
this: stress 11.6 is really fine.
I think that if you get stress down to 5% (0.05) or less, then there is
something fishy in your data or in your model specification, like
overfitting.
Cheers, Jari Oksanen
But,
of course, our goal is to reduce the observed complexity of nature
. They are
not the same as the strict rotation scores for factors in Gower metric (but
should be the same as the Legendre scores for continuous variables), but may
be more intuitive.
Cheers, jari oksanen
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tests available in several
packages in R, but what are the things you want to solve by using
dissimilarities?
Cheers, Jari Oksanen
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their conflicting
arguments make sense, they are not yet an optimal solution.
Cheers, Jari Oksanen
so we thought it would be a good idea not to use mantel and friends
since the problem of IBD seems to need a different approach here.
best,
Jens
Sarah Goslee schrieb:
That doesn't make much
easily
spot those changes (probably in BiodiversityRGUI, diversityresult,
diversityresult0). I have cc'ed this to Roeland Kindt, but I think the
Internet connection is not always so good so that it may take some time
before he answers. I can look if I can hack around this in vegan.
Cheers, Jari
On 12/10/09 19:54 PM, Roman Luštrik roman.lust...@gmail.com wrote:
Hello list,
I have a felling this is a generic error but nonetheless, it has been
bugging me extensively. If anyone can chip in, I would most appreciate.
I'm trying to calculate expected species richness, following
On 1/10/09 20:36 PM, Sarah Goslee sarah.gos...@gmail.com wrote:
I can only speak for the mantel() within ecodist, but I can tell you that it
will not take full matrices - the upper triangle will be dropped. You could
roll your own very easily, but it would be exceedingly slow, eg:
mat1 -
of the other parameters (c-g) turn out to be,
as well as the model fit when using the forced parameters in conjunction
with the free parameters.
Cheers, Jari Oksanen
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that species are not points nor arrows. Vegan
tutorial (from the Web) gives an example.
Cheers, Jari Oksanen
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E. C. Pielou may be one of the first who wrote about this. Check her book
'Mathematical ecology' (J. Wiley, 1977).
Best wishes, Jari Oksanen
-Original Message-
From: Paulo Inácio de Knegt López de Prado
Sent: 04.07.2009, 17:35
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco
in which Gavin Simpson and Jari Oksanen
states that are not available routines in vegan to retrieve this
information.
I am interested in the length of the DCCA/pCCA axis as I would like to
perform a similar analyses to the one Lancaster et al. 1996 performed
to measure community persistence
(and go
along the axes), then it would be meaningful to look a the
relationship of axis and something else.
And indeed, there is no constrained NMDS in vegan. It is unconstrained
with an interpretation through vector fitting.
cheers, jari oksanen
Stephen Sefick
On Sat, Dec 6, 2008 at 11:58 AM
effect on the scales. The choice of
clustering method has a huge impact.
cheers, Jari Oksanen
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them to draw the surface with the contour()
command. The grid item is available from vegan working version 1.16-3
(revision 532) in R-Forge, and Windows binary is available (probably)
from tomorrow morning (Central European Standard Time).
Best wishes, Jari Oksanen
--
Jari Oksanen [EMAIL
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