API for reconhub/outbreaker2
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
| Global functions | |
|---|---|
| .are_possible_alpha | Source code |
| .choose_possible_alpha | Source code |
| .clean_cycles | Source code |
| .decycle_tree | Source code |
| .ll_genetic | Source code |
| .ll_reporting | Source code |
| .ll_timing_infections | Source code |
| .ll_timing_sampling | Source code |
| .onAttach | Source code |
| .prior_eps | Source code |
| .prior_lambda | Source code |
| .prior_mu | Source code |
| .prior_pi | Source code |
| add_convolutions | Source code |
| add_to_function_environment | Source code |
| bind_moves | Source code |
| bind_to_function | Man page Source code |
| can_be_swapped | Source code |
| can_move_alpha | Source code |
| cases_pal | Man page Source code |
| chains_pal | Man page Source code |
| check_i | Source code |
| convolve_log | Source code |
| cpp_are_possible_ancestors | Source code |
| cpp_find_descendents | Source code |
| cpp_find_local_cases | Source code |
| cpp_get_n_mutations | Source code |
| cpp_ll_all | Source code |
| cpp_ll_contact | Source code |
| cpp_ll_genetic | Source code |
| cpp_ll_reporting | Source code |
| cpp_ll_timing | Source code |
| cpp_ll_timing_infections | Source code |
| cpp_ll_timing_sampling | Source code |
| cpp_lookup_sequenced_ancestor | Source code |
| cpp_move_alpha | Source code |
| cpp_move_eps | Source code |
| cpp_move_kappa | Source code |
| cpp_move_lambda | Source code |
| cpp_move_mu | Source code |
| cpp_move_pi | Source code |
| cpp_move_swap_cases | Source code |
| cpp_move_t_inf | Source code |
| cpp_pick_possible_ancestor | Source code |
| cpp_prior_all | Source code |
| cpp_prior_eps | Source code |
| cpp_prior_lambda | Source code |
| cpp_prior_mu | Source code |
| cpp_prior_pi | Source code |
| cpp_sample1 | Source code |
| cpp_swap_cases | Source code |
| create_config | Man page Source code |
| create_param | Man page Source code |
| custom_likelihoods | Man page Source code |
| custom_moves | Man page Source code |
| custom_priors | Man page Source code |
| fake_outbreak | Man page |
| find_descendents | Source code |
| get_cpp_api | Man page Source code |
| log_sum | Source code |
| log_sum_vec | Source code |
| look_for_trouble | Source code |
| modify_defaults | Source code |
| outbreaker | Man page Source code |
| outbreaker_chains | Man page |
| outbreaker_data | Man page Source code |
| outbreaker_find_imports | Source code |
| outbreaker_init_mcmc | Source code |
| outbreaker_mcmc_shape | Source code |
| outbreaker_mcmc_store | Source code |
| outbreaker_move | Source code |
| outbreaker_package | Man page |
| outbreaker_palettes | Man page |
| outbreaker_param | Man page |
| outbreaker_store | Man page |
| plot.outbreaker_chains | Man page Source code |
| print.custom_likelihoods | Man page Source code |
| print.custom_priors | Man page Source code |
| print.outbreaker_chains | Man page Source code |
| print.outbreaker_config | Man page Source code |
| print.outbreaker_moves | Man page Source code |
| ralpha | Source code |
| replace_formals | Source code |
| select_alpha_to_move | Source code |
| sim_ctd | Man page Source code |
| summary.outbreaker_chains | Man page Source code |
