API for outbreaker2
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Global functions
add_convolutions Source code
add_to_function_environment Source code
are_possible_alpha 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
choose_possible_alpha 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
ll_genetic Source code
ll_reporting Source code
ll_timing_infections Source code
ll_timing_sampling Source code
log_sum Source code
log_sum_vec Source code
look_for_trouble Source code
modify_defaults Source code
onAttach 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_store Man page
plot.outbreaker_chains Man page 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
prior_eps Source code
prior_lambda Source code
prior_mu Source code
prior_pi 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 Man page Source code
outbreaker2 documentation built on March 18, 2018, 1:19 p.m.