rarefy_FPD: Rarefied Function-Phylogenetic Distances
In levisc8/Fun_Phylo_Package: Helpers to Power the Fun Phylo Shiny App

Description Usage Arguments Value Author(s)

rare_FPD resamples a phylogenetic and functional distance matrix a set number of times so that communities of different sizes can be compared to each other.

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rarefy_FPD(focal.species, phylo.mat, fun.mat, metric = c("MPD", "NND"),
  n.resamp = 1000, n.rare, a, p, abundance.weighted = FALSE,
  community.data = NULL)

`focal.species`	The name of the focal species in the community to be rarefied.
`phylo.mat, fun.mat`	A phylogenetic or functional distance matrix with species names as row names and column names. Can either be a `data frame`, `matrix`, or `dist`.
`metric`	Either MPD (`MPD`) or nearest neighbor distance (`NND`). The default is to calculate both metrics.
`n.resamp`	The number of rarefied resamplings to perform. Default is 1000.
`n.rare`	The number of species to rarefy the community down to. Must be less than the total in the community.
`a`	The phylogenetic scaling factor for the calculation of functional-phylogenetic distances
`p`	The power to raise each distance value to in the functional- phylogenetic distance calculation
`abundance.weighted`	A logical value indicating whether or not to weight species by their relative abundances
`community.data`	The community data file. Each observation of a species in a community should be its own row. For now, the column specifiy which community is which is called `exotic_species`, but this will be generalized later using an argument to specifiy which column marks community separators and which column holds the actual species names