[R-sig-eco] Question on using strata in a pRDA

[Gavin Simpson]

On Tue, 2011-11-08 at 13:19 -0200, Diogo B. Provete wrote:
> Dear list,
> I've got an issue on using a partial RDA (space with PCNM + environment)
> coupled with a variation partitionning, with randomization (strata).
> 
> 1) I sampled  11 ponds during 6 months, obtaining both tadpoles species
> abundance ("species") and environmental data ("env"). I was running the
> anova() to test the significance of the rda with randomization only between
> ponds, by using the function with(). I'd like to know if my procederes are
> correct.
> 
> > rda.global =
> rda(species~ph+temp+CO+cond+area+as.factor(month)+as.factor(pond)+Condition
> (pcnm.matrix),     na.action=na.exclude, data=env)
> 
> > anova(rda.global)
> 
>    Permutation test for rda under reduced model
> 
> Model: rda(formula = species.pad ~ temp + pH + DO + turb + cond + veg +
> canopy + dep + area + as.factor(month) + as.factor(pools) +
> Condition(as.matrix(pcnm.mat)), data = abiotic.pad, na.action = na.exclude)
>             Df      Var      *F*      N.Perm *Pr(>F) *
> Model    15 0.212182* 3.7405 *   199  *0.005 ***
> Residual 16 0.060508
> ---
> Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1
> 
> 
> >  with(env, anova(rda.global, strata=pond))
> Permutation test for rda under reduced model
> Permutations stratified within 'pools'
> 
> Model: rda(formula = species.pad ~ temp + pH + DO + turb + cond + veg +
> canopy + dep + area + as.factor(month) + as.factor(pools) +
> Condition(as.matrix(pcnm.mat)), data = abiotic.pad, na.action = na.exclude)
>             Df      Var      *F *     N.Perm *Pr(>F)*
> Model    15 0.212182 *3.7405*    199   *0.01 ***
> Residual 16 0.060508
> ---
> Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1
> 
> As you can see, the F statistic are precisely the same in the two
> procedures, but the p-values are different. Is that right?

Why do you wish for the permutation to be stratified by a variable that
you included in the analysis?

Anyway, you are testing the *observed* F against a null distribution of
F under permutation. The null distribution so generated will depend on
the permutation and permutation scheme used. The *observed* F will not
change, just the permutation p-value of this observed F stat.

> 2) I have some NAs in my original environmental data matrix, but I couldn't
> remove them using na.action argument from rda. Thus, I actually couldn't
> run the varpart function. Do you know how can I couple with Nas in the
> varpart?

Remove them first by applying na.omit():

dat2 <- na.omit(dat)
varpart(...., data = dat2)

HTH

G

> Thank you all for your attention and (future) willingness to give me some
> feedback.
> 
> Diogo
> 
> 
> --
> Atenciosamente,
> Diogo Borges Provete
> 
> ==============================
> Bilogo
> Mestre em Biologia Animal (UNESP)
> Doutorando PPG Ecologia e Evoluo
> Laboratrio de Ecologia de Insetos (sl. 222)
> Departamento de Ecologia
> Instituto de Cincias Biolgicas - ICB 1
> Universidade Federal de Gois, campus II - UFG
> Goinia-GO
> CP: 131
> 74001-970
> Brazil
> 
> > Tel. Lab. +55 62 3521-1732
> > Cel. +55 62 8231-5775
> > : diogoprovete
> > : diogoprov at yahoo.com.br
> > Personal web page
> > Traduza conosco:
> > <<<D-Lang  Solues linguisticas>>>
> > <<<Perfil no ProZ>>>
> > ==============================
> 
> 
> 
> --
> Thiago Gonalves-Souza, Ms.
> Universidade Estadual Paulista (UNESP)
> Departamento de Zoologia e Botnica
> Programa de Ps-Graduao em Biologia Animal (Doutorado)
> E-mail alternativo: thiagoaracno at gmail.com
> Home page:<http://www.wix.com/thiagocalvesouza/tg-s>
> 
> 
> 
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