Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/procrustesFit.2.R
Given a list of landmark coordinate data, this function performs Generalized Procrustes Analysis (GPA) and extracts the GPA-coordinates.
1 2 | procrustesFit.2(x, e, makeplot = FALSE, reflect = FALSE, swap = TRUE,
axispointscale = 0.8, sgn = c(1, -1))
|
x |
a list containing landmark coordinate data of anchors from the specimens of interest |
e |
a constant specifying the anchor of interest: ventral right(1), ventral left(2), dorsal right(3), dorsal left(4) |
makeplot |
if TRUE, returns a scatter plot of the GPA-coordinates |
reflect |
logical; if TRUE, x-coordinates are reflected around the x=0 axis |
swap |
logical; if TRUE, the x and y-coordinates are swapped |
axispointscale |
a numeric constant for controlling the font size of numeric values on the xy axes |
sgn |
a numeric vector; two choices 1 and -1; defaults to c(1,-1) |
This function is essentially a wrapper for procrustesFit
and stdLM
to ease extraction of GPA-coordinates
from list data. Both require the geomorph
package (Version 3.0.0).
an array containing GPA-coordinates of the specimens of interest
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.
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.
1 2 3 4 5 6 7 8 9 10 11 12 | data(ligophorus_tpsdata)
vright <- procrustesFit.2(ligophorus_tpsdata$johorensis, 1,
makeplot=TRUE, reflect=FALSE, swap=TRUE, sgn=c(-1,1))
vleft <- procrustesFit.2(ligophorus_tpsdata$johorensis, 2,
makeplot=TRUE, reflect=TRUE, swap=TRUE, sgn=c(-1,1))
va <- (vright+vleft)/2
plotLM(va, "VA", pointscale=0.8, meansize=1.2, polygon.outline=TRUE,
axispointscale=0.8, c(-.6,.6),c(-.6,.6))
|
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