get_node_range_BioGeoBEARS: Get node ranges from BioGeoBEARS biome reconstruction model

In GabrielNakamura/Rrodotus: Tools for Historical Biogeography analysis

Get node ranges from BioGeoBEARS biome reconstruction model

Description

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

GabrielNakamura/Rrodotus documentation built on Aug. 31, 2023, 2:13 p.m.