facefuns Overview

2021-03-15

Convenience functions

Function name	Brief description
facefuns	Conducts GPA and PCA, selects and creates PCs for plotting of 2-D and 3-D data
read_lmdata	Read landmark data from TPS, webmorph_list or Webmorph template files
read_vertices	Read vertex data from PLY and OBJ files
select_pcs	Select PCs based on broken stick, Kaiser Guttman or total variance explained criterion
make_pcs	Creates coordinates for a reference face at +/- x units of standard deviations for a (list of) given principal component(s)
plot_2dpcs	Create and save TPS grid plots for 2-D PCs
plot_3dpcs	Create and plot 3-D PCs
mirror_templates	Mirror landmark templates
symm_templates	Symmetrise landmark templates

Shape metrics

Functions for calculating commonly derived morphometric descriptives

Function name	Brief description	Vignette
calc_avg	Calculate averageness (reversed distance between original template(s) and sample average)	calcED
calc_as	Calculate asymmetry (distance between original and symmetrized template)	calcAsym
calc_fa	Calculate fluctuating asymmetry (distance between FA component and symmetric average)	calcAsym
calc_ed	Calculate Euclidean distance	calcED
calc_ds	Calculate group membership based on linear discriminant analysis	calcSD
calc_shapevs	Calculate group membership based on vector projection (from facefuns object, allows for symmetrizing of templates)	calcSD
calc_vs	Calculate group membership based on vector projection (from PC scores)	calcSD

Utility functions

Functions for formatting data

Function name	Brief description	Vignette
bind_arrays	Bind matrices/arrays into one 3-D array
convert_array_to_matrix	Convert 3-D array to 2-D matrix
convert_points_to_mesh	Convert 3-D coordinates to 3-D mesh using ashape3d
convert_points_to_knownmesh	Convert 3-D coordinates to 3-D mesh using reference mesh
convert_tem_to_tps	Read Webmorph template files and save as TPS
frl_features	Get point indices of FRL standard template features
remove_points	Remove points from 2-D landmark templates

Example data

Data included in facefuns

Data	Content
LondonSet_data	FRL London set: original templates (p=132, k=2, n=102)
LondonSet_aligned	FRL London set: Procrustes-aligned templates (p=132, k=2, n=102)
LondonSet_scores	FRL London set: principal component scores (first eight PCs)
LondonSet_info	FRL London set: basic demographic data
mirroredlandmarks	FRL London set: index of mirrored landmarks (p=132)