Question on using strata in a pRDA
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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