Uses stochastic character mapping to propagate ASR uncertainty through speciation classifications. Posterior distribution of in-situ event counts

When multiple trees are provided, the function propagates ASR uncertainty from the stochastic mapping itself, and phylogenetic uncertainty from the distribution of trees.

Usage

simmap_insitu(phy, PAM, model = "ER", nsim = 10)

Arguments

phy

The phylogenetic tree associated with your data

PAM

A presence-absence matrix reflecting where each species of interest is located. The match_island_phylo function will create this PAM, but if the user would prefer to input a custom PAM, make sure that it has a column titled "locale" with the name of an island in each row, and each subsequent column is titled with a species name. Each species column should include either a 0 (absence) or a 1 (presence), signifying whether that species occurs on the island in a given row.

model

The transition model to use in phytools::make.simmap. See documentation for ape::ace for more information. Default: ER

nsim

The number of simulations to use in phytools::make.simmap Default: 10

Value

A list of island-specific ancestral state reconstructions