get_nodes_info_core: Auxiliary function to compute information of node path and...

In GabrielNakamura/Rrodotus: Tools for Historical Biogeography analysis

Auxiliary function to compute information of node path and dispersal path for each species

Description

Auxiliary function to compute information of node path and dispersal path for each species

Usage

get_nodes_info_core(W, tree, ancestral.area, biogeo)

Arguments

W	Numerical matrix, rows are assemblages and columns are species
tree	Phylogenetic tree in newick format
ancestral.area	Single column data frame with nodes in rows and ancestral area/Ecoregion of occurrence in columns. If the reconstruction comes from BioGeoBears this data frame can be obtained with (get_node_range_BioGeoBEARS)
biogeo	Data frame containing the information of the biome/area/ecoregion of each assemblage

Value

A list with auxiliary information on nodes and species

Examples

## Not run: 
# hypothetical occurrence matrix with species in columns and assemblages in lines
 W_toy<- matrix(c(0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0),
     nrow= 3,ncol= 5,
     dimnames=list(c("Comm 1", "Comm 2", "Comm 3"),
     c(paste("s", 1:5, sep=""))))
 
 #toy tree
 data(toy_treeEx)
 
 # hypothetical data indicating the ecoregions of each assemblage
 biogeo_toy <- data.frame(Ecoregion= c("A", "B", "C"))
 
 # hypothetical data indicating the ancestral range of each node
 ancestral_area_toy <- data.frame(state= c("ABC", "B", "C", "ABC"))
 
get_nodes_info_core(W=W_toy,tree=toy_treeEx,ancestral.area=ancestral_area_toy,biogeo=biogeo_toy)

## End(Not run)

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