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On Jan 8, 2019, at 11:54 AM, Pedro Neves
mailto:pedro.ne...@oom.arditi.pt>> wrote:
On 08/01/19 14:01, Steve Brewer wrote:
Pedro,
In my opinion, the problem is that adonis can only use the residual error to
test effects. It doesn’t
I’ve generated a function called “centroidmatrix” that might be helpful to you.
I think this could allow you to test the season and habitat and their
interaction effects using the correct error term.
#' centroidmatrix
#' This function allows you to generate a matrix of centroids from a
Gian,
I am bit confused by what your concern is. First, if the imbalance is not that
severe, the approach you take to analyzing a two-way permanova (type I, type
II, type III ss) is not going to matter that much. Indeed, if the design were
balanced, they would give you identical results.
David,
Assuming the distance/similarity measure is non-euclidean (e.g., Bray-Curtis),
see attached pdf document containing a previous post on this subject. This
approach is based on the one that Marti Anderson describes in Primer.
Good luck,
Steve
Stephen Brewer
David,
Thanks for your response to Martijn's question. I too am interested in
using manyglm in analyzing multifactor experiments, and I think I've
figured out how to do this. One question though regarding the model and
sequential sums of squares. I think understand correctly that the anova
Ecology Research
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phone (61)(2) 9385-7031
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http://www.eco-stats.unsw.edu.au/ecostats15.html
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Date: Wed, 10 Jun 2015 09:57:37 -0500
From: Steve
Thanks Phillip
That's helpful. I hadn't thought about the one-tailed aspect of it. The
idea came from path analysis, wherein the goodness-of-fit test is a sum of
the chi squares for the unspecified paths. I'll look into this further.
Steve
J. Stephen Brewer
Professor
Department of Biology
PO
100
1.00
mesocosm 12.8188 15.8910100
0.009901 **
Residuals 127 22.5277 0.1774
---
Signif. codes: 0 �***� 0.001 �**� 0.01 �*� 0.05 �.� 0.1 � � 1
Thank you very much
Paul Moquin
[R-sig-eco] Permanova with nested data
Steve
PERMANOVA
tests on a reduced data set, I could be evaluating differences between the
levels of a main effect?
Could anyone provide a citation for a paper that uses a similar procedure?
On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer jbre...@olemiss.edu wrote:
Brandon,
Are you asking if you can use
effect?
Could anyone provide a citation for a paper that uses a similar
procedure?
On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer jbre...@olemiss.edu
wrote:
Brandon,
Are you asking if you can use betadisper as a substitute for post-anova
pairwise comparisons among levels? After using
Brandon,
Are you asking if you can use betadisper as a substitute for post-anova
pairwise comparisons among levels? After using betadisper to obtain
dispersions, I believe you can plot the centroids for each level. In
addition to telling you if the dispersions differ among levels, you could
see
Alicia
One more thought. I wonder if part of the problem is that you're
attempting to use ISA to do something it was not designed to deal with.
Sometimes that can work and result in a clever new approach, but in this
case, I don't see how it can work. As a recall, ISA is done by taking the
Alexandre,
I'll leave it to Sarah to advise you on MRM (and I agree with Jari that
the method you're describing is not going to work). I'll just add that it
is not clear to me why the predictors (even geographic distance) have to
be treated as distances to partition the variance in composition.
Peter,
For my purposes (I.e., estimating exposure and drying potential in
northern hemisphere temperate forests), I simply subtract 45 degrees from
the measured aspect in degrees, convert to radians, and then take the
cosine of the adjusted angle. If I want to make exposure positive, I then
Sharon,
I've had difficulty trying to figure out how to do a split-split-plot
anova on bray-curtis distances in R and thus may not be much help to you.
If you didn't have the habitat effect and associated subplots, you could
do a simple split-plot analysis using two separate analyses (two-way
Beth and others,
Given several recent queries regarding how to analyze repeated-measures
and split-plot perManova using adonis, I thought I would pass along what I
think is a reasonable solution.
I just saw the recent exchange over the use of BiodiversityR to do nested
perMANOVA. I was unaware
Valerie,
Adonis does not define fixed or random effects, and you therefore cannot
define multiple error terms. However, if your model statement looks
something like this - isolation*year + site, strata = site - then you will
get the correct test for the isolation x year interaction and the
an additional question: I have also an environemental
gradient (continuous, one value pro site, constant over the years). Is it
possible to include it?
Best wishes
Valerie
Message du 18/02/13 à 15h41
De : Steve Brewer
A : v_coudr...@voila.fr, r-sig-ecology@r-project.org
Copie à :
Objet : Re: [R-sig
Erin,
There have been a lot of similar queries (e.g., repeated measures, nested
permanova). Jari can correct me if I am wrong, but as far as I know, no
one has developed a way to define multiple error terms in adonis.
You can use adonis, however, to get the split-plot effects. If you want to
From: r-sig-ecology-boun...@r-project.org
[r-sig-ecology-boun...@r-project.org] on behalf of Steve Brewer
[jbre...@olemiss.edu]
Sent: 29 November 2012 16:42
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] summing F stats and permutation
Dear Colleagues,
I'm
Chris,
Another thing to keep in mind is that when you run the regression analysis
using residuals, as opposed to putting all predictors in the multiple
regression from the beginning (oceanographic data and productivity data),
you are in effect inflating the error df for the analysis of catch
Kay,
Seems like a clever and reasonable approach, but I have a couple of
comments/questions.
First, it seems that with this approach, you cannot evaluate the sediment
x hydrology, the sediment x depth or the sediment x hydrology x depth
interactions. I'm not sure if Arnaud is interested in these
/8/12 1:07 PM, Steve Brewer jbre...@olemiss.edu wrote:
Kay,
Seems like a clever and reasonable approach, but I have a couple of
comments/questions.
First, it seems that with this approach, you cannot evaluate the sediment
x hydrology, the sediment x depth or the sediment x hydrology x depth
Edi and Kay,
Assuming one is using Bray-Curtis distances for the species composition
matrix, how are the bc distances among the larger plots (e.g., whole plots
or sites) or the split-plots (site/hydro combos) being calculated here?
I understand that one can use permutation to shuffle the sites
Arnaud,
Have you already tried to run the analysis using the Site_Hydro
interaction as the strata effect? If so, can you show us the anova table?
One thing I'm wondering about is how adonis is dealing with the apparent
nesting of sites within sediment types. From your description, site does
not
Hey Folks,
I am new to R and am trying to modify my multivariate eco-statistics course
by giving my students the option of doing all of the assignments in R.
One of the exercises I've been doing in Primer, but would like to do in R,
is a repeated measures permutation MANOVA, wherein I examine
Hey folks,
I am new to R and am trying to modify my multivariate eco-statistics course
by giving my students the option of doing all of the assignments in R.
Currently, all the assignments are done in either JMP, PC-Ord, or Primer.
One difficulty I'm having is figuring out how to do a
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