Package index • codiv

Main Functions

Core codiversification analysis

codiv(): Perform codiversification scan between host and symbiont trees
check_inputs(): Validate inputs to codiv()
codiv_null_scans(): Second-order permutation test for scan-wide co-diversification
host_codiv_summary(): Summarize which hosts have co-diversifying symbionts

Working with Results

Methods for the codiv result object

print(<codiv>): Print a codiv result
summary(<codiv>): Summarize a codiv result
as.data.frame(<codiv>): Coerce a codiv result to a plain data frame
filter_results(): Filter a codiversification scan, optionally collapsing nested calls

Codiversification Methods

Statistical methods used at each node

hommola(): Calculate Hommola correlation coefficient
hommola_wf(): Hommola correlation with permutation significance testing
paco_wf(): Phylogenetic Association with Co-diversification (PACo) analysis
topology_wf(): Topology-congruence test with permutation significance

Helper Functions

Tree and data manipulation utilities

collapse_monophyletic(): Collapse monophyletic groups in a phylogenetic tree
host_symbiont_links(): Convert host-symbiont associations to binary presence-absence matrix

Secondary Analyses

Robustness, interpretation, and visualization

loo_host_analysis(): Leave-One-Host-Out Analysis
sensitivity_analysis(): Parameter Sensitivity Analysis
molecular_clock(): Molecular-clock corroboration of co-diversification
plot_codiv_trees(): Visualize Host-Symbiont Codiversification

Simulation

Generate host/symbiont data with known co-diversification

simulate_codiv_data(): Simulate host and symbiont trees with known co-diversification