Skip to contents

Calculate the posterior probability of ancestral host repertoires

Source: R/posterior_at_nodes.R
posterior_at_nodes.Rd

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)