| %*%,struc,struc-method |
Man page
|
| %+% |
Man page
|
| %_% |
Man page
|
| %~% |
Man page
|
| *,struc,struc-method |
Man page
|
| +,struc,struc-method |
Man page
|
| .onLoad |
Source code
|
| .onUnload |
Source code
|
| McMasterPandemic |
Man page
|
| McMasterPandemic-package |
Man page
|
| `%+%` |
Source code
|
| `%_%` |
Source code
|
| `%||%` |
Source code
|
| `%~%` |
Source code
|
| `pars_base_sim<-.flexmodel` |
Source code
|
| `pars_base_sim<-` |
Source code
|
| add_conv |
Man page
Source code
|
| add_d_log |
Man page
Source code
|
| add_error_dist |
Man page
Source code
|
| add_factr |
Man page
Source code
|
| add_lag_diff |
Man page
Source code
|
| add_lag_diff_uneven |
Man page
Source code
|
| add_linearized_outflow |
Man page
Source code
|
| add_opt_params |
Man page
Source code
|
| add_opt_tv_params |
Man page
Source code
|
| add_outflow |
Man page
Source code
|
| add_parallel_accumulators |
Man page
Source code
|
| add_piece_wise |
Man page
Source code
|
| add_pow |
Man page
Source code
|
| add_rate |
Man page
Source code
|
| add_sim_report_expr |
Man page
Source code
|
| add_state_mappings |
Man page
Source code
|
| add_state_param_sum |
Man page
Source code
|
| add_tmb_indices |
Man page
Source code
|
| add_updated_vaxrate |
Man page
Source code
|
| adjust_params |
Source code
|
| adjust_symbols |
Source code
|
| ageify |
Man page
Source code
|
| aggregate.pansim |
Man page
|
| aggregate_agecats |
Man page
Source code
|
| all_except |
Man page
Source code
|
| all_in |
Man page
|
| alt_group |
Man page
Source code
|
| any_var |
Man page
Source code
|
| as.character.struc |
Man page
Source code
|
| as.flexmodel |
Man page
Source code
|
| as.flexmodel.flexmodel_obs_error |
Source code
|
| as.flexmodel.flexmodel_to_calibrate |
Source code
|
| as.flexmodel_obs_error |
Man page
Source code
|
| as.flexmodel_obs_error.flexmodel_to_calibrate |
Source code
|
| as.flexmodel_one_step |
Man page
Source code
|
| as.flexmodel_one_step.flexmodel |
Source code
|
| as.flexmodel_to_calibrate |
Man page
Source code
|
| as.matrix.struc |
Man page
Source code
|
| as.struc |
Man page
Source code
|
| as_data_frame_no_row_names |
Source code
|
| as_vector_no_attr |
Source code
|
| assert_len1_char |
Source code
|
| assert_len1_int |
Source code
|
| asymp_cat |
Man page
|
| avail_for_conv |
Man page
Source code
|
| avail_for_expr |
Man page
Source code
|
| avail_for_factr |
Man page
Source code
|
| avail_for_lag |
Man page
Source code
|
| avail_for_pow |
Man page
Source code
|
| avail_for_rate |
Man page
Source code
|
| avail_for_sum |
Man page
Source code
|
| badness |
Source code
|
| bbmle_flexmodel |
Man page
Source code
|
| bd |
Man page
|
| block |
Source code
|
| bundle_def |
Source code
|
| calc_conv |
Man page
Source code
|
| calc_reports |
Source code
|
| calc_variant_adjustment |
Source code
|
| calibrate |
Man page
Source code
|
| calibrate_comb |
Man page
Source code
|
| calibrate_flexmodel |
Man page
Source code
|
| capitalize |
Source code
|
| changing_ratemat_elements |
Man page
Source code
|
| check_age_cat_compatibility |
Man page
Source code
|
| check_contact_rate_setting |
Man page
Source code
|
| check_def |
Source code
|
| check_def.def_logical |
Source code
|
| check_dots |
Source code
|
| check_from_to |
Source code
|
| check_in_rate_fun |
Source code
|
| check_len |
Source code
|
| check_len_bounds |
Source code
|
| check_spec_ver_archived |
Source code
|
| check_var_names |
Source code
|
| colSums,struc-method |
