Thierry and Hadley,
Sorry to be late coming into this (I forgot I subscribed to sig-eco).
package labdsv has a function called matrify() which takes a three
column data.frame (sample,taxa,abundance) and creates a full (sparse)
matrix representation. I've never tried it on a data set
Chris,
One (sub-optimal) solution would be to fit GAMS and then have the
gam.predict estimate values immediately near your data points which you
could use to calculate a local gradient. If the GAM is reasonably
smooth, I would think you could get estimates that were reasonable.
Dave
--
of a
# plot to itself
apply(as.matrix(demodis),1,mean) # calcualte the mean dissimilarity
# of every plot to the others
This is all done as part of function disana() in package labdsv along
with some other simple dissimilarity analyses.
Dave Roberts
Dear List,
Earlier this year on an (undoubtedly ill-advised) lark I coded up
an R version of TWINSPAN. It's far from a polished package at this
point, but the code does run. One of the interesting features is that
you can partition a PCO or NMDS in addition to the traditional CA. To be
Modified
TWINSPAN classification in which the hierarchy respects cluster
heterogeneity Journal of Vegetation Science 20(4): 596–602
http://onlinelibrary.wiley.com/doi/10./j.1654-1103.2009.01062.x/abstract
Zoltan
2011.04.26. 23:40 keltezéssel, Dave Roberts írta:
Dear List,
Earlier
Hi Kátia,
Sorry to be so late; just back in the office.
Pedro is correct that adonis will help establish statistical
significance to potential differences, but I think NMDS could still be
very helpful. One approach would be to code the sites by glyph (e.g.
site 1 = circle, site 2 =
On 10/07/2011 08:51 AM, Dr N.A. Cutler wrote:
Dear All,
I have a query about multivariate analysis of community data.
In my experiment, 24 microbial communities in different locations were
sampled using Sampling Technique 1 (ST1). A site X species matrix was
then derived by molecular
On 10/10/2011 02:15 PM, Gavin Simpson wrote:
On Mon, 2011-10-10 at 09:11 -0700, Rich Shepard wrote:
On Mon, 10 Oct 2011, Dave Roberts wrote:
I want to compare the results of the two sampling exercises in order to
test the performance of the two sampling techniques.
I would try
the duplicate
plots you can change the zero to a small value
d[d==0] - 0.0001
and run the isoMDS on the resulting revised dissimilarity matrix.
Undoubtedly someone from the vegan group will respond to your second
question.
Dave Roberts
On 12/05/2011 01:28 AM, 坪井 隼 wrote:
Dear Madam / Sir,
I have two
in.
Dave Roberts
On 01/15/2012 12:10 PM, Laura S wrote:
Dear all:
May you recommend an R package for analyzing this data set? I would greatly
appreciate any thoughts you can provide.
I. Study goals
This study examines soil crust (lichens and bryophytes) recovery and succession
in fields
is available in the ecodist package you already have loaded.
Dave Roberts
On 01/23/2012 05:51 AM, Sacha Viquerat wrote:
Hello dear list!
Maybe I am demanding too much, but I am having problems finding the
right way to tackle a seemingly trivial problem:
We counted fish at different sites. In order
(clustid)
and see if cluster size is unique.
Dave Roberts
On 07/03/2012 07:12 AM, Caitlin Porter wrote:
Dear all,
I am working with a large data set to examine plant community structure on
barrens habitats and have a couple of questions regarding Indval (labdsv
package) on Wards Clusters (hclust
Philip,
IS there an online errata,or do you just have to be smart and diligent?
Thanks, Dave
On 11/29/2012 07:30 AM, Dixon, Philip M [STAT] wrote:
I agree with all the previous comments and second Tom's recommendations of Faraway
as an 'in between' Zuur and Piniehro Bates. One thing to
=;, header=TRUE)
any(is.na(newveg))
newveg[1:10,1:10]
and then
spc.pres- apply(newveg0,2,sum)
any(is.na(spc.pres))
Dave Roberts
On 04/19/2013 06:49 AM, lisa couet wrote:
Hi,
I have an issue concerning the fonction spc.pres in package labdsv.
the message is:
Erreur dans plot.window
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