plot_index_at_ages: Plot network structure indices across ancestral summary,...

In maribraga/evolnets: Reconstruct Ancestral Networks Inferred In RevBayes

Plot network structure indices across ancestral summary, sampled and extant networks

Description

Plot z-scores for nestedness (NODF) and/or modularity (Q) for sampled and summary networks at time points in the past, calculated by index_at_ages_samples and index_at_ages_summary.

Usage

plot_index_at_ages(
  nodf_sampled,
  q_sampled = NULL,
  nodf_summary = NULL,
  q_summary = NULL,
  col_sampled = "#3B9AB2",
  col_summary = "#E67D00"
)

Arguments

nodf_sampled	Output of index_at_ages_samples when index = "NODF".
q_sampled	Output of index_at_ages_samples when index = "Q".
nodf_summary	Output of index_at_ages_summary when index = "NODF".
q_summary	Output of index_at_ages_summary when index = "Q".
col_sampled	Color used to represent values from sampled networks.
col_summary	Color used to represent values from summary networks.

Value

A plot of z-scores over time. Violins show the posterior distribution of z-scores of sampled networks, with dots and lines showing the mean values. Z-scores of summary networks and extant network are shown as dots and line. Use different colors to differentiate values from sampled and summary 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)

# calculate posterior probabilities at ages
ages <- c(60, 50, 40, 0)
at_ages <- posterior_at_ages(history, ages, tree, host_tree)

# summary networks
summary_networks <- get_summary_networks(at_ages, threshold = 0.5, weighted = TRUE)
Nz_sum <- index_at_ages_summary(summary_networks, index = "NODF", nnull = 10)

# sampled networks
sampled_networks <- get_sampled_networks(at_ages)
Nz_sam <- index_at_ages_samples(sampled_networks, index = "NODF", nnull = 10)

# plot
plot_index_at_ages(nodf_sampled = Nz_sam, nodf_summary = Nz_sum)

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