ada: Ancestral Diversity Analysis

In GabrielNakamura/Herodotools: Tools for Historical Biogeography analysis

Ancestral Diversity Analysis

Description

This function computes different assemblage level metrics using an ancestral community reconstruction

Usage

ada(
  x,
  phy,
  sp.bin = "Sturges",
  marginal = FALSE,
  lik.threshold = FALSE,
  threshold = 0.7,
  compute.fields = F
)

Arguments

x	Community occurrence matrix. Rows are sites and columns are species
phy	Phylogenetic tree
sp.bin	Character indicating the methods to be used to compute the number of time slices in which metrics will be computed. Default is "Sturges"
marginal	Logical indicating
lik.threshold	Logical indicating if some threshold value will be used to select the likelihood values of ancestor species in a site. Default is TRUE
threshold	Scalar indicating the threshold value used to select the likelihood of a given species be present at a site
compute.fields	Logical, indicates if phylogenetic fields will be computed. Default is FALSE

Details

ada function calculates an ancestral assemblage reconstruction for each assemblage in a matrix using for this reconstruction ace function from ape package

Value

A list of size eight containing the following objects

Phylogeny	Phylogenetic tree
Root.Age	Numeric containing root age of the tree used
Per.node.ancestral.area	Matrix containing the ancestors (nodes) for each species
Diversity.Through.Time	Age of each node in the phylogeny
Cell.Metric	Matrix containing the assemblage level metrics for richness and ancestral diversity

GabrielNakamura/Herodotools documentation built on Aug. 27, 2023, 2:33 p.m.