Function reference • evolnets

All functions

count_events() effective_rate() count_gl() rate_gl(): Calculate the rate of host-repertoire evolution

evolnets: evolnets: a package for summarizing inference of network evolution

extant_net: Extant network

get_sampled_networks(): Get posterior samples of networks of interactions of extant lineages at given time points in the past

get_summary_networks(): Get summary networks from posterior probabilities of interactions of extant lineages at given time points in the past

history: Data for Pieridae butterflies and their host plants from Braga et al. 2021

host_tree: Host plants tree

index_at_ages_samples(): Posterior distribution of network structure indices across ancestral networks

index_at_ages_summary(): Network structure indices across ancestral summary networks and extant network

match_modules(): Match modules of different ancestral networks across time.

modules_across_ages(): Evolution of modules: find and match modules across time slices

modules_from_samples(): Find modules in networks sampled across MCMC at specific time slices

modules_from_summary_networks(): Identify modules for each summary network at each age

mycomputeModules(): Modified version of bipartite's computeModules function

plot_ancestral_networks(): Plot ancestral networks with module information

plot_ancestral_states(): Plot ancestral states on the phylogeny.

plot_extant_matrix(): Plot a network with modules as an adjacency matrix

plot_index_at_ages(): Plot network structure indices across ancestral summary, sampled and extant networks

plot_matrix_phylo(): Plot a network with modules as an adjacency matrix, with aligned phylogenies.

plot_network_at_age(): Plot one ancestral network with module information at a given time

posterior_at_ages(): Calculate the posterior probability of ancestral host repertoires at time points in the past (ages)

posterior_at_nodes(): Calculate the posterior probability of ancestral host repertoires

read_history(): Read history.txt file produced by RevBayes

read_tree_from_revbayes(): Read symbiont tree file produced by RevBayes containing node indices

support_for_modules(): Calculate support for modules from summary networks based on modules of sampled networks

tree: Pieridae tree