estimated_ancestral_va: Estimated Generalized Procrustes Analysis (GPA) coordinates...
In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description Usage Format Details Author(s) Source References See Also Examples

Estimated GPA landmark configuration of the ventral anchors of the root ancestor of 13 Ligophorus species.

1	data(estimated_ancestral_va)

A matrix of 11 rows (landmarks) and 2 columns (xy-coordinates) representing the estimated GPA landmark configuration of the ventral anchors of the root ancestor (left and right anchors averaged).

The root ancestor's GPA landmark configuration is unknown, but can be estimated using similar data from extant species. The estimation is done using fastAnc function in the phytools package (Revell, 2012). Root ancestor mean GPA coordinates of anchor landmarks are required for shape evolution analysis.

Tsung Fei Khang tfkhang@um.edu.my

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

Revell LJ. (2012). phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217-223.

shapeEvo

library(gplots)
library(circular)

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

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)