Man page
|
| col_multiply |
Man page
Source code
|
| comb_sub |
Man page
|
| combine_rates |
Source code
|
| compare_grads |
Man page
Source code
|
| compare_hessians |
Man page
Source code
|
| compare_sims |
Man page
Source code
|
| compare_sims_cbind |
Man page
Source code
|
| compare_sims_diffmat |
Man page
Source code
|
| compare_sims_plot |
Man page
Source code
|
| compare_sims_unlist |
Man page
Source code
|
| complement |
Man page
Source code
|
| compute_factr_from_indices |
Source code
|
| compute_factrs |
Source code
|
| compute_num_iters |
Source code
|
| compute_rate_from_indices |
Source code
|
| compute_rates |
Source code
|
| concatenated_state_vector |
Man page
Source code
|
| condense |
Man page
|
| condense.pansim |
Man page
|
| condense_age |
Man page
Source code
|
| condense_flexmodel |
Man page
Source code
|
| condense_names |
Source code
|
| condense_params_vax |
Man page
Source code
|
| condense_state |
Man page
Source code
|
| condense_vax |
Man page
Source code
|
| condensed_sim_report_names |
Source code
|
| const_named_vector |
Man page
Source code
|
| contract_struc |
Source code
|
| conv_indices |
Source code
|
| convergence_info |
Man page
Source code
|
| convergence_info.default |
Source code
|
| convergence_info.flexmodel_bbmle |
Source code
|
| convergence_info.flexmodel_calibrated |
Source code
|
| convergence_info.flexmodel_failed_calibration |
Source code
|
| cross |
Source code
|
| cross_mat |
Man page
Source code
|
| cryptic_cat |
Man page
|
| date_count |
Source code
|
| date_logist |
Source code
|
| deprecated_simulation_functions |
Man page
|
| describe_params |
Man page
|
| dev_is_tikz |
Man page
Source code
|
| dfs |
Source code
|
| dim,struc-method |
Man page
|
| dim_hyperparam |
Source code
|
| discountGap |
Source code
|
| disease_free_indices |
Source code
|
| disease_free_state |
Source code
|
| distribute_counts |
Man page
Source code
|
| do_debug_plot |
Source code
|
| do_step |
Man page
Source code
|
| do_variant |
Source code
|
| eval_formulas |
Source code
|
| exclude_states |
Source code
|
| exists_opt_params |
Source code
|
| expand_names |
Man page
Source code
|
| expand_params_S0 |
Man page
Source code
|
| expand_params_age |
Man page
Source code
|
| expand_params_desc_age |
Man page
Source code
|
| expand_params_desc_variant |
Man page
Source code
|
| expand_params_desc_vax |
Man page
Source code
|
| expand_params_mistry |
Man page
Source code
|
| expand_params_nb_disp |
Source code
|
| expand_params_normal_sd |
Source code
|
| expand_params_variant |
Man page
Source code
|
| expand_params_vax |
Man page
Source code
|
| expand_state_age |
Man page
Source code
|
| expand_state_vax |
Man page
Source code
|
| expand_stateval_testing |
Man page
Source code
|
| expand_struc |
Man page
Source code
|
| extend_end_date |
Man page
Source code
|
| extend_end_date.flexmodel |
Source code
|
| extend_end_date.flexmodel_calibrated |
Source code
|
| factor_table |
Source code
|
| factory_fresh_macpan_options |
Man page
Source code
|
| factr |
Source code
|
| factr_algo |
Source code
|
| factr_indices |
Source code
|
| feature_check |
Man page
Source code
|
| ff |
Source code
Source code
|
| fill_edge_values |
Source code
|
| filter_loss_params |
Source code
|
| final_sim_report_names |
Source code
|
| final_state_ratio |
Man page
Source code
|
| final_state_vector |
Man page
Source code
|
| find_operators |
Source code
|
| find_pos_grep |
Source code
|
| find_vec_indices |
