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Get node ranges from BioGeoBEARS biome reconstruction model

get_node_range_BioGeoBEARS.Rd

This is an auxiliary function that can be with a ancestral area reconstruction from BioGeoBEARS to obtain a data frame containing the ancestral area of occurrence (biome range) for all ancestors (nodes)

Usage

get_node_range_BioGeoBEARS(
  BioGeoBEARS.data,
  phyllip.file,
  tree,
  max.range.size
)

Arguments

BioGeoBEARS.data

An object containing the result of BioGeoBEARS reconstruction

phyllip.file

Phylip file, the same used in BioGeoBEARS package

tree

A phylogenetic tree

max.range.size

Scalar indicating the maximum number of biomes in which each node can occupy

Value

Data frame with two columns, one indicating the node and other the ancestral biome range

Examples

data(resDEC) # ancestral area reconstruction from biogeobears
data(akodon_newick)
extdata_dir = system.file("extdata", package="Herodotools")
fn = paste(extdata_dir, "/geo_area_akodon.data", sep="")
node_area <- get_node_range_BioGeoBEARS(resDEC,phyllip.file = fn, akodon_newick,
                                        max.range.size = 4) # obtaining area for each node