LOST (version 2.1.2)

unbend.tps.poly: TPS-style unbend specimens

Description

Remove dorsoventral arching effect from fish specimen landmark data. Function similar to "unbend specimens" utility in the TPS software suite. Fits a polynomial function along the length and height of the specimen, determines the perpendicular residuals and arc length along the polynomial, and these are used as the new length and width landmarks.

Usage

unbend.tps.poly(coords, reference, axes = NULL, deg = 2)

Value

Returns a matrix or array (depending on original data) of landmark data with the effect of dorso-ventral arching removed.

Arguments

coords

A matrix or array of landmark coordinate data. Columns should be coordinates, and rows landmarks. Data may be 2D or 3D. If array is given, process will repeat on each slice individually.

reference

The rows of the matrix over which the polynomial function will be fit. Should represent the spine or other proxy for the long axis of the body.

axes

A vector with 2 values representing the "lateral" view of the fish. The first entry should be the "long" (anterior-posterior) axis and the second should be the vertical (dorso-central) axis. If not provided it is assumed the first column is X and the second is Y.

deg

The degrees for the polynomial function, passed to "poly". Typically 2 or 3 (default = 2, quadratic fit).

Author

J.H. Arbour

Details

It is advisable to remove lateral bending with unbend.spine prior to using this function. Otherwise data should be at least bilaterally aligned to a plane (and seebilat.align) Resulting landmark data is in the same scale as the original landmark configuration. Can be applied over multiple specimens using for-loops or apply functions.

References

Arbour,J.H. In Prep. Get Unbent! R Tools for the removal of arching and bending of fish specimens in geometric morphometric shape analysis

See Also

bilat.align, unbend.spine

Examples

# \donttest{
library(rgl)
data(darters)
## bilaterally aligned using only head landmarks
lands.unbent<-unbend.spine(darters$coords[,,3],
darters$land.pairs,deg=3, restricted=darters$restricted)$unbent

plot(lands.unbent[,c(1,3)],asp=1)

lands.unbent<-unbend.tps.poly(lands.unbent,darters$reference,axes=c(1,3),deg=3)
plot(lands.unbent[,c(1,2)],asp=1)

plot3d(lands.unbent, aspect=FALSE)
# }