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R Scripts — Functional Space

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Functional Space

Functional space construction, KDE and visualisation

make.PCA(TRAITS, dimensionsAux, savePCA)

Run PCA on a functional trait matrix and save axes and loadings.

density_threshold(z, p)

Find the density value at a given cumulative probability threshold from a KDE grid.

compute_kde(scores, n_grid, lims, thresholds, ...)

Kernel density estimation on PCA scores with multiple threshold contours.

compute_phylopic_positions(scores, species, ...)

Compute x/y positions for phylopic silhouette overlays on a functional space plot.

plot_FS_new(pca_sub, ...)

Plot a functional space with KDE contours, convex hulls and optional phylopic images.