fgProcrustes: Full Generalized Procrustes alignment between shapes

In Momocs: Morphometrics using R

Full Generalized Procrustes alignment between shapes

Description

Directly borrowed from Claude (2008), called there the fgpa2 function.

Usage

fgProcrustes(x, tol, coo)

Arguments

x	an array, a list of configurations, or an Out, Opn or Ldk object
tol	numeric when to stop iterations
coo	logical, when working on Out or Opn, whether to use $coo rather than $ldk

Details

If performed on an Out or an Opn object, will try to use the $ldk slot, if landmarks have been previousy defined, then (with a message) on the $coo slot, but in that case, all shapes must have the same number of coordinates (coo_sample may help).

Value

a list with components:

• rotated array of superimposed configurations

• iterationnumber number of iterations

• Q convergence criterion

• Qi full list of Q

• Qd difference between successive Q

• interproc.dist minimal sum of squared norms of pairwise differences between all shapes in the superimposed sample

• mshape mean shape configuration

• cent.size vector of centroid sizes.

or an Out, Opn or an Ldk object.

Note

Slightly less optimized than procGPA in the shapes package (~20% on my machine). Will be optimized when performance will be the last thing to improve! Silent message and progress bars (if any) with options("verbose"=FALSE).

References

Claude, J. (2008). Morphometrics with R. Analysis (p. 316). Springer.

See Also

Other procrustes functions: fProcrustes(), fgsProcrustes(), pProcrustes()

Examples

# on Ldk
w <- wings %>% slice(1:5) # for the sake of speed
stack(w)
fgProcrustes(w, tol=0.1) %>% stack()

# on Out
h <- hearts %>% slice(1:5) # for the sake of speed
stack(h)
fgProcrustes(h) %>%  stack()

Momocs documentation built on Nov. 13, 2023, 5:07 p.m.