Source code
|
| first_letter_cap |
Source code
|
| fitted.flexmodel_calibrated |
Man page
Source code
|
| fix_pars |
Man page
Source code
|
| fix_stored |
Man page
Source code
|
| flexmodel |
Man page
Source code
|
| forecast_ensemble |
Man page
Source code
|
| forecast_sim |
Man page
Source code
|
| getData |
Man page
Source code
|
| get_DE_lims |
Source code
|
| get_GI_moments |
Man page
Source code
|
| get_Gbar |
Man page
Source code
|
| get_R0 |
Man page
Source code
|
| get_age |
Source code
|
| get_and_set_model_parameters |
Man page
|
| get_attr |
Source code
|
| get_dim |
Source code
|
| get_doses_per_day |
Man page
Source code
|
| get_evec |
Man page
Source code
|
| get_factr_formula |
Source code
|
| get_factr_info |
Source code
|
| get_factr_initial_value |
Source code
|
| get_form_dim |
Source code
|
| get_hyperparam_list |
Source code
|
| get_indices_per_rate |
Source code
|
| get_kernel_moments |
Man page
Source code
|
| get_macpan_options |
Man page
Source code
|
| get_n_factors |
Source code
|
| get_n_products |
Source code
|
| get_n_variables |
Source code
|
| get_opt_pars |
Man page
Source code
|
| get_params_timevar_impute |
Source code
|
| get_params_timevar_orig |
Source code
|
| get_params_timevar_series |
Source code
|
| get_r |
Man page
Source code
|
| get_rate_factors |
Source code
|
| get_rate_formula |
Source code
|
| get_rate_from |
Source code
|
| get_rate_info |
Source code
|
| get_rate_state_dependent |
Source code
|
| get_rate_sum_dependent |
Source code
|
| get_rate_time_varying |
Source code
|
| get_rate_to |
Source code
|
| get_rate_vars |
Source code
|
| get_rates |
Source code
|
| get_rates_with_vars |
Source code
|
| get_schedule |
Source code
|
| get_sum_indices |
Source code
|
| get_sum_info |
Source code
|
| get_sum_initial_value |
Source code
|
| get_sum_summands |
Source code
|
| get_tmb_data |
Source code
|
| get_tmb_hist |
Source code
|
| get_tmb_hist_stoch |
Source code
|
| get_tmb_params |
Source code
|
| get_tmb_report |
Source code
|
| get_tmb_simulate |
Source code
|
| get_tmb_tv_mult |
Source code
|
| get_var_counts |
Source code
|
| get_var_indx |
Source code
|
| get_var_list |
Source code
|
| get_var_modifiers |
Source code
|
| get_variables |
Source code
|
| get_vax |
Source code
|
| get_vax_model_type |
Source code
|
| gradfun |
Man page
Source code
|
| has_age |
Source code
|
| has_inflow |
Source code
|
| has_testing |
Source code
|
| has_time_varying |
Source code
|
| has_vacc |
Source code
|
| has_vax |
Source code
|
| has_zeta |
Source code
|
| hyperparam_to_vec |
Source code
|
| index_sep |
Man page
Source code
|
| init_def |
Source code
|
| init_def.def_character |
Source code
|
| init_def.def_dataframe |
Source code
|
| init_def.def_double |
Source code
|
| init_def.def_formula |
Source code
|
| init_def.def_integer |
Source code
|
| init_def.def_list |
Source code
|
| init_def.def_logical |
Source code
|
| init_def.def_nlist |
Source code
|
| init_def.def_struc |
Source code
|
| init_model |
Man page
Source code
|
| initial_population |
Man page
Source code
|
| initial_population_indices |
Source code
|
| initial_ratemat |
Man page
Source code
|
| initial_sim_report_names |
Source code
|
| initial_state_vector |
Man page
Source code
|
| initialization_mapping_indices |
Source code
|
| initialize_opt_params |
Man page
Source code
|
| initialize_opt_tv_params |
Man page
Source code
|
| initialize_piece_wise |
Man page
Source code
|
| int0_to_0 |
