warpRefOutline {geomorph}

Creates a 2D outline warped to the mean shape

Description

A function to take an outline (defined by many points) and use thin-plate spline method to warp the outline into the estimated mean shape for a set of aligned specimens.

Usage

warpRefOutline(file, coord, ref)

Arguments

file

A .txt or .csv file of the outline point coordinates, or a .TPS file with OUTLINES= or CURVES= elements

coord

A p x k matrix of 2D fixed landmark coordinates

ref

A p x k matrix of 2D coordinates made by mshape

Details

Function takes an outline (defined by many points) with a set of fixed landmark coordinates and uses the thin-plate spline method (Bookstein 1989) to warp the outline into the shape defined by a second set of landmark coordinates, usually those of the mean shape for a set of aligned specimens. It is highly recommended that the mean shape is used as the reference for warping (see Rohlf 1998). The workflow is as follows:

1. Calculate the mean shape using mshape

2. Choose an actual specimen to use for the warping. The specimen used as the template for this warping is recommended as one most similar in shape to the average of the sample, but can be any reasonable specimen - do this by eye, or use findMeanSpec

3. Warp this specimen into the mean shape using warpRefOutline

4. Use this average outline where it asks for a outline= in the analysis functions and visualization functions

The returned outline object is for use in geomorph functions where shape deformations are plotted (picknplot.shape, two.b.pls, bilat.symmetry, and plotRefToTarget).

Value

Function returns an outline object

Author(s)

Emma Sherratt

References

Bookstein, F. L. 1989 Principal Warps: Thin-Plate Splines and the Decomposition of Deformations. IEEE Transactions on Pattern Analysis and Machine Intelligence 11(6):567-585.

Rohlf, F. J. 1998. On Applications of Geometric Morphometrics to Studies of Ontogeny and Phylogeny. Systematic Biology. 47:147-158.

See Also

findMeanSpec