coralPreprocess: coralPreprocess

In hmsc-r/HMSC: Hierarchical Model of Species Communities

coralPreprocess

Description

Splits typical Hmsc data into common and rare partitions for CORAL analysis

Usage

coralPreprocess(
  Y,
  spNames.common,
  TrData = NULL,
  phyloTree = NULL,
  Taxa = NULL,
  TaxaFormula = NULL
)

Arguments

Y	community matrix of both common and rare species
spNames.common	vector of species that are considered common in CORAL analysis
TrData	trait matrix for both common and rare species
phyloTree	phylogeny tree covering both common and rare species
Taxa	dataframe with
TaxaFormula	formula for calculating phylogeny from taxonomy, as in as.phylo.formula(...)

Details

This functions implies that all column names of Y that are not listed in spNames.common argument are considered rare species in the context of CORAL analysis.

Exactly one argument of phyloTree and Taxa must be specified.

Value

A named list containing Y.xyz and TrData.xyz parts for common and rare partitions, phylogeny tree phyloTree.common for common part and phylogeny similarity matrix C.common.rare between common and rare species

hmsc-r/HMSC documentation built on March 5, 2025, 10:52 p.m.