Source code
|
| intermediate_sim_report_names |
Source code
|
| inverse |
Man page
Source code
|
| invlink_trans |
Man page
Source code
|
| is_1by1 |
Man page
Source code
|
| is_empty |
Source code
|
| is_fitted_by_bbmle |
Source code
|
| is_len1_char |
Source code
|
| is_len1_int |
Source code
|
| kappaGap |
Source code
|
| kernelMoments |
Source code
|
| kronecker,struc,struc-method |
Man page
|
| lag_diff_indices |
Source code
|
| lag_diff_uneven_indices |
Source code
|
| layered_zero_state |
Man page
Source code
|
| legacy |
Source code
|
| legacy_break_dates |
Source code
|
| legacy_sim_fun |
Source code
|
| legacy_time_args |
Source code
|
| length_tv_mult_series |
Source code
|
| lin_state_timevar_params |
Source code
|
| linearized_param_indices |
Source code
|
| linearized_params |
Source code
|
| lookup_pairwise |
Source code
|
| loss_params |
Source code
|
| make_ageified_model |
Man page
Source code
|
| make_base_model |
Man page
Source code
|
| make_beta |
Man page
Source code
|
| make_betavec |
Man page
Source code
|
| make_def_function |
Source code
|
| make_delay_kernel |
Man page
Source code
|
| make_hello_world_model |
Man page
Source code
|
| make_jac |
Man page
Source code
|
| make_latex_flows |
Source code
|
| make_latex_rates |
Source code
|
| make_latex_symbols |
Source code
|
| make_nested_indices |
Source code
|
| make_omicron_model |
Man page
Source code
|
| make_ratemat |
Man page
Source code
|
| make_sir_model |
Man page
Source code
|
| make_state |
Man page
Source code
|
| make_test_posvec |
Man page
Source code
|
| make_test_wtsvec |
Man page
Source code
|
| make_vaccination_model |
Man page
Source code
|
| make_vaxrate |
Man page
Source code
|
| mat |
Man page
Source code
|
| mat_rate |
Man page
Source code
|
| merge_named_vec_attr |
Man page
Source code
|
| merge_named_vectors |
Man page
Source code
|
| mk_Nvec |
Man page
Source code
|
| mk_agecats |
Man page
Source code
|
| mk_contact_rate_setting |
Man page
Source code
|
| mk_mistry_Nvec |
Man page
Source code
|
| mk_pmat |
Man page
Source code
|
| mk_vaxcats |
Man page
Source code
|
| mk_zero_vec |
Source code
|
| mle_fun |
Man page
Source code
|
| model |
Source code
|
| names_or_values |
Source code
|
| nlist |
Man page
Source code
|
| nlminb_flexmodel |
Man page
Source code
|
| non_expanded_states |
Man page
|
| norm_vec |
Source code
|
| null_to_0 |
Source code
|
| null_to_char0 |
Source code
|
| null_to_charNA |
Source code
|
| null_to_int0 |
Source code
|
| null_to_intNA |
Source code
|
| null_to_log0 |
Source code
|
| null_to_logNA |
Source code
|
| null_to_num0 |
Source code
|
| null_to_numNA |
Source code
|
| num_prod |
Source code
|
| omit_empty |
Source code
|
| ont_all |
Man page
|
| ont_all_sub |
Man page
|
| ont_cal1 |
Man page
|
| ont_cal_2brks |
Man page
|
| ont_cal_mob1 |
Man page
|
| opt_obj |
Man page
Source code
|
| optim_flexmodel |
Man page
Source code
|
| outflow |
Source code
|
| outflow_indices |
Source code
|
| pad_convs |
Source code
|
| pad_lag_diffs |
Source code
|
| parallel_accumulators |
Source code
|
| pars_base_init |
Man page
Source code
|
| pars_base_init.flexmodel_calibrated |
Source code
|
| pars_base_init.flexmodel_to_calibrate |
Source code
|
| pars_base_opt |
Man page
Source code
|
| pars_base_opt.flexmodel_calibrated |
Source code
|
| pars_base_sim |
Man page
Source code
|
| pars_base_sim.flexmodel |
Source code
|
| pars_base_sim<- |
Man page
|
| pars_infer_conf |
Man page
Source code
|
