plot.procD.allometry: Plot Function for geomorph

Description

The following are brief descriptions of the different plotting methods, with references.

If "method=CAC" (the default) the function calculates the common allometric component of the shape data, which is an estimate of the average allometric trend within groups (Mitteroecker et al. 2004). The function also calculates the residual shape component (RSC) for the data.
If "method=RegScore" the function calculates shape scores from the regression of shape on size, and plots these versus size (Drake and Klingenberg 2008). For a single group, these shape scores are mathematically identical to the CAC (Adams et al. 2013).
If "method=PredLine" the function calculates predicted values from a regression of shape on size, and plots the first principal component of the predicted values versus size as a stylized graphic of the allometric trend (Adams and Nistri 2010).

Usage

"plot"(x, method = c("CAC", "RegScore", "PredLine"), warpgrids = TRUE, label = NULL, gp.label = FALSE, pt.col = NULL, mesh = NULL, shapes = FALSE, ...)

Arguments

plot object (from procD.allometry)

method

Method for estimating allometric shape components

warpgrids

A logical value indicating whether deformation grids for small and large shapes should be displayed (note: if groups are provided no TPS grids are shown)

label

An optional vector indicating labels for each specimen that are to be displayed

gp.label

A logical value indicating labels for each group to be displayed (if group was originally included); "PredLine" only

pt.col

An optional vector of colours to use for points (as in points(bg=))

mesh

A mesh3d object to be warped to represent shape deformation of the minimum and maximum size if warpgrids=TRUE (see warpRefMesh).

shapes

Logical argument whether to return the the shape coordinates shape coordinates of the small and large shapes

...

other arguments passed to plot

Value

If shapes = TRUE, function returns a list containing the shape coordinates of the small and large shapes

References

Adams, D.C., F.J. Rohlf, and D.E. Slice. 2013. A field comes of age: geometric morphometrics in the 21st century. Hystrix. 24:7-14.

Adams, D. C., and A. Nistri. 2010. Ontogenetic convergence and evolution of foot morphology in European cave salamanders (Family: Plethodontidae). BMC Evol. Biol. 10:1-10.

Drake, A. G., and C. P. Klingenberg. 2008. The pace of morphological change: Historical transformation of skull shape in St Bernard dogs. Proc. R. Soc. B. 275:71-76.

Mitteroecker, P., P. Gunz, M. Bernhard, K. Schaefer, and F. L. Bookstein. 2004. Comparison of cranial ontogenetic trajectories among great apes and humans. J. Hum. Evol. 46:679-698.