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Statistical analyses

Core functions

stat_pca()
Principal Component Analysis for morphometric data
stat_lda()
Linear Discriminant Analysis for morphometric data
stat_lm()
Linear Model for morphometric data
stat_kmeans()
K-means clustering for morphometric data
stat_hclust()
Hierarchical clustering for morphometric data

Verbs

That applies to all stat_*

collect()
Collect results from statistical analyses
transduce()
Transduce model positions to coefficients and shapes

Morphospace

That applies to all stat_*

morphospace_axes()
Morphospace visualization: shapes along axes
morphospace_centroids()
Morphospace visualization: group centroids
morphospace_grid()
Morphospace visualization: uniform grid
morphospace_range()
Morphospace visualization: data range grid

Misc

Todo

collect()
Collect results from statistical analyses
collect(<stat_hclust>)
Collect cluster assignments from hierarchical clustering
collect(<stat_kmeans>)
Collect cluster assignments from k-means
collect(<stat_lm>)
Collect fitted values from linear model
plot(<stat_hclust>)
Plot hierarchical clustering tree
plot(<stat_kmeans>)
Plot k-means clustering results
plot(<stat_lm>)
Plot linear model results
predict(<stat_lda>)
Predict method for LDA
predict(<stat_pca>)
Predict method for PCA
transduce(<stat_hclust>)
Transduce hierarchical clustering nodes to shapes
transduce(<stat_kmeans>)
Transduce k-means cluster centers to shapes
transduce(<stat_lm>)
Transduce linear model positions to shapes

Morphospaces

Smart way to reconstruct shapes from coefficients encoded by stat_*

transduce()
Transduce model positions to coefficients and shapes

Methods

to be reorganized

collect(<stat_lda>)
Collect predictions and LD scores from LDA results
collect(<stat_pca>)
Collect PC scores from PCA results
plot(<stat_lda>)
Plot LDA results
plot(<stat_pca>)
Plot PCA results
collect(<stat_meanshape>)
Collect mean shapes and add to original data
plot(<stat_meanshape>)
Plot mean shapes
stat_meanshape()
Calculate mean (or aggregated) shapes

Data

To play with

boteft
Bottle outlines with elliptic Fourier transform coefficients
vitis
Grapevine pips outlines (two views) with elliptic Fourier transform coefficients