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.
warpRefOutline(file, coord, ref)A .txt or .csv file of the outline point coordinates, or a .TPS file with OUTLINES= or CURVES= elements
A p x k matrix of 2D fixed landmark coordinates
A p x k matrix of 2D coordinates made by mshape
Function returns an outline object
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:
Calculate the mean shape using mshape
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
Warp this specimen into the mean shape using warpRefOutline
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 (plotTangentSpace,
two.b.pls, bilat.symmetry, and plotRefToTarget).
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.