stdLM: Standardization of landmark configuration by a reference...
In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

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

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.

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

`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)

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).

an array of landmark coordinates

Tsung Fei Khang tfkhang@um.edu.my

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.

procrustesFit, plotLM

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) )