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?

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?

Thank you all for your attention and (future) willingness to give me some
feedback.

Diogo


--
Atenciosamente,
Diogo Borges Provete

==============================
Biólogo
Mestre em Biologia Animal (UNESP)
Doutorando PPG Ecologia e Evolução
Laboratório de Ecologia de Insetos (sl. 222)
Departamento de Ecologia
Instituto de Ciências Biológicas - ICB 1
Universidade Federal de Goiás, campus II - UFG
Goiânia-GO
CP: 131
74001-970
Brazil

> Tel. Lab. +55 62 3521-1732
> Cel. +55 62 8231-5775
> : diogoprovete
> : diogoprov@yahoo.com.br
> Personal web page
> Traduza conosco:
> <<<D-Lang  Soluções linguisticas>>>
> <<<Perfil no ProZ>>>
> ==============================



--
Thiago Gonçalves-Souza, Ms.
Universidade Estadual Paulista (UNESP)
Departamento de Zoologia e Botânica
Programa de Pós-Graduação em Biologia Animal (Doutorado)
E-mail alternativo: thiagoaracno@gmail.com
Home page:<http://www.wix.com/thiagocalvesouza/tg-s>



-- 
Atenciosamente,
Diogo Borges Provete

==============================
Biólogo
Mestre em Biologia Animal (UNESP)
Doutorando PPG Ecologia e Evolução
Laboratório de Ecologia de Insetos (sl. 222)
Departamento de Ecologia
Instituto de Ciências Biológicas - ICB 1
Universidade Federal de Goiás, campus II - UFG
Goiânia-GO
CP: 131
74001-970
Brazil

Tel. Lab. +55 62 3521-1732
Cel. +55 62 8231-5775
: diogoprovete
: diogoprov@yahoo.com.br
Personal web page
Traduza conosco:
<<<D-Lang  Soluções linguisticas>>>
<<<Perfil no ProZ>>>
==============================

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