shapeEvo: Statistical test of deviation from directional uniformity and...
In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description Usage Arguments Value Author(s) References See Also Examples

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).

1 2	shapeEvo(x, ancestor, col.lab = "black", coltones = redgreen(101), clade, exfac = 1, tit = NULL)

`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

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

Tsung Fei Khang tfkhang@um.edu.my

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.

plotCircular, anglecheck

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")