monogeneaGM (version 1.1)

stdLM: Standardization of landmark configuration by a reference landmark

Description

This function provides options for reflecting GPA coordinates around x=0, swapping of GPA xy-coordinates, and rotating all GPA coordinates in such a way that landmark 7 is standardized at x=0.

Usage

stdLM(x, reflect = FALSE, swap = FALSE, sgn = c(1, 1))

Arguments

x

an array containing landmark coordinate data of anchor from the specimens of interest

reflect

if TRUE, x-coordinates are reflected around the x=0 axis

swap

if TRUE, the x and y-coordinates are swapped

sgn

a numeric vector; two choices 1 and -1; defaults to c(1,1)

Value

an array of landmark coordinates

Details

The values in the sgn vector should be tuned to obtain the desired orientation of landmark configuration. This function processes the output from procrustesFit, which requires the geomorph package (Version 3.0.0; Adams & Otarola-Castillo, 2013).

References

Adams DC, Otarola-Castillo E. (2013). geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution 4:393-399.

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

See Also

procrustesFit, plotLM

Examples

library(geomorph)

data(ligophorus_tpsdata)
#A data processing step to parse out the orientation of landmarks
#from samples of L.parvicopulatrix

O <- matrix(0, length(ligophorus_tpsdata$parvicopulatrix), 4)
for(w in 1:length(ligophorus_tpsdata$parvicopulatrix)){
	result <- mapply(function(k)
	anglePolygon(matrix2list(ligophorus_tpsdata$parvicopulatrix[[w]][(11*(k-1)+1):(11*k),]),
	degree=TRUE), k=1:4)

	result_angle <- mapply(function(k) list(result[[2*k-1]]), k=1:4)
	result_orientation <- mapply(function(k) list(result[[2*k]]), k=1:4)
	names(result_angle) <- names(result_orientation) <- c("VR","VL","DR","DL")
	O[w,] <- unlist(result_orientation)
}

mdir <- apply(O, 2, function(k) which(k == "m") )
pdir <- apply(O, 2, function(k) which(k == "p") )

e <- 1 #Ventral right anchor
result <- procrustesFit(ligophorus_tpsdata$parvicopulatrix, e,
list(mdir[[e]], pdir[[e]]), PrinAxes=TRUE, showplot=TRUE)
#Standardize the x-coordinate of Landmark 7 by rotating the x-coordinate
#of its mean GPA xy-coordinate to x=0.
coordinates <- stdLM(result$coords, reflect=FALSE, swap=TRUE, sgn=c(1,-1))

plotLM(coordinates, "VR", pointscale=0.8,axispointscale=0.8,
meansize=1.2,polygon.outline=TRUE,c(-.6,.6),c(-.6,.6) )