| pars_infer_init |
Man page
Source code
|
| pars_infer_init.flexmodel_calibrated |
Source code
|
| pars_infer_init.flexmodel_to_calibrate |
Source code
|
| pars_infer_opt |
Man page
Source code
|
| pars_infer_opt.flexmodel_calibrated |
Source code
|
| pars_time_opt |
Man page
Source code
|
| pars_time_opt.flexmodel_calibrated |
Source code
|
| pars_time_series |
Man page
Source code
|
| pars_time_series.flexmodel |
Source code
|
| pars_time_sim |
Man page
Source code
|
| pars_time_sim.flexmodel |
Source code
|
| pars_time_spec |
Man page
Source code
|
| pars_time_spec.flexmodel |
Source code
|
| parse_and_resolve_loss_form |
Source code
|
| parse_and_resolve_opt_form |
Source code
|
| parse_formula |
Man page
Source code
|
| parse_loss_form |
Source code
|
| parse_name_sum |
Source code
|
| parse_opt_form |
Source code
|
| parse_opt_param |
Source code
|
| penultimate_state_vector |
Man page
Source code
|
| pfun |
Source code
|
| pivot |
Man page
|
| plot.fit_pansim |
Man page
|
| plot.pansim |
Man page
|
| plot.predict_pansim |
Man page
|
| plot_res_by_age |
Man page
|
| plot_res_by_state |
Man page
|
| pluralizer |
Source code
|
| pop_pred_samp |
Source code
|
| pow |
Source code
|
| pow_indices |
Source code
|
| predict.fit_pansim |
Man page
|
| prep_res_for_plotting |
Man page
Source code
|
| print.pansim |
Source code
|
| print.params_pansim |
Man page
|
| print_globals |
Source code
|
| prod,struc-method |
Man page
|
| profile_obj_fun |
Source code
|
| profile_obj_fun.flexmodel_to_calibrate |
Source code
|
| put_attr |
Source code
|
| pwise |
Source code
|
| rExp |
Man page
Source code
|
| r_mode |
Man page
Source code
|
| r_tmb_comparable |
Man page
Source code
|
| rate |
Source code
|
| rate_matrix_lookup |
Source code
|
| rate_summary |
Man page
Source code
|
| rateform_as_char |
Man page
Source code
|
| ratemat_indices |
Source code
|
| read_params |
Man page
Source code
|
| recompress |
Source code
|
| reduce_rates |
Source code
|
| regen_model |
Source code
|
| regen_rates |
Source code
|
| regen_sim_report_expr |
Source code
|
| remove_opt_param |
Source code
|
| rename_params |
Source code
|
| rep_rate |
Man page
Source code
|
| repair_names_age |
Man page
Source code
|
| reset_error_dist |
Man page
Source code
|
| reset_spec_version |
Man page
Source code
|
| resolve_param |
Source code
|
| restore |
Man page
Source code
|
| rmult |
Source code
|
| rowSums,struc-method |
Man page
|
| run_sim |
Man page
Source code
|
| run_sim_ageify |
Man page
Source code
|
| run_sim_break |
Man page
Source code
|
| run_sim_break2 |
Source code
|
| run_sim_decay |
Source code
|
| run_sim_loglin |
Man page
Source code
|
| run_sim_mobility |
Man page
Source code
|
| run_sim_range |
Man page
Source code
|
| same_dims |
Man page
Source code
|
| scal |
Man page
Source code
|
| set_hyperparam_dims |
Source code
|
| set_spec_version |
Man page
Source code
|
| severe_cat |
Man page
|
| show_ratemat |
Man page
Source code
|
| sim_report_expr |
Source code
|
| sim_report_expr_indices |
Source code
|
| simple_mult |
Source code
|
| simulate.flexmodel |
Man page
Source code
|
| simulate_changing_ratemat_elements |
Man page
Source code
|
| simulate_ensemble |
Man page
Source code
|
| simulate_state_vector |
Man page
Source code
|
| simulation_condensed |
Man page
Source code
|
| simulation_dates |
Source code
|
| simulation_fitted |
Man page
Source code
|
| simulation_history |
Man page
Source code
|
| smart_round |
Source code
|
| spec_check |
