├── .Rbuildignore ├── .github ├── .gitignore ├── R-version └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── test_environment.yaml ├── .gitignore ├── CONTRIBUTING.md ├── ChangeLog.md ├── DESCRIPTION ├── LICENSE ├── Makefile ├── McMasterPandemic.Rproj ├── NAMESPACE ├── R ├── afuns.R ├── ageify.R ├── avail_for.R ├── calibrate.R ├── constructing_vectors.R ├── data.R ├── expandify.R ├── flexmodel_calibrate.R ├── flexmodel_convert.R ├── flexmodel_parameters.R ├── flexmodel_simulate.R ├── flexstruc.R ├── getters_for_devs.R ├── globals.R ├── impsamp.R ├── kfuns.R ├── methods.R ├── models.R ├── models_IP.R ├── names_and_strings.R ├── opt_info.R ├── pkgname.R ├── sim_funs.R ├── specs.R ├── structure.R ├── testify.R ├── tmb.R ├── tmb_indices.R ├── tmbutils.R ├── topological_sort.R ├── utils.R └── zzz.R ├── README.md ├── ROADMAP.md ├── TODO.md ├── assets ├── architecture.drawio ├── architecture.png ├── architecture.svg ├── roadmap.drawio ├── roadmap.svg ├── target_architecture.drawio ├── target_architecture.png └── target_architecture.svg ├── data ├── ONcalib.rda ├── ONcalib_2brks.rda ├── ONcalib_mob1_2020Jun01.rda ├── ONdata_2020Jun01.rda └── mobility_comb.rda ├── dockerfile ├── docs ├── .nojekyll ├── 404.html ├── CONTRIBUTING.html ├── ChangeLog.html ├── ROADMAP.html ├── TODO.html ├── articles │ ├── calibration.html │ ├── calibration_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── farr.html │ ├── farr_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── flex_intro.html │ ├── flex_intro_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── flex_specs.html │ ├── flex_specs_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── getting_started.html │ ├── getting_started.pdf │ ├── getting_started_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── index.html │ ├── model.html │ ├── model_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── testing_flow.html │ ├── testing_flow_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── vaxify_implementation.html │ └── vaxify_implementation_files │ │ └── accessible-code-block-0.0.1 │ │ └── empty-anchor.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── McMasterPandemic-package.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── add_conv.html │ ├── add_d_log.html │ ├── add_factr.html │ ├── add_lag_diff.html │ ├── add_opt_params.html │ ├── add_outflow.html │ ├── add_parallel_accumulators.html │ ├── add_pow.html │ ├── add_rate.html │ ├── add_sim_report_expr.html │ ├── add_state_mappings.html │ ├── add_state_param_sum.html │ ├── add_updated_vaxrate.html │ ├── aggregate.pansim.html │ ├── aggregate_agecats.html │ ├── as.character.struc.html │ ├── as.flexmodel.html │ ├── as.matrix.struc.html │ ├── avail_for.html │ ├── calc_conv.html │ ├── calibrate.html │ ├── calibrate_comb.html │ ├── calibrate_flexmodel.html │ ├── check_age_cat_compatibility.html │ ├── check_contact_rate_setting.html │ ├── col_multiply.html │ ├── compare_grads.html │ ├── compare_sims.html │ ├── complement.html │ ├── condense.html │ ├── condense.pansim.html │ ├── condense_age.html │ ├── condense_params_vax.html │ ├── condense_state.html │ ├── condense_vax.html │ ├── const_named_vector.html │ ├── cross_mat.html │ ├── deprecated_simulation_functions.html │ ├── describe_params.html │ ├── dev_is_tikz.html │ ├── distribute_counts.html │ ├── do_step.html │ ├── expand_contract_struc.html │ ├── expand_names.html │ ├── expand_params_S0.html │ ├── expand_params_age.html │ ├── expand_params_desc_age.html │ ├── expand_params_desc_variant.html │ ├── expand_params_desc_vax.html │ ├── expand_params_mistry.html │ ├── expand_params_variant.html │ ├── expand_params_vax.html │ ├── expand_state_age-1.png │ ├── expand_state_age-2.png │ ├── expand_state_age.html │ ├── expand_state_vax.html │ ├── expand_stateval_testing.html │ ├── extend_end_date.html │ ├── factory_fresh_macpan_options.html │ ├── fix_pars.html │ ├── fix_stored.html │ ├── flexmodel.html │ ├── forecast_ensemble.html │ ├── forecast_sim.html │ ├── getData.html │ ├── get_GI_moments.html │ ├── get_Gbar.html │ ├── get_R0.html │ ├── get_and_set_model_parameters.html │ ├── get_doses_per_day.html │ ├── get_evec.html │ ├── get_kernel_moments.html │ ├── get_macpan_options.html │ ├── get_opt_pars.html │ ├── get_r.html │ ├── gradfun.html │ ├── index.html │ ├── index_sep.html │ ├── initial_population.html │ ├── invlink_trans.html │ ├── is_1by1.html │ ├── layered_zero_state.html │ ├── macpan_regex_helpers.html │ ├── make_ageified_model.html │ ├── make_base_model.html │ ├── make_beta.html │ ├── make_betavec.html │ ├── make_delay_kernel.html │ ├── make_hello_world_model.html │ ├── make_jac.html │ ├── make_omicron_model.html │ ├── make_ratemat-1.png │ ├── make_ratemat.html │ ├── make_sir_model.html │ ├── make_state.html │ ├── make_test_wtsvec-1.png │ ├── make_test_wtsvec-2.png │ ├── make_test_wtsvec-3.png │ ├── make_test_wtsvec.html │ ├── make_vaccination_model.html │ ├── make_vaxrate.html │ ├── mat_rate.html │ ├── merge_named_vec_attr.html │ ├── merge_named_vectors.html │ ├── mk_Nvec.html │ ├── mk_agecats.html │ ├── mk_contact_rate_setting.html │ ├── mk_mistry_Nvec.html │ ├── mk_pmat.html │ ├── mk_vaxcats.html │ ├── mle_fun.html │ ├── nlist.html │ ├── non_expanded_states.html │ ├── ontario_data.html │ ├── ontario_fits.html │ ├── opt_obj.html │ ├── optim_flexmodel.html │ ├── parse_formula.html │ ├── pivot.html │ ├── plot.pansim.html │ ├── plot.predict_pansim-1.png │ ├── plot.predict_pansim-2.png │ ├── plot.predict_pansim-3.png │ ├── plot.predict_pansim-4.png │ ├── plot.predict_pansim.html │ ├── plot_res_by_age.html │ ├── plot_res_by_state.html │ ├── predict.fit_pansim-1.png │ ├── predict.fit_pansim.html │ ├── prep_res_for_plotting.html │ ├── print.params_pansim.html │ ├── rExp.html │ ├── r_mode.html │ ├── r_tmb_comparable.html │ ├── rate_summary.html │ ├── read_params.html │ ├── rep_rate.html │ ├── repair_names_age.html │ ├── restore.html │ ├── run_sim-1.png │ ├── run_sim.html │ ├── run_sim_ageify.html │ ├── run_sim_break-1.png │ ├── run_sim_break-2.png │ ├── run_sim_break.html │ ├── run_sim_loglin.html │ ├── run_sim_mobility.html │ ├── run_sim_range-1.png │ ├── run_sim_range.html │ ├── same_dims.html │ ├── set_spec_version.html │ ├── show_ratemat-1.png │ ├── show_ratemat-2.png │ ├── show_ratemat.html │ ├── simulate_ensemble.html │ ├── simulation_history.html │ ├── spec_check.html │ ├── spec_version.html │ ├── string_concatenation_operators.html │ ├── struc-class.html │ ├── struc.html │ ├── struc_block.html │ ├── struc_eval.html │ ├── struc_expanded-class.html │ ├── struc_expanded.html │ ├── struc_stretch.html │ ├── summary.params_pansim.html │ ├── testify-1.png │ ├── testify.html │ ├── texify.html │ ├── tibble_row_to_named_vec.html │ ├── time_wrap.html │ ├── tmb_fun.html │ ├── tmb_mode.html │ ├── tmb_params.html │ ├── tmb_params_trans.html │ ├── topological_sort.html │ ├── trans_state_vars.html │ ├── unpack.html │ ├── update.params_pansim.html │ ├── update_condense_map.html │ ├── update_contact_rate_setting.html │ ├── update_disease_free_state.html │ ├── update_error_dist.html │ ├── update_foi.html │ ├── update_initial_state.html │ ├── update_linearized_params.html │ ├── update_loss_params.html │ ├── update_observed.html │ ├── update_params.html │ ├── update_params_mistry.html │ ├── update_piece_wise.html │ ├── update_ranef_params.html │ ├── update_simulation_bounds.html │ ├── update_tmb_indices.html │ ├── v2d.html │ ├── vec_factr.html │ ├── vec_rate.html │ ├── vis_model-1.png │ ├── vis_model-2.png │ ├── vis_model-3.png │ ├── vis_model.html │ └── write_params.html ├── rename.html └── sitemap.xml ├── dottarget.mk ├── git_push ├── McMasterReport.pdf ├── ageify.html ├── ageify_phac-report.html ├── demo_vaccination_switch.png ├── epiestim.Rout.pdf ├── explore_caltest.pdf ├── ont_fac_1011_fit.rds ├── ontario_R0_cal1.rds ├── ontario_calibration.html ├── ontario_calibration_report.html └── plot_caltest.Rout.pdf ├── inst ├── params │ ├── CI_base.csv │ ├── CI_updApr1.csv │ ├── ICU1.csv │ ├── ICU_diffs.csv │ ├── PHAC.csv │ ├── PHAC_testify.csv │ ├── midas_estimates.csv │ ├── midas_estimates_ali.csv │ ├── mistry-cmats │ │ ├── AB_F_community_setting_85.csv │ │ ├── AB_F_household_setting_85.csv │ │ ├── AB_F_school_setting_85.csv │ │ ├── AB_F_work_setting_85.csv │ │ ├── AB_M_overall_contact_matrix_85.csv │ │ ├── AB_age_distribution_85.csv │ │ ├── BC_F_community_setting_85.csv │ │ ├── BC_F_household_setting_85.csv │ │ ├── BC_F_school_setting_85.csv │ │ ├── BC_F_work_setting_85.csv │ │ ├── BC_M_overall_contact_matrix_85.csv │ │ ├── BC_age_distribution_85.csv │ │ ├── CA_F_community_setting_85.csv │ │ ├── CA_F_household_setting_85.csv │ │ ├── CA_F_school_setting_85.csv │ │ ├── CA_F_work_setting_85.csv │ │ ├── CA_M_overall_contact_matrix_85.csv │ │ ├── CA_age_distribution_85.csv │ │ ├── MB_F_community_setting_85.csv │ │ ├── MB_F_household_setting_85.csv │ │ ├── MB_F_school_setting_85.csv │ │ ├── MB_F_work_setting_85.csv │ │ ├── MB_M_overall_contact_matrix_85.csv │ │ ├── MB_age_distribution_85.csv │ │ ├── NB_F_community_setting_85.csv │ │ ├── NB_F_household_setting_85.csv │ │ ├── NB_F_school_setting_85.csv │ │ ├── NB_F_work_setting_85.csv │ │ ├── NB_M_overall_contact_matrix_85.csv │ │ ├── NB_age_distribution_85.csv │ │ ├── NL_F_community_setting_85.csv │ │ ├── NL_F_household_setting_85.csv │ │ ├── NL_F_school_setting_85.csv │ │ ├── NL_F_work_setting_85.csv │ │ ├── NL_M_overall_contact_matrix_85.csv │ │ ├── NL_age_distribution_85.csv │ │ ├── NS_F_community_setting_85.csv │ │ ├── NS_F_household_setting_85.csv │ │ ├── NS_F_school_setting_85.csv │ │ ├── NS_F_work_setting_85.csv │ │ ├── NS_M_overall_contact_matrix_85.csv │ │ ├── NS_age_distribution_85.csv │ │ ├── NT_F_community_setting_85.csv │ │ ├── NT_F_household_setting_85.csv │ │ ├── NT_F_school_setting_85.csv │ │ ├── NT_F_work_setting_85.csv │ │ ├── NT_M_overall_contact_matrix_85.csv │ │ ├── NT_age_distribution_85.csv │ │ ├── NU_F_community_setting_85.csv │ │ ├── NU_F_household_setting_85.csv │ │ ├── NU_F_school_setting_85.csv │ │ ├── NU_F_work_setting_85.csv │ │ ├── NU_M_overall_contact_matrix_85.csv │ │ ├── NU_age_distribution_85.csv │ │ ├── ON_F_community_setting_85.csv │ │ ├── ON_F_household_setting_85.csv │ │ ├── ON_F_school_setting_85.csv │ │ ├── ON_F_work_setting_85.csv │ │ ├── ON_M_overall_contact_matrix_85.csv │ │ ├── ON_age_distribution_85.csv │ │ ├── PE_F_community_setting_85.csv │ │ ├── PE_F_household_setting_85.csv │ │ ├── PE_F_school_setting_85.csv │ │ ├── PE_F_work_setting_85.csv │ │ ├── PE_M_overall_contact_matrix_85.csv │ │ ├── PE_age_distribution_85.csv │ │ ├── QC_F_community_setting_85.csv │ │ ├── QC_F_household_setting_85.csv │ │ ├── QC_F_school_setting_85.csv │ │ ├── QC_F_work_setting_85.csv │ │ ├── QC_M_overall_contact_matrix_85.csv │ │ ├── QC_age_distribution_85.csv │ │ ├── SK_F_community_setting_85.csv │ │ ├── SK_F_household_setting_85.csv │ │ ├── SK_F_school_setting_85.csv │ │ ├── SK_F_work_setting_85.csv │ │ ├── SK_M_overall_contact_matrix_85.csv │ │ ├── SK_age_distribution_85.csv │ │ ├── YT_F_community_setting_85.csv │ │ ├── YT_F_household_setting_85.csv │ │ ├── YT_F_school_setting_85.csv │ │ ├── YT_F_work_setting_85.csv │ │ ├── YT_M_overall_contact_matrix_85.csv │ │ └── YT_age_distribution_85.csv │ └── stanford_estimates.csv ├── pix │ ├── sir_test1.jpg │ ├── testify.png │ ├── testing_flow.png │ ├── testing_flow_graph.R │ └── testing_flow_v2-crop.pdf ├── testdata │ ├── ON.short.spline.RDS │ ├── ONcalib_2020Jun01.rda │ ├── ONcalib_2brks_2020Jun01.rda │ ├── Ontario_basic.rda │ ├── calib_test.RData │ ├── ccS.rds │ ├── ontario_flex_test.rda │ ├── ontario_flex_test_better.rda │ ├── ontario_flex_test_better_fit.rda │ ├── ontario_flex_test_better_forecasts.rda │ ├── report_data_yukon_h_and_i.csv │ ├── yukon.csv │ └── yukon_no_flex.rda └── tmb │ ├── 0.0.1 │ └── macpan.cpp │ ├── 0.0.2 │ └── macpan.cpp │ ├── 0.0.4 │ └── macpan.cpp │ ├── 0.0.5 │ └── macpan.cpp │ ├── 0.0.6 │ └── macpan.cpp │ ├── 0.1.0 │ └── macpan.cpp │ ├── 0.1.1 │ └── macpan.cpp │ ├── 0.1.2 │ └── macpan.cpp │ ├── 0.2.0 │ └── macpan.cpp │ ├── 0.2.1 │ └── macpan.cpp │ └── recommended_spec_version ├── make_pkglist.sh ├── man ├── McMasterPandemic-package.Rd ├── add_conv.Rd ├── add_d_log.Rd ├── add_factr.Rd ├── add_lag_diff.Rd ├── add_opt_params.Rd ├── add_outflow.Rd ├── add_parallel_accumulators.Rd ├── add_pow.Rd ├── add_rate.Rd ├── add_sim_report_expr.Rd ├── add_state_mappings.Rd ├── add_state_param_sum.Rd ├── add_updated_vaxrate.Rd ├── aggregate.pansim.Rd ├── aggregate_agecats.Rd ├── as.character.struc.Rd ├── as.flexmodel.Rd ├── as.matrix.struc.Rd ├── avail_for.Rd ├── calc_conv.Rd ├── calibrate.Rd ├── calibrate_comb.Rd ├── calibrate_flexmodel.Rd ├── check_age_cat_compatibility.Rd ├── check_contact_rate_setting.Rd ├── col_multiply.Rd ├── compare_grads.Rd ├── compare_sims.Rd ├── complement.Rd ├── condense.Rd ├── condense.pansim.Rd ├── condense_age.Rd ├── condense_params_vax.Rd ├── condense_state.Rd ├── condense_vax.Rd ├── const_named_vector.Rd ├── cross_mat.Rd ├── deprecated_simulation_functions.Rd ├── describe_params.Rd ├── dev_is_tikz.Rd ├── distribute_counts.Rd ├── do_step.Rd ├── expand_contract_struc.Rd ├── expand_names.Rd ├── expand_params_S0.Rd ├── expand_params_age.Rd ├── expand_params_desc_age.Rd ├── expand_params_desc_variant.Rd ├── expand_params_desc_vax.Rd ├── expand_params_mistry.Rd ├── expand_params_variant.Rd ├── expand_params_vax.Rd ├── expand_state_age.Rd ├── expand_state_vax.Rd ├── expand_stateval_testing.Rd ├── extend_end_date.Rd ├── factory_fresh_macpan_options.Rd ├── fix_pars.Rd ├── fix_stored.Rd ├── flexmodel.Rd ├── forecast_ensemble.Rd ├── forecast_sim.Rd ├── getData.Rd ├── get_GI_moments.Rd ├── get_Gbar.Rd ├── get_R0.Rd ├── get_and_set_model_parameters.Rd ├── get_doses_per_day.Rd ├── get_evec.Rd ├── get_kernel_moments.Rd ├── get_macpan_options.Rd ├── get_opt_pars.Rd ├── get_r.Rd ├── gradfun.Rd ├── index_sep.Rd ├── initial_population.Rd ├── invlink_trans.Rd ├── is_1by1.Rd ├── layered_zero_state.Rd ├── macpan_regex_helpers.Rd ├── make_ageified_model.Rd ├── make_base_model.Rd ├── make_beta.Rd ├── make_betavec.Rd ├── make_delay_kernel.Rd ├── make_hello_world_model.Rd ├── make_jac.Rd ├── make_omicron_model.Rd ├── make_ratemat.Rd ├── make_sir_model.Rd ├── make_state.Rd ├── make_test_wtsvec.Rd ├── make_vaccination_model.Rd ├── make_vaxrate.Rd ├── mat_rate.Rd ├── merge_named_vec_attr.Rd ├── merge_named_vectors.Rd ├── mk_Nvec.Rd ├── mk_agecats.Rd ├── mk_contact_rate_setting.Rd ├── mk_mistry_Nvec.Rd ├── mk_pmat.Rd ├── mk_vaxcats.Rd ├── mle_fun.Rd ├── nlist.Rd ├── non_expanded_states.Rd ├── ontario_data.Rd ├── ontario_fits.Rd ├── opt_obj.Rd ├── optim_flexmodel.Rd ├── parse_formula.Rd ├── pivot.Rd ├── plot.pansim.Rd ├── plot.predict_pansim.Rd ├── plot_res_by_age.Rd ├── plot_res_by_state.Rd ├── predict.fit_pansim.Rd ├── prep_res_for_plotting.Rd ├── print.params_pansim.Rd ├── rExp.Rd ├── r_mode.Rd ├── r_tmb_comparable.Rd ├── rate_summary.Rd ├── read_params.Rd ├── rep_rate.Rd ├── repair_names_age.Rd ├── restore.Rd ├── run_sim.Rd ├── run_sim_ageify.Rd ├── run_sim_break.Rd ├── run_sim_loglin.Rd ├── run_sim_mobility.Rd ├── run_sim_range.Rd ├── same_dims.Rd ├── set_spec_version.Rd ├── show_ratemat.Rd ├── simulate_ensemble.Rd ├── simulation_history.Rd ├── spec_check.Rd ├── spec_version.Rd ├── string_concatenation_operators.Rd ├── struc-class.Rd ├── struc.Rd ├── struc_block.Rd ├── struc_eval.Rd ├── struc_expanded-class.Rd ├── struc_expanded.Rd ├── struc_stretch.Rd ├── summary.params_pansim.Rd ├── testify.Rd ├── texify.Rd ├── tibble_row_to_named_vec.Rd ├── time_wrap.Rd ├── tmb_fun.Rd ├── tmb_mode.Rd ├── tmb_params.Rd ├── tmb_params_trans.Rd ├── topological_sort.Rd ├── trans_state_vars.Rd ├── unpack.Rd ├── update.params_pansim.Rd ├── update_condense_map.Rd ├── update_contact_rate_setting.Rd ├── update_disease_free_state.Rd ├── update_error_dist.Rd ├── update_foi.Rd ├── update_initial_state.Rd ├── update_linearized_params.Rd ├── update_loss_params.Rd ├── update_observed.Rd ├── update_params.Rd ├── update_params_mistry.Rd ├── update_piece_wise.Rd ├── update_ranef_params.Rd ├── update_simulation_bounds.Rd ├── update_tmb_indices.Rd ├── v2d.Rd ├── vec_factr.Rd ├── vec_rate.Rd ├── vis_model.Rd └── write_params.Rd ├── misc ├── calibration_sbatch.sh ├── calibration_sbatch_test.txt ├── change_notation.csh ├── dependencies.R ├── git_push.sh ├── macpan_lint.R ├── macpan_style.R ├── ont_cal_NelderMead.R ├── rename_mistry.R ├── scalibration_sbatch.sh └── test_file.txt ├── notes ├── IP_explore_codebase.Rmd ├── IP_to-do-ageify.Rmd ├── MRE_neg-jumps.Rmd ├── Makefile ├── R0est.R ├── Rt.R ├── SIR.cpp ├── SIR_try_to_break_tmb.R ├── SIR_try_to_break_tmb.cpp ├── TMB_SIR.R ├── TMB_do_step.cpp ├── absolute.R ├── absolute_keepall.R ├── ageify.Rmd ├── ageify_calibrate.Rmd ├── ageify_calibrate.html ├── ageify_demo.Rmd ├── ageify_demo.html ├── ageify_model.Rmd ├── ageify_model.html ├── ageify_severity.Rmd ├── ageify_severity.html ├── ali_simple_run1.R ├── ali_simple_run1.makeR.script ├── ali_test_sir.Rmd ├── ali_test_sir.html ├── alt_cal.R ├── bad_nonsense.R ├── basic.R ├── basic_keepall.R ├── batch_aliases.rc ├── batch_notes.md ├── batchtools.R ├── break_check.R ├── break_test.R ├── brief_model_description.md ├── calibration.md ├── call_graph.R ├── clean_testing.R ├── collect_calib.R ├── collect_recalib.R ├── collect_spline_shape_calib.R ├── combine_testing.R ├── contact_matrices_152_countries │ ├── MUestimates_all_locations_1.xlsx │ ├── MUestimates_all_locations_2.xlsx │ ├── MUestimates_home_1.xlsx │ ├── MUestimates_home_2.xlsx │ ├── MUestimates_other_locations_1.xlsx │ ├── MUestimates_other_locations_2.xlsx │ ├── MUestimates_school_1.xlsx │ ├── MUestimates_school_2.xlsx │ ├── MUestimates_work_1.xlsx │ └── MUestimates_work_2.xlsx ├── covid19testing_funs.R ├── curve_shapes.R ├── diagnose_repfit.R ├── do_step.cpp ├── estimability.md ├── example.R ├── exampleTMB.R ├── expandify_implementation.Rmd ├── explore_caltest.R ├── explore_nobreaks.R ├── explore_ontcal.R ├── explore_ontcal.Rmd ├── explore_testify.R ├── focus.csv ├── funcresp.cpp ├── get_mistry_cmats.R ├── git_push │ ├── basic.testify_calibration.Rout.pdf │ ├── biased_testing.pdf │ ├── combine_testing.Rout.pdf │ ├── explore_nobreaks.Rout.pdf │ ├── ode.simplots.Rout.pdf │ ├── plot_caltest.Rout.pdf │ ├── plot_caltest_nobreak.Rout.pdf │ ├── random_testing.pdf │ ├── simcalib_plot.Rout.pdf │ ├── spline_compare.Rout.pdf │ ├── spline_fitplots.Rout.pdf │ ├── spline_forecast_plot.Rout.pdf │ ├── spline_plots.Rout.pdf │ ├── spline_recalib_compare.Rout.pdf │ ├── testify_simplot.Rout.pdf │ ├── testify_sims.1.5.pdf │ ├── testify_sims.2.pdf │ ├── testify_sims.pdf │ ├── testsim.plots.Rout │ ├── testsim.plots.Rout.pdf │ ├── testwt_N.simcalib_plot.Rout.pdf │ ├── testwt_N.simplots.Rout.pdf │ ├── testwt_N.testify_simreportplot.Rout.pdf │ └── very_biased_testing.pdf ├── graham_notes.md ├── horrid_loops.md ├── indexing.R ├── indexing.md ├── indexing │ ├── Makefile │ ├── doc-output │ │ ├── indexing.md │ │ └── indexing_files │ │ │ └── figure-markdown_strict │ │ │ ├── unnamed-chunk-11-1.png │ │ │ └── unnamed-chunk-12-1.png │ ├── eigen.md │ ├── experiment_0.0.3.R │ ├── flex_architecture │ │ ├── flex_architecture.drawio │ │ ├── flex_architecture.md │ │ └── limitations_of_tmb.md │ ├── indexing.Rmd │ ├── jacobian_test.R │ ├── jacobian_theory │ │ └── jacobian_theory.Rmd │ ├── make_state.R │ ├── old_ideas_on_0.0.3.R │ ├── ourParser.R │ ├── ourParser.cpp │ ├── outflow_test.R │ ├── sir.R │ ├── speedup_comparisons │ │ └── speedup_comparisons.Rmd │ ├── structure-experimentation.R │ ├── sums.txt │ ├── test-tmb-0.0.4.R │ ├── test-tmb-0.0.5.R │ ├── test-tmb-0.0.6.R │ ├── test-tmb-0.0.7.R │ ├── test-tmb-0.1.0.R │ ├── test-tmb-0.2.0-1.R │ ├── test-tmb-0.2.0-2.R │ ├── test-tmb-0.2.0.R │ ├── test-tmb-0.2.1.R │ ├── test-tmb-002.R │ ├── test_other_dists.R │ ├── testing_model_structure.R │ ├── tinyexpr.c │ ├── tinyexpr.h │ ├── tinyexpr_test.sh │ ├── tinyexpr_test1 │ ├── tinyexpr_test1.cpp │ ├── tinyexpr_test2.cpp │ ├── tmb_data_struct.md │ ├── tmb_data_struct_v2.md │ ├── utilities.R │ ├── vaccine_model_structure.R │ ├── vax.md │ └── vax_model_from_irena.R ├── loglin_spatial.R ├── ltcf.Rmd ├── midas_estimates.R ├── mlefit.R ├── nested_testify.R ├── ode.R ├── outputs │ └── testing_distrib.html ├── phac_handover.md ├── pkg_versions.R ├── plot_caltest.R ├── random.csv ├── ratemat_vis.Rmd ├── refactor │ ├── refactor.Rmd │ ├── refactor.bib │ └── refactor.pdf ├── reimplementation.md ├── renewal.md ├── run_DEoptim.R ├── run_caltest.R ├── run_caltest_1break.R ├── run_params_breaks.R ├── run_params_breaks_DE.R ├── run_params_mobility_DE.R ├── run_params_nobreak.R ├── selection_coefficient.rmd ├── sharcnet_kickoff.md ├── sim_funs.cpp ├── sim_funs_cpp.md ├── simcalib_plot.R ├── simcalib_tidy.R ├── simple.R ├── simple_spline_sim.R ├── simplify_macpan.md ├── simplots.R ├── slow.csv ├── sparse_benchmark.R ├── spline.csv ├── spline_calib.R ├── spline_compare.R ├── spline_fit.R ├── spline_fitplots.R ├── spline_forecast.R ├── spline_forecast_plot.R ├── spline_plots.R ├── spline_projection1.R ├── spline_projection2.R ├── spline_recalib.R ├── spline_recalib_compare.R ├── spline_shape_calib.R ├── spline_sim.R ├── spline_test_macpan.R ├── stable_tmb.md ├── steve_TMB_do_step.cpp ├── steve_test_TMB.R ├── stoch_forecasts.R ├── structure.md ├── symptomatic.csv ├── test.log ├── test_TMB.R ├── test_calibration.R ├── test_calibreaks.R ├── test_exp.R ├── test_hosp.R ├── test_pps.R ├── test_sir.R ├── testify_calibration.R ├── testify_check.R ├── testify_funs.R ├── testify_makesim.R ├── testify_sim.R ├── testify_simreportplot.R ├── testify_testcatplot.R ├── testing.md ├── testing_distrib.Rmd ├── testing_flow.md ├── testing_flow_graph.R ├── testsim.R ├── testwt_N.R ├── time_series.Rmd ├── vacc_test.R └── weekly_calibrations_work.md ├── ontario ├── .gitignore ├── Makefile ├── McMasterReport.Rnw ├── ON_june1.R ├── ONepigrowthfit.R ├── Ontario_Mobility.R ├── Ontario_PH.R ├── Ontario_calibration_setup.R ├── Ontario_calibration_setup_nomake.R ├── Ontario_current.R ├── Ontario_splines.R ├── README.md ├── batchtools.R ├── codegraph.R ├── collect_spline_factorial.R ├── comb_calib.R ├── compare_calib.R ├── de_pop.R ├── epiestim.R ├── epiestim_plot.R ├── example.rmd ├── git_push │ ├── example.pdf │ ├── ont_cal_factorial.RData │ ├── ont_cal_factorial_plot.Rout.pdf │ └── plot_spline_factorial.Rout.pdf ├── mobility.R ├── nlipreamble.tex ├── ont_cal.R ├── ont_cal_1brks.R ├── ont_cal_2brks.R ├── ont_cal_2brks_ndt.R ├── ont_cal_H.R ├── ont_cal_HD_2brks.R ├── ont_cal_factorial.R ├── ont_cal_factorial_plots.R ├── ont_cal_factorial_plots.Rmd ├── ont_cal_forecast.R ├── ont_cal_mob1.R ├── ont_cal_mob1_HD.R ├── ont_cal_noICU.R ├── ont_cal_noICU_1brks.R ├── ont_cal_noICU_2brks.R ├── ont_cal_noICU_2brks_prior.R ├── ont_cal_spline1.R ├── ont_cal_splinecomp.R ├── ont_cal_splinecomp_plots.R ├── ont_cal_splinemob1.R ├── ont_cal_zeta.R ├── ont_keep.R ├── ont_single_var.R ├── ont_spline_factorial.R ├── ontario_ICU.Rmd ├── ontario_calibration_report.Rmd ├── ontario_clean.R ├── ontario_de_cal.R ├── ontario_nbfit.R ├── ontario_quadmod.R ├── plot_spline_factorial.R └── reference_mod_forecast.R ├── refactor ├── benchmark_inplace.R ├── coverage │ └── coverage.R ├── dependencies │ ├── dependency_visualization.R │ └── function_locations.R ├── hpc │ ├── comparison.R │ └── setup.sh ├── no-anydate │ └── find_dates.R ├── optimization_ideas.md ├── profiling │ ├── benchmark_sweep.R │ ├── profvis_everything.R │ ├── profvis_grepl.R │ ├── profvis_specifics.R │ └── test.R └── test-autotest.R ├── rename.md ├── sandbox ├── ON.short.breaks.RDS ├── ON.short.spline.RDS ├── ageify_workshop.R ├── break_tests.R ├── calibrate_gif │ ├── animation.gif │ └── sims.R ├── calibrate_timeargs_reprex.R ├── calibration_2021-06-18_ON.RDS ├── demo_vaccination_switch.R ├── do_make_state_segfault.R ├── fix_stored_plot.R ├── forecast2.R ├── jaggy.R ├── kernel_test.R ├── odin.R ├── ontario_vaccine.RDS ├── ontario_vaccine_plot.R ├── reprex_flex_timevar_backcompatibility.R ├── run_sim_mre.R ├── run_sim_mre_tmb.R ├── sample_vaxify_sim.R ├── santaclara_ex.R ├── sim.RData ├── spline_tests.R ├── test_mob_breaks.R ├── threedosewane.R ├── time_varying_mre.R ├── time_varying_run_sim.R ├── tmb-sandbox │ ├── debug_stuff.R │ ├── mre_tmb_obj_fun_nans.R │ ├── opt_params_tmb.R │ └── tmb-condense-to-tmb.R ├── tmb_forecast.R ├── variant_demo.R ├── vaxify_demo.R ├── visNetwork.R └── yukon │ ├── PHAC_Yukon_brian.csv │ ├── new_yukon │ ├── animation.gif │ ├── fitted.mod.rda │ ├── report_data_yukon_h_and_i.csv │ └── yukon_steve_lisa_works_reports_hosp_forecast.R │ ├── report_data_yukon.csv │ ├── report_data_yukon_h_and_i-1.csv │ ├── report_data_yukon_h_and_i.csv │ ├── report_data_yukon_hosp.csv │ ├── yukon.R │ ├── yukon_steve_lisa.R │ └── yukon_steve_lisa_forecast_V2.R ├── src └── McMasterPandemic.cpp ├── tests ├── AAAtest-all.R ├── moments.R ├── prior_tests.R ├── test_calibrate.R └── testthat │ ├── _snaps │ └── snapshots.md │ ├── test-ageify.R │ ├── test-basic.R │ ├── test-calibrate.R │ ├── test-exp.R │ ├── test-expandify.R │ ├── test-methods.R │ ├── test-plots.R │ ├── test-rda.R │ ├── test-simfuns.R │ ├── test-snapshots.R │ ├── test-testify.R │ ├── test-tmb-calibrate.R │ ├── test-tmb-condense.R │ ├── test-tmb-forecast.R │ ├── test-tmb-formula.R │ ├── test-tmb-make-state.R │ ├── test-tmb-pars.R │ ├── test-tmb-simulate.R │ ├── test-tmb-struc.R │ ├── test-tmb-timevar.R │ ├── test-tmb.R │ ├── test-utils.R │ ├── test-zzzDE.R │ └── utils.R ├── vignettes ├── calibration.rmd ├── farr.rmd ├── flex_intro.Rmd ├── flex_specs.rmd ├── getting_started.Rnw ├── model.rmd ├── nlipreamble.tex ├── testing_flow.rmd └── vaxify_implementation.Rmd └── weekly_calibrations ├── ONcalib_2021Aug02.rda ├── ONcalib_2021Aug09.rda ├── ONcalib_2021Aug16.rda ├── ONcalib_2021Aug23.rda ├── ONcalib_2021Aug30.rda ├── ONcalib_2021Dec06.rda ├── ONcalib_2021Dec13.rda ├── ONcalib_2021Dec20.rda ├── ONcalib_2021Dec27.rda ├── ONcalib_2021Jul07.rda ├── ONcalib_2021Jul08.rda ├── ONcalib_2021Jul13.rda ├── ONcalib_2021Jul16.rda ├── ONcalib_2021Jul19.rda ├── ONcalib_2021Jul26.rda ├── ONