If you want to stick with or at least compare a mulivariate tree with
other approaches (like CCA or mvabund or boral) then the partykit
package provides an implementation of a multivariate tree model, using
conditional inference trees (i.e. you use conditional inference to
decide if spits are
Right, but mvabund fits quite different types of model to that fitted
in a multivariate tree, which can be seen as an unsupervised
constrained clustering of the multivariate species response matrix.
All the best
Gavin
On 24 June 2017 at 10:02, Torsten Hauffe wrote:
>
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rda) will only have one data= argument.
> However, in addition to variables in the data frame given in data=, you can
> mix variables in the work environment in your formula. If you think you
> need to have several data frames for the data= argument, please consider
> cbind().
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as is it is too complex for your data. You can;t test for an
interaction but you could remove the interaction and just test for main
effects, unless you can get some more data.
G
Andrew
On 24 October 2014 04:08, Gavin Simpson ucfa...@gmail.com wrote:
This all looks bogus to me; you've fit the data
419 473
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...@oulu.fi wrote:
On 23/10/2014, at 18:17 PM, Gavin Simpson wrote:
On 22 October 2014 17:24, Chris Howden ch...@trickysolutions.com.au
wrote:
A good place to start is by looking at your residuals to determine if
the normality assumptions are being met, if not then some form of glm
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On 17 October 2014 10:04, Bob O'Hara boh...@senckenberg.de wrote:
On 10/17/2014 05:36 PM, Gavin Simpson wrote:
On 17 October 2014 06:44, Bob O'Hara boh...@senckenberg.de wrote:
On 17/10/14 13:54, José M. Blanco Moreno wrote:
Dear users
I have been checking the values returned
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FAX - 662-915-5144
Phone - 662-915-1077
On 3/27/14 10:47 AM, Gavin Simpson ucfa...@gmail.com wrote:
Note that `betadisper()` only considers statistically dispersions
about the group centroids. It might show the centroids and return
their values, but it doesn't consider
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it works
with this data. I can't quite figure out how I would go about interrogating
the fitted spline to deterine when the peak value happens with respect to
DoY. Any suggestions?
-Jacob
On Tue, Mar 25, 2014 at 9:06 PM, Gavin Simpson ucfa...@gmail.com wrote:
I would probably attack
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- predict(mod$gam, newdata = newdat, type = terms)
take - which(pred[,s(DoY)] == max(pred[,s(DoY)]))
or
take - as.numeric(which.max(pred[,s(DoY)]))
Cheers,
-Jacob
On Wed, Mar 26, 2014 at 9:46 AM, Gavin Simpson ucfa...@gmail.com wrote:
1) Visually - unless it actually matters exactly on which
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to do it, I would really
appreciate it.
Thanks in advance.
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-rda(spe~1+Condition(env))
plot(partial.pca)
Is this a reasonable approach?
Some feedback would be great.
Thanks,
Duarte
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# sites as text
text(island.NMDS, display = 'sites')
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will the dune.env be in the case of metaMDS instead of rda?
Thank you again
Elaine
On Tue, Aug 20, 2013 at 12:08 AM, Gavin Simpson ucfa...@gmail.com wrote:
I have some posts on my blog that explain how to do this, ain the vein
of Vit's reply (indexing via a factor). This way is preferable
am wrong in any point, will be glad if someone corrects me.
Cheers,
Vit
Dne 2013-08-09 19:25, Gavin Simpson napsal:
What Jari meant was if you use `betadisper()` on your data then it will
give you an object that has a `plot()` method which will give you
something
of relevance to what
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a mixed intercept model on the residuals to deal with the nested
structure (and also the heterogeneity between plots). This runs,
gives reasonable results that agree with the graphs, but is it
statistically valid?
Thanks,
Jonathan
From: Gavin Simpson
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, hence it makes sense to model
it this way. For the record, as simple AR1 model better account for
the seasonal fluctuation than a gam, and my ARMA(2,0) model does an
even better job.
Hope this helps, J
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not to use it for `strata` in the permutation test if the null
distribution you are testing needs to retain the archipelago-based
clustering of samples.
HTH
G
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is one of the machine learning tools that
might usefully be applied.
HTH
G
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523 Research
.
As for the species scores; metaMDS adds these as a convenience feature
if the species data is available to it. They are added as a weighted
average of the site scores and then possibly expanded.
G
thanks for any input on this!
adrien
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Gillet
[francois.gil...@univ-fcomte.fr]
Date d'envoi : samedi 20 avril 2013 10:59
À : Gavin Simpson
Cc: Aurélie Boissezon; r-sig-ecology@r-project.org
Objet : Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf
2013/4/19 Gavin Simpson
gavin.simp...@ucl.ac.ukmailto:gavin.simp...@ucl.ac.uk
I
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A contrary view in-lined below:
On Fri, 2013-04-19 at 15:19 +0200, François Gillet wrote:
A lot of questions, some responses below...
snip /
Why not explore unconstrained ordination methods and went further with
NMDS (V2 mission in Anderson et al 2011)?
Just because your purpose is to
On Thu, 2013-03-07 at 11:13 -0800, Rich Shepard wrote:
On Thu, 7 Mar 2013, Philippi, Tom wrote:
I would look at packages bio.infer, paltran, fossil, and analogue, and
search to see if anyone has pushed them in the direction you want to go.
To this list I would add Steve Juggins' excellent
to *several* questions I've had
already then I couldn't even have made it this far. Thank you!
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On Thu, 2013-03-07 at 10:48 -0400, carolina monmany wrote:
Hi all,
I would like to use ordipointlabel() to plot a RDA but the function
only displays species and sites. How can I include environmental
variables as vectors?
Thanks!
You can use
text(ord, display = bp)
(where `ord` is
On Thu, 2013-03-07 at 15:37 +, Mark Fulton wrote:
There's probably something off the shelf, but
I use a little function written in R:
#A function for doing an xyz bubbleplot.
bubbleplot - function(x, y, z, bmax=4, bmin=.5) {
plot(x,y, type=n)
z - z-min(z); z - z/max(z)
for (i in
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On Mon, 2013-02-25 at 13:18 -0500, Sarah Loboda wrote:
Hi,
I have trouble to obtain the ordination graph I want. I want to have 4 RDA
biplot on the same page and I don't want to have (or I want to modify) the
axis numbers. I want the marks on the axis without numbers to maximize the
space for
!
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-vegdist(cen.si,method=euclidean)
sites_main - factor(c(rep(1,4), rep(2,4)), labels = c(grazed,ungrazed))
mod3 - betadisper(time.dist,sites_main)
boxplot(mod3)
Cheers,
Gustaf
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Dr. Gavin Simpson [t] +44
if the within-site variation also differs. For
example, a site may show little compositional variation over time
overall, but the subplots may show large variation.
Gustaf
On 2012-10-22 13:57, Gavin Simpson wrote:
betadisper() will give you a test of homogeneity of variance between
groups
On Fri, 2012-07-27 at 09:45 +0100, Gavin Simpson wrote:
On Mon, 2012-07-23 at 10:31 -0200, Alexandre Fadigas de Souza wrote:
Dear friends,
In performing a PERMANOVA in VEGAN's 'adonis' function, we can use strata
to indicate a blocking variable. Contrary to standard statistical
-ecology
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, append) :
argument 2 (type 'list') cannot be handled by 'cat'
what is meaning it?
do i allow use it for continue?
thanks
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Dr. Gavin Simpson [t] +44 (0)20 7679
I've removed R-Help from this now...
On Thu, 2012-05-10 at 10:13 +, Jari Oksanen wrote:
On 10/05/2012, at 11:45 AM, Gavin Simpson wrote:
snip /
As you provide little or no context I'll explain what envfit() does etc.
The idea goes back a long way (!) and is in my 1995 edition
...@gmail.com
Mobile: +41794385586
Skype: aghaynes
On 10 May 2012 12:53, Gavin Simpson gavin.simp...@ucl.ac.uk wrote:
I've removed R-Help from this now...
On Thu, 2012-05-10 at 10:13 +, Jari Oksanen wrote:
On 10/05/2012, at 11:45 AM, Gavin Simpson wrote
help that anyone can
offer.
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Dr. Gavin Simpson
have any further questions, please do not hesitate to contact me.
We look forward to seeing you in August.
Gavin
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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-ecology
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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data, yes, presence absence data can be analysed using CoCA.
HTH
G
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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Pearson Building, [e
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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.
You could always do a procrustes rotation on the two configurations to
see how well they compare.
G
Gian
2012/2/20 Gavin Simpson gavin.simp...@ucl.ac.uk
On Mon, 2012-02-20 at 16:28 +0100, Gian Maria Niccol Benucci wrote:
Hi r-sig-ecology Members,
I would please you to examine
can find it, maybe it escapes me...
Thank you very much for your aid,
Gian
2012/2/20 Gavin Simpson gavin.simp...@ucl.ac.uk
On Mon, 2012-02-20 at 17:24 +0100, Gian Maria Niccol Benucci wrote:
Dear Gavin,
Thank you very much. I tried with your advice but the result
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,SIMa,SIMb,SZV,BM,BRE))
levels(groups)
[1] SIG BA SIMa SIMb SZV BM BRE
Do check that code you use creates the expected results!
HTH
G
Gian
2011/11/17 Gavin Simpson gavin.simp...@ucl.ac.uk
On Thu, 2011-11-17 at 10:01 +0100, gabriel singer wrote:
... dangerous wording
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