get_sampled_networks: Get posterior samples of networks of interactions of extant...

In maribraga/evolnets: Reconstruct Ancestral Networks Inferred In RevBayes

Get posterior samples of networks of interactions of extant lineages at given time points in the past

Description

Get posterior samples of networks of interactions of extant lineages at given time points in the past

Usage

get_sampled_networks(at_ages, state = 2, ages = NULL)

Arguments

at_ages	List of lists, with samples and posterior probabilities for each interaction of extant lineages at given ages. Usually calculated posterior_at_ages, see example.
state	Which state? Default is 2. For analyses using the 3-state model, choose 1, 2 or both using c(1, 2) (where 1 is a potential host and 2 an actual host). Note that this is also applied to the extant network.
ages	Vector of ages (time points in the past) at which samples were retrieved. By default, uses all ages present in pp_at_ages.

Value

A list of arrays, one for each age. Arrays contain sampled networks.

Examples

# read data that comes with the package
data_path <- system.file("extdata", package = "evolnets")
tree <- read_tree_from_revbayes(paste0(data_path,"/tree_pieridae.tre"))
host_tree <- ape::read.tree(paste0(data_path,"/host_tree_pieridae.phy"))
history <- read_history(paste0(data_path,"/history_thin_pieridae.txt"), burnin = 0)

# choose ages
ages <- c(60, 50, 40, 0)

# calculate posterior probability of interactions
at_ages <- posterior_at_ages(history, ages, tree, host_tree)

# get sampled networks
sampled_nets <- get_sampled_networks(at_ages)

maribraga/evolnets documentation built on Feb. 3, 2025, 6:46 p.m.