Man page
Source code
|
| spec_ver_btwn |
Man page
Source code
|
| spec_ver_eq |
Man page
Source code
|
| spec_ver_gt |
Man page
Source code
|
| spec_ver_lt |
Man page
Source code
|
| spec_version |
Man page
Source code
|
| state_dependent_rates |
Source code
|
| state_mapping_indices |
Source code
|
| state_param_sum |
Source code
|
| state_round |
Source code
|
| statefun |
Source code
|
| struc |
Man page
Source code
|
| struc-class |
Man page
|
| struc_block |
Man page
Source code
|
| struc_eval |
Man page
Source code
|
| struc_expanded |
Man page
Source code
|
| struc_expanded-class |
Man page
|
| struc_stretch |
Man page
Source code
|
| structure_state_vector |
Source code
|
| sub_vars |
Source code
|
| sum,struc-method |
Man page
|
| sum_dependent_rates |
Source code
|
| sum_indices |
Source code
|
| summary.params_pansim |
Man page
|
| t,struc-method |
Man page
|
| test_accumulators |
Man page
|
| test_extensions |
Man page
|
| testify |
Man page
Source code
|
| texify |
Man page
Source code
|
| thin |
Source code
|
| tibble_row_to_named_vec |
Man page
Source code
|
| time_varying_rates |
Source code
|
| time_wrap |
Man page
Source code
|
| timevar_order_indices |
Source code
|
| tmb_fun |
Man page
Source code
|
| tmb_fun_args |
Man page
Source code
|
| tmb_indices |
Man page
Source code
|
| tmb_map_indices |
Source code
|
| tmb_mode |
Man page
Source code
|
| tmb_observed_data |
Source code
|
| tmb_opt_form |
Source code
|
| tmb_opt_params |
Source code
|
| tmb_param_names |
Source code
|
| tmb_params |
Man page
Source code
|
| tmb_params_init |
Source code
|
| tmb_params_trans |
Man page
Source code
|
| topological_sort |
Man page
Source code
|
| transKernel |
Source code
|
| trans_state_vars |
Man page
Source code
|
| uniroot_target |
Source code
|
| unlist_params |
Source code
|
| unpack |
Man page
Source code
|
| untestify_statenames |
Source code
|
| update.list |
Source code
|
| update.params_pansim |
Man page
|
| update_condense_map |
Man page
Source code
|
| update_contact_rate_setting |
Man page
Source code
|
| update_debug_hist |
Source code
|
| update_disease_free_state |
Man page
Source code
|
| update_error_dist |
Man page
Source code
|
| update_foi |
Man page
Source code
|
| update_full_condensation_map |
Source code
|
| update_initial_state |
Man page
Source code
|
| update_linearized_params |
Man page
Source code
|
| update_loss_params |
Man page
Source code
|
| update_observed |
Man page
Source code
|
| update_opt_params |
Man page
Source code
|
| update_opt_tv_params |
Man page
Source code
|
| update_opt_vec |
Source code
|
| update_params |
Man page
Source code
|
| update_params_calibrated |
Source code
|
| update_params_mistry |
Man page
Source code
|
| update_piece_wise |
Man page
Source code
|
| update_ranef_params |
Man page
Source code
|
| update_ratemat |
Source code
|
| update_simulation_bounds |
Man page
Source code
|
| update_tmb_indices |
Man page
Source code
|
| update_tmb_indices.flexmodel |
Source code
|
| update_tmb_indices.flexmodel_to_calibrate |
Source code
|
| v2d |
Man page
Source code
|
| valid_dim_hyperparam |
Source code
|
| variable_regex |
Source code
|
| vec |
Man page
|
| vec_factr |
Man page
Source code
|
| vec_rate |
Man page
Source code
|
| vis_model |
Man page
Source code
|
| which_time_varying_rates |
Source code
|
| which_unwraped |
Source code
|
| wrap_exact |
Man page
Source code
|
| wrap_paren |
Source code
|
| write_params |
Man page
Source code
|
