compare.physignal.z: Comparisons of Phylogenetic Signal Effect Sizes

In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

Comparisons of Phylogenetic Signal Effect Sizes

Description

Function performs an analysis to compare the effect sizes of two or more phylogenetic effect sizes

Usage

compare.physignal.z(..., two.tailed = TRUE)

Arguments

...	saved analyses of class physignal.z
two.tailed	A logical value to indicate whether a two-tailed test (typical and default) should be performed.

Details

The function statistically compares the effect sizes of two or more physignal.z analyses. This can be performed on different traits from the same tree, same or different traits from different trees, or modules of landmark configurations.

To use this function, perform physignal.z on as many samples as desired. Any number of objects of class physignal.z can be input. Note that some values of Z can be NaN, if the scaling parameter, lambda, is optimized at 0. In these cases, the standard error is also 0, and pairwise comparisons might not make sense.

Value

An object of class compare.physignal.z, returns a list of the following

sample.z	A vector of effect sizes for each sample.
sample.r.sd	A vector of standard deviations for each sampling distribution (following Box-Cox transformation).
pairwise.z	A matrix of pairwise, two-sample z scores between all pairs of effect sizes.
pairwise.p	A matrix of corresponding P-values.

Author(s)

Michael Collyer

References

Collyer, M.L., E.K. Baken, & D.C. Adams. 2022. A standardized effect size for evaluating and comparing the strength of phylogenetic signal. Methods in Ecology and Evolution. 13:367-382.

Examples

# Example: Compare phylogenetic signal of head components in Plethodon

data(plethspecies) 
Y.gpa<-gpagen(plethspecies$land)    #GPA-alignment

## landmarks of the jaw and cranium
jaw <- 1:5
cranium <- 6:11

PS.jaw <- physignal.z(A = Y.gpa$coords[jaw,,], phy = plethspecies$phy, 
lambda = "front", PAC.no = 7, iter=999)

PS.cranium <- physignal.z(A = Y.gpa$coords[cranium,,], phy = plethspecies$phy, 
lambda = "front", PAC.no = 7, iter=999)

PS.list <-list(PS.jaw, PS.cranium)
names(PS.list) <- c("jaw", "cranium")

PS.Z <- compare.physignal.z(PS.list)
summary(PS.Z)

geomorph documentation built on Sept. 1, 2023, 1:07 a.m.