Just to clarify the point - the null distribution for the test-statistic
(F) in this method is generated by Brownian motion simulation on the
phylogeny. The P-value of the ANOVA is thus obtained by comparing the
observed test-statistic to simulated test-statistics (for an arbitrarily
large number of simulations). The reference to this is:
Garland, T. Jr., A. W. Dickerman, C. M. Janis, & J. A. Jones. 1993.
Phylogenetic analysis of covariance by computer simulation. Syst. Biol.
42: 265-292. (http://www.jstor.org/stable/2992464)
Thus, if you have a test-statistic (F) more extreme then that obtained
for every last one of your simulated datasets, then the P-value will be
entirely determined by the number of simulations that are used (as Luke
says). This seems to be case for your data (not surprising given the
very large values for F that were obtained).
- Liam
Liam J. Revell
NESCent, Duke University
web: http://anolis.oeb.harvard.edu/~liam/
NEW email: lrev...@nescent.org
Luke Harmon wrote:
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
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Luke Harmon
Assistant Professor
Biological Sciences
University of Idaho
208-885-0346
lu...@uidaho.edu
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