phy.anova {geiger} | R Documentation |
Calculates ANOVA or MANOVA, and returns p-value based on Brownian motion simulations
phy.anova(y, factor, phy, nsim=1000) phy.manova(y, factor, phy, nsim=1000, test="Wilks")
y |
Independent variable(s) - continuous |
factor |
Dependent variable - factor |
phy |
Phylogenetic tree |
nsim |
Number of simulations for calculating p-value |
test |
The name of the test statistic to be used. Partial matching is used so the name can be abbreviated. |
Simulations are run under a Brownian motion model. For MANOVA the estimates vcv matrix from ic.sigma is used as a model.
You can specify the test statistic for the summary table. Wilks' statistic is most popular in the literature.
Standard ANOVA or MANOVA table and p-value based on simulations
Luke J. Harmon
Garland
data(geospiza) attach(geospiza) drop.tip(geospiza.tree, "olivacea")->g.tree f<-as.factor(c(rep(0, 7), rep(1, 6))) phy.manova(geospiza.data, f, g.tree) x<-geospiza.data[,1] names(x)<-rownames(geospiza.data) phy.anova(x, f, g.tree)