Re: [R-sig-eco] AIC in R: back-transforming standardized model parameters (slopes)

Hi Matt, This isn't going to be a complete answer, but it might help. I wasn't 100% sure what standardize() was doing, or how it was doing it, so I did getMethod("standardize","glm") to see the source code. That function calls standardize.default() which is a bit hard to get but

Re: [R-sig-eco] Number of Groups in SpeciesMix

Dear Alexandre, I'm glad that you are using species archetypes models (SAMs). I hope that SAMs can answer your questions succinctly. I think that a lot will be clarified if you look at the example in the help file for clusterSelect(). There you will see that: 1) obs is just a dummy -- you

Re: [R-sig-eco] NMDS axes scores

Contrary to common misbelief, NMDS ordination space is **metric**. In vegan, the ordination space (= the ordination result) is even guaranteed to be Euclidean (in isoMDS it can be Minkowski, but this is not allowed with vegan). What is non-metric is the regression from observed dissimilarities

Re: [R-sig-eco] NMDS axes scores

Thank you Jari for an, as always, insightful email. It has been a gut feeling of mine for quite some time that using PCA scores as independent variables is at least little wrong but never found any reference to substantiate it. I would like to use this opportunity to ask you or other readers if

Re: [R-sig-eco] NMDS axes scores

Hi Conny, AFAIK NMDS is *non-metric* and represents distances among objects, not gradients along axes (known or unknown): distances along axes are stretched as needed locally (NMDS works with rank order), even order of the elements along axes does not tell anything. NMDS is great if you want to

Re: [R-sig-eco] NMDS axes scores

On 11/01/16 12:08, Roman Luštrik wrote: Thank you Jari for an, as always, insightful email. It has been a gut feeling of mine for quite some time that using PCA scores as independent variables is at least little wrong but never found any reference to substantiate it. I would like to use this

Re: [R-sig-eco] NMDS axes scores

> On 11 Jan 2016, at 14:13 pm, Bob O'Hara wrote: > > > Whilst I'm filling bandwidth, I'm not sure Jari's suggestion that you need > the interaction term is correct. If a model is linear in axis1 and axis2, > then any rotation is also linear, i.e. the transformation is

Re: [R-sig-eco] NMDS axes scores

Zoltan, You’d better ask Bob… If you really want to get a synthetic (latent) variable with reduced noise, I think you really should be doing Factor Analysis. In particular, you should have confirmatory factor analysis, a.k.a. measurement model in latent linear structural models. Often

Re: [R-sig-eco] NMDS axes scores

Dear Jari, What is your opinion about using first few axes of a metric ordination? I'm aware that it is meaningless using first two axes of NMDS ordination that calculated for three dimensions. But in my experience, it is often useful to use only first few axes of metric ordination instead

[R-sig-eco] Number of Groups in SpeciesMix

Dear friends, I am willing to apply the SAM analytical framework to a dataset of plant species in coastal Brazil using the SpeciesMix package. The SpeciesMix package fits Species Archtype Models, a special type of finite mixture of regression model motivated by the analysis of multi-species data.