API for dhelekal/CaveDive
Phylodynamics for Clonal Expansion
| Global functions | |
|---|---|
| build_coal_tree | Man page Source code |
| build_coal_tree.structured | Man page Source code |
| build_correlate_map | Source code |
| choose_reaction | Source code |
| clade_lookup | Source code |
| clade_node_recursion | Source code |
| clade_tip_recursion | Source code |
| coalescent_loglh | Man page Source code |
| compute_ci | Source code |
| compute_persistence | Source code |
| constant.rate.int_inv | Source code |
| discard_burn_in | Source code |
| discard_burn_in.expansionsMCMC | Man page Source code |
| exp.loglh | Source code |
| exp.prob | Source code |
| expansionsMCMC | Man page Source code |
| expansions_infer | Man page Source code |
| expansions_simulate | Man page Source code |
| exponential_coalescent_loglh | Man page Source code |
| extract_lineage_times | Man page Source code |
| extract_lineage_times_native | Source code |
| extract_partition_times_fast | Source code |
| fn_log_J | Source code |
| fn_log_J_inv | Source code |
| homogenous_coal.log_lh | Man page Source code |
| homogenous_coal.simulate | Man page Source code |
| inhomogenous_coal.log_lh | Man page Source code |
| inhomogenous_coal.simulate | Man page Source code |
| inhomogenous_exp.loglh | Source code |
| inhomogenous_exp.prob | Source code |
| inhomogenous_poi_0.loglh | Source code |
| inv_rates | Man page Source code |
| inv_t_conditional_exp | Source code |
| inv_t_inhomogenous_exp_conditional | Source code |
| log_posterior | Source code |
| logexp_coalescent_loglh | Man page Source code |
| make_move | Source code |
| mcmc2data.frame | Man page Source code |
| model_lh2 | Source code |
| move_update_N | Source code |
| move_update_branch2 | Source code |
| move_update_mid.time | Source code |
| move_update_probs | Source code |
| para.initialiser | Source code |
| para.log_lh | Source code |
| plot.expansionsMCMC | Man page Source code |
| plot_event_summary | Man page Source code |
| plot_mode_summary | Source code |
| plot_mode_traces | Source code |
| plot_persistence | Source code |
| plot_pop_fn | Source code |
| plot_pop_fn_facet | Source code |
| plot_structured_tree | Man page Source code |
| plot_traces | Source code |
| plot_tree | Source code |
| plot_tree_freq | Man page Source code |
| poi_0.loglh | Source code |
| preprocess_phylo | Man page Source code |
| print.expansionsMCMC | Source code |
| print.preprocessedPhy | Source code |
| priorList | Source code |
| prior_mixture | Source code |
| prop_lh | Source code |
| rate_int_sum | Source code |
| rjmcmc | Source code |
| run_expansion_inference | Man page Source code |
| sat.rate | Source code |
| sat.rate.int | Source code |
| sat.rate.int_inv | Source code |
| sat_coalescent_loglh | Man page Source code |
| simulate_clonal_tree | Man page Source code |
| simulate_expansion_phylo | Man page Source code |
| standard_priors | Man page Source code |
| structured_coal.likelihood | Man page Source code |
| structured_coal.simulate | Man page Source code |
| transdimensional.sampler | Source code |
| within_model.sampler | Source code |
