[R-sig-eco] Unbalanced data and random effects

2013-10-17 Thread v_coudrain
Thank you very much for these explanations. It is quite technical and I am not 
sure that I got it all, but I will try to find the book of GelmanHill to get 
more insight into 
shrinkage. I read the book of Zuur and as you said the topic is not extensively 
covered.

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Re: [R-sig-eco] envfit() in vegan

2013-10-17 Thread Paolo Piras
Thankyou very much Jari,
actually this clarifies anything in my mind about this topic. 
What I was looking for is plotting the correlation vectors of my environmental 
variables (that in my hypothesis are the independent variables) on to my 
ordination scores of my dependent table. 
Graphically, envfit returns the plot I want but the orientation of these 
vectors are build under the opposite hypothesis that environmental variables 
are the dependent table.
Maybe a manual solution for my need is to build a list of centered vectors each 
of which orientated upon the correlation between environmental variables and 
the ordination scores
best
paolo



Da: Jari Oksanen jari.oksa...@oulu.fi
Inviato: giovedì 17 ottobre 2013 9.32
A: Paolo Piras
Cc: r-sig-ecology@r-project.org
Oggetto: Re: [R-sig-eco] envfit() in vegan

On 17/10/2013, at 02:49 AM, Paolo Piras wrote:

 Dear list,
 I write you because I do not understand the behavior of envfit() in vegan.
 Basically, it takes a matrix coming from an ordination procedure and it fits 
 on it another matrix  (often an environmental matrix).
 The projections of points onto vectors have maximum correlation with 
 corresponding environmental variables.

 A permutation test is associated to this procedure and it basically performs 
 a series of correlations between any column in the environmental matrix and 
 the ordnation matrix.
 Maybe my question is trivial (or simply ...wrong) but..intuitively, this 
 should return the same results found from a series of separate multivariate 
 regressions between any single column in the environmental matrix and the 
 entire ordination matrix.
 However it is not the case, being the envfit() results much more liberal when 
 compared to regression (i.e. using rda) and the r2 are drastically larger 
 than R-sq from rda.
 I suspect that the metric undergoing the permutation test of significance in 
 envfit() that is squared correlation coefficient (r^2) does not correspond to 
 the R-sq calculated using rda.

Paolo,

I am afraid I cannot quite understand your problems. A reproducible example 
with some numbers could be useful.

I did not quite catch your comparison of RDA and envfit. They are quite 
different methods, and their R2's really are for different things (but with 
special tricks these things can be made similar). In RDA, the R2 tells how well 
the ordination predicts the species abundances, and in envfit() the R2 tells 
how well the ordination predicts the environmental variables. For a basic and 
normal usage of RDA let us compare the following cases:

library(vegan)
data(varespec, varechem)
mod - rda(varespec ~ Al + P + K, varechem)
## gives unadjusted R2=0.377
envfit(mod ~ Al + P + K, varechem, display=lc, choices=1:3)
## **should** give for all vars r2=1 because they were the constraints

Cheers, Jari Oksanen



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Re: [R-sig-eco] angular statistics

2013-10-17 Thread Michael Marsh
If you want a measure of exposure, i. e., heat, I suggest using the 
heatload transformation suggested by McCune and Grace (2002). Their 
assumption is that mid-afternoon, when the sun is in the southwest, is 
usually the warmest time of day. The formula at the end of Chapter 3 
follows:


heat load index=(1-cos(degrees-45))/2

McCune, Bruce and James B. Grace. 2002. Analysis of ecological 
communities. MJM Software Design. Gleneden Beach, Oregon. USA


Mike Marsh


On 10/16/2013 3:00 AM, r-sig-ecology-requ...@r-project.org wrote:

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Today's Topics:

1. angular statistics (Peter Nelson)
2. Re: angular statistics (Holland, Jeffrey D)
3. Re: angular statistics (Don McKenzie)
4. Re: angular statistics (Peter Nelson)
5. Re: angular statistics (Donald McKenzie)


--

Message: 1
Date: Tue, 15 Oct 2013 09:59:38 -0700
From: Peter Nelson pnel...@cfr-west.org
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] angular statistics
Message-ID: 0c3c26ea-5599-4570-b205-5feecb70b...@cfr-west.org
Content-Type: text/plain; charset=us-ascii

I want to include the exposure (measured in degrees, for example, East-facing 
is 90) of various coastal sites in GLM and CCA analyses. Is there an 
appropriate transformation that I can apply to these measurements that will 
allow me to do this? I've found plenty of information on comparing headings, 
calculating means, etc, but nothing on how exposure might be used as a 
continuous independent variable.

Treating exposure as a categorical variable (East, Southwest, etc) seems like a 
fallback option, but then there is just as much of a 'difference' between SE 
and E sites as there is between SE and NW sites!

Thanks, Pete


--

Message: 2
Date: Tue, 15 Oct 2013 17:10:43 +
From: Holland, Jeffrey D jdhol...@purdue.edu
To: R-sig-ecology@r-project.org R-sig-ecology@r-project.org
Subject: Re: [R-sig-eco] angular statistics
Message-ID:
30a9cce0a986f74c837d6f87f9c581861367e...@wpvexcmbx01.purdue.lcl
Content-Type: text/plain; charset=us-ascii

Hello Pete,
You could include the sine and cosine of the angles.  A good book on this 
kind of analysis:
Fisher, N.I. 1993. Statistical Analysis of Circular Data. Cambridge Univ. Press.
To make this closer to exposure, perhaps you could first rotate the compass 
so that 360' is facing the direction of maximum exposure, and back-transform later?  Just 
a thought.
Cheers,  Jeff


Jeffrey D. Holland  (765) 494-7739
Assoc. Prof. of Landscape Ecology  Biodiversityjdhollan #at# purdue.edu
Dept. of Entomology, Purdue University  Smith Hall B17, 901 W. 
State St., West Lafayette, IN 47907


-Original Message-
From: r-sig-ecology-boun...@r-project.org 
[mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Peter Nelson
Sent: Tuesday, October 15, 2013 1:00 PM
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] angular statistics

I want to include the exposure (measured in degrees, for example, East-facing 
is 90) of various coastal sites in GLM and CCA analyses. Is there an 
appropriate transformation that I can apply to these measurements that will 
allow me to do this? I've found plenty of information on comparing headings, 
calculating means, etc, but nothing on how exposure might be used as a 
continuous independent variable.

Treating exposure as a categorical variable (East, Southwest, etc) seems like a 
fallback option, but then there is just as much of a 'difference' between SE 
and E sites as there is between SE and NW sites!

Thanks, Pete
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Message: 3
Date: Tue, 15 Oct 2013 11:45:14 -0700
From: Don McKenzie d...@u.washington.edu
To: Peter Nelson pnel...@cfr-west.org
Cc: r-sig-ecology@r-project.org
Subject: Re: [R-sig-eco] angular statistics
Message-ID: cd8bb4be-0db6-4863-b8af-1d7443d79...@u.washington.edu
Content-Type: text/plain

There is precedent in the ecological literature for using a cosine transformation IF you have 
reason to believe that your predictor varies continuously and symmetrically in its effects around a 
circle.  For example, if due east were the most exposure, and due west the least, with 
due north and south being roughly equal, you could 

Re: [R-sig-eco] angular statistics

2013-10-17 Thread Ivailo
On Fri, Oct 18, 2013 at 6:16 AM, Michael Marsh sw...@blarg.net wrote:

 If you want a measure of exposure, i. e., heat, I suggest using the 
 heatload transformation suggested by McCune and Grace (2002). Their 
 assumption is that mid-afternoon, when the sun is in the southwest, is 
 usually the warmest time of day. The formula at the end of Chapter 3 follows:

 heat load index=(1-cos(degrees-45))/2

 McCune, Bruce and James B. Grace. 2002. Analysis of ecological communities. 
 MJM Software Design. Gleneden Beach, Oregon. USA

Thanks for the interesting discussion!

I'd like to add that although I don't have the book, I found the
radiation measures presented in the following paper:
McCune, B. and D. Keon. 2002. Equations for potential annual direct
incident radiation and heat load. Journal of Vegetation Science
13:603–606.

Cheers,
Ivailo
-- 
UBUNTU: a person is a person through other persons.

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