posterior_at_nodes: Calculate the posterior probability of ancestral host...

In maribraga/evolnets: Reconstruct Ancestral Networks Inferred In RevBayes

Calculate the posterior probability of ancestral host repertoires

Description

Group of functions to calculate the posterior probabilities of ancestral host repertoires at internal nodes of the symbiont tree.

Usage

posterior_at_nodes(history, tree, host_tree, nodes = NULL, state = c(2))

Arguments

history	Data frame with posterior samples of interaction histories returned from read_history().
tree	Symbiont tree
host_tree	Host tree
nodes	Vector of internal nodes for which to calculate the posterior probability of state.
state	Which state? Default is 2. For analyses using the 3-state model, give c(1, 2) to include both states (where 1 is a potential host and 2 an actual host).

Value

A list with three elements:

• "samples" An array of samples x nodes x hosts, containing the state of each sample.

• "post_states" An array of nodes x hosts x state containing the posterior probability for each state.

• "post_repertoires" An array of nodes x hosts x repertoire containing the posterior probability for 1) the "realized" repertoire which is defined as state 2, and 2) the "fundamental" repertoire which is defined as having any state (usually 1 or 2).

The number of samples is the number of iterations in history.

Examples

# read parasite and host tree
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"))

# read histories sampled during MCMC
history <- read_history(paste0(data_path,"/history_thin_pieridae.txt"), burnin = 0)

# calculate the posterior probability of host repertoires
# at chosen internal nodes of the parasite tree
nodes <- c(129:131)
pp_at_nodes <- posterior_at_nodes(history, tree, host_tree, nodes)

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