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R Scripts — Functional Diversity

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Functional Diversity

TPD estimation, functional richness and overlap

make.TPD.2D.high.def(targetGroupName, PCAImpute, alphaUse=0.95, ...)

High-resolution 2D TPD (Trait Probability Density) estimation for a taxonomic group.

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make.TPD.2D.low.def(targetGroupName, PCAImpute, alphaUse=0.95, ...)

Low-resolution 2D TPD estimation — faster, suited for large datasets.

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make.TPDLarge(targetGroupName, PCAImpute, alphaUse=0.95, TPDsMean_large, ...)

TPD computation for very large assemblages using a pre-computed reference TPD.

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TPDRichness(TPDc=NULL, TPDs=NULL)

Compute functional richness (FRIC) from community or species TPD objects.

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imageTPD(x, thresholdPlot=0.99)

Plot a TPD object as a filled image at a given probability threshold.

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overlapF(x, y)

Functional overlap between two TPD distributions (Bhattacharyya coefficient).

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percentileTPD(x)

Percentile-based summary statistics of a TPD probability distribution.

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quantileTPD(x, thresholdPlot=0.99)

Extract contour lines at given probability quantiles from a 2D TPD.

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MAE_TPD(x, y)

Mean absolute error between two TPD probability distributions.

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compute_FRic()

Functional Richness via convex hull (FD::dbFD)

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null_model_FD()

SES and p-value against species-shuffling null model

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