API for mrc-ide/squire
SEIR transmission model of COVID-19
| Global functions | |
|---|---|
| R0_date_particle_filter | Source code |
| Rt_args_list | Source code |
| `%||%` | Source code |
| adjusted_eigen | Man page Source code |
| align | Man page Source code |
| assert_2d | Source code |
| assert_atomic | Source code |
| assert_bounded | Source code |
| assert_custom_class | Source code |
| assert_dataframe | Source code |
| assert_date | Source code |
| assert_decreasing | Source code |
| assert_dim | Source code |
| assert_eq | Source code |
| assert_file_exists | Source code |
| assert_gr | Source code |
| assert_greq | Source code |
| assert_in | Source code |
| assert_increasing | Source code |
| assert_int | Source code |
| assert_le | Source code |
| assert_length | Source code |
| assert_leq | Source code |
| assert_limit | Source code |
| assert_list | Source code |
| assert_logical | Source code |
| assert_matrix | Source code |
| assert_ncol | Source code |
| assert_neg | Source code |
| assert_neq | Source code |
| assert_noduplicates | Source code |
| assert_non_null | Source code |
| assert_not_in | Source code |
| assert_nrow | Source code |
| assert_null | Source code |
| assert_numeric | Source code |
| assert_pos | Source code |
| assert_pos_int | Source code |
| assert_same_length | Source code |
| assert_same_length_multiple | Source code |
| assert_single | Source code |
| assert_single_bounded | Source code |
| assert_single_int | Source code |
| assert_single_logical | Source code |
| assert_single_numeric | Source code |
| assert_single_pos | Source code |
| assert_single_pos_int | Source code |
| assert_single_string | Source code |
| assert_square_matrix | Source code |
| assert_string | Source code |
| assert_symmetric_matrix | Source code |
| assert_vector | Source code |
| beta_est | Man page Source code |
| beta_est_explicit | Man page Source code |
| beta_est_simple | Man page Source code |
| calc_loglikelihood | Source code |
| calc_loglikelihood_drjacoby | Source code |
| calibrate | Man page Source code |
| cases_total_index | Source code |
| check_drjacoby_list | Source code |
| check_drjacoby_loglike | Source code |
| check_drjacoby_logprior | Source code |
| check_pcr_df | Source code |
| check_sero_df | Source code |
| check_squire | Man page Source code |
| check_time_change | Man page Source code |
| compare_output | Man page Source code |
| conduct_replicate | Man page Source code |
| contact_matrices | Man page |
| convert_drjacoby_mcmc | Source code |
| convert_log_likelihood_func_for_drjacoby | Source code |
| convert_log_prior_func_for_drjacoby | Source code |
| country_specific_healthcare_capacity | Man page |
| create_master_chain | Man page Source code |
| default_durations | Man page Source code |
| default_probs | Man page Source code |
| deterministic_model | Man page Source code |
| div_pop | Man page Source code |
| drjacoby_mcmc | Man page Source code |
| elderly_pop | Man page |
| evaluate_Rt_pmcmc | Source code |
| explicit_SEIR | Source code |
| explicit_SEIR_deterministic | Source code |
| explicit_model | Man page Source code |
| extract_ICU_occ | Man page Source code |
| extract_deaths | Man page Source code |
| extract_hospital_occ | Man page Source code |
| extract_infection_incidence | Man page Source code |
| format_deterministic_output | Man page Source code |
| format_output | Man page Source code |
| format_output_simple_model | Man page Source code |
| get_ICU_bed_capacity | Source code |
| get_elderly_population | Man page Source code |
| get_healthcare_capacity | Man page Source code |
| get_hosp_bed_capacity | Source code |
| get_lmic_countries | Man page Source code |
| get_mixing_matrix | Man page Source code |
| get_population | Man page Source code |
| income_group | Man page |
| income_strata_healthcare_capacity | Man page |
| init_check | Man page Source code |
| init_check_explicit | Man page Source code |
| intervention_dates_for_odin | Man page Source code |
| interventions_unique | Source code |
| is_ptr_null | Source code |
| jc_prop_update | Man page Source code |
| less_basic_model_for_js | Source code |
| ll_nbinom | Source code |
| matrix_check | Man page Source code |
| matrix_set | Man page Source code |
| matrix_set_explicit | Source code |
| nice_format | Source code |
| numeric_to_offset | Source code |
| numeric_to_start_date | Source code |
| odin_index | Source code |
| odin_is_discrete | Source code |
| odin_sv | Source code |
| offset_to_numeric | Source code |
| offset_to_start_date | Source code |
| parameters_explicit_SEEIR | Man page Source code |
| parameters_simple_SEEIR | Man page Source code |
| parse_country_population_mixing_matrix | Source code |
| parse_country_severity | Man page Source code |
| parse_durations | Source code |
| particle_filter | Man page Source code |
| particle_filter_data | Man page Source code |
| particle_run_model | Source code |
| plot.squire_pmcmc | Source code |
| plot.squire_pmcmc_list | Source code |
| plot.squire_scan | Man page Source code |
| plot.squire_simulation | Man page Source code |
| plot_particles | Source code |
| plot_pmcmc_sample | Source code |
| plot_sample_grid_search | Source code |
| pmcmc | Man page Source code |
| population | Man page |
| pos_num | Man page Source code |
| print.squire_simulation | Man page Source code |
| process_contact_matrix | Man page Source code |
| process_contact_matrix_scaled_age | Man page Source code |
| projection_inputs | Source code |
| projection_plotting | Man page Source code |
| projections | Man page Source code |
| propose_parameters | Source code |
| reflect_proposal | Source code |
| resample | Source code |
| run_deterministic_SEIR_model | Man page Source code |
| run_deterministic_comparison | Man page Source code |
| run_drjacoby_mcmc | Source code |
| run_explicit_SEEIR_model | Man page Source code |
| run_mcmc_chain | Source code |
| run_mcmc_chain_gibbs | Source code |
| run_particle_filter | Man page Source code |
| run_simple_SEEIR_model | Man page Source code |
| sample_3d_grid_scan | Man page Source code |
| sample_drjacoby | Man page Source code |
| sample_grid_scan | Man page Source code |
| sample_pmcmc | Man page Source code |
| scale_log_weights | Source code |
| scan_R0_date | Man page Source code |
| scan_R0_date_Meff | Man page Source code |
| simple_SEIR | Source code |
| simple_model | Man page Source code |
| squire_file | Source code |
| squire_simulation_plot_prep | Source code |
| start_date_to_offset | Source code |
| summary.squire_pmcmc | Source code |
| summary.squire_pmcmc_list | Source code |
| summary.squire_simulation | Man page Source code |
| systematic_resample | Source code |
| t0_variables | Source code |
| trigger_projections | Man page Source code |
