monogeneaGM (version 1.1)

shapeEvo: Statistical test of deviation from directional uniformity and estimation of average magnitude of directional change

Description

This function performs the Rayleigh test (Batschelet, 1981) for detecting deviation from uniformity of directional change at each landmark. Additionally, it estimates the mean magnitude of directional change, and then summarizes the result graphically using a wireframe-lollipop plot (Klingenberg, 2013).

Usage

shapeEvo(x, ancestor, col.lab = "black", coltones = redgreen(101), clade, exfac = 1, tit = NULL)

Arguments

x

a list of objects that are matrices containing average GPA coordinates of anchor landmarks. The species names should be the names of this list

ancestor

a matrix specifying the GPA coordinates of the root ancestor, estimated using fastAnc function in the phytools package

col.lab

color for arrows in the wireframe-lollipop plot

coltones

color tones for p-values; defaults to red-black-green spectrum

clade

a character vector specifying the species that form a clade of interest

exfac

an expansion factor for the magnitude of direction change

tit

title for the wireframe-lollipop plot

Value

A wireframe-lollipop plot and a list containing:

magnitude

a matrix of the mean magnitude of directional change (column) of each landmark for each species (row)

pvalue

p-values for each landmark from the Rayleigh test

References

Batschelet E. (1981). Circular Statistics in Biology. London: Academic Press.

Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4:e1668.

Klingenberg CP. (2013). Visualizations in geometric morphometrics: how to read and how to make graphs showing shape changes. Hystrix 24:15-24.

See Also

plotCircular, anglecheck

Examples

library(gplots)
library(circular)

data(va_mean)
data(estimated_ancestral_va)
data(spcolmap)

nf <- layout(matrix(c(1,1,1,2),1, 4,byrow=TRUE))
layout.show(nf)

cladeII <- spcolmap$species[spcolmap$host %in% "L.subviridis"]
shapeEvo(va_mean, estimated_ancestral_va, col.lab="dodgerblue",
clade=cladeII, exfac=2, tit="Ventral anchors")
#Some journals want the title to be left-adjusted, so set tit="" and then:
#title("a)", adj=0)

#Add a nice color bar
par(mar=c(5,6,4,2))
colorBar(redgreen(101),min=0, max=1, tit="p-value")