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 |

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