Yes that's a direct result of the number of simulations - if all of the simulated F statistics are smaller than the test statistics, then you will get:
p = 1/(n+1) where n is the number of simulated data sets. lh On Jul 26, 2010, at 8:44 AM, Alejandro Gonzalez V wrote: > Hello, > > Some colleagues and I are running some phylogenetic ANOVAS using the geiger > package. In some of the analyses we get the same phylogentic p-value (very > small p-value) even though the F-statistic differs between the two analyses, > albeit it being relatively high in both instances. We were wondering why this > arises, to get better grip on how the analysis works. We thought it may have > to do with the randomizations to calculate the phylogenetic p-value. Or that > the F-statistics are quite high... > Below are two examples : > > m11<-phy.anova(tree1,tmax,biozone,data.names=X,nsim=1000) > Standard ANOVA: > Analysis of Variance Table > > Response: td$data > Df Sum Sq Mean Sq F value Pr(>F) > group 1 967.96 967.96 155.88 3.057e-12 *** > Residuals 25 155.24 6.21 > --- > Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > > > Phylogenetic p-value: 0.000999001 > > > m12<-phy.anova(tree1,wt,biozone,data.names=X,nsim=1000) > Standard ANOVA: > Analysis of Variance Table > > Response: td$data > Df Sum Sq Mean Sq F value Pr(>F) > group 1 602.88 602.88 109.01 1.333e-10 *** > Residuals 25 138.26 5.53 > --- > Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > > > Phylogenetic p-value: 0.000999001 > > > Cheers, > > Alejandro > __________________________________ > > Alejandro Gonzalez Voyer > Post-doc > > NEW ADDRESS & NEW E-MAIL > > Estación Biológica de Doñana (CSIC) > Avenida Américo Vespucio s/n > 41092 Sevilla > Spain > > E-mail: alejandro.gonza...@ebd.csic.es > > Tel: +34- 954 466700, ext 1749 > > Website (From my previous position): > http://www.iee.uu.se/zooekol/default.php?type=personalpage&lang=en&id=146 > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Luke Harmon Assistant Professor Biological Sciences University of Idaho 208-885-0346 lu...@uidaho.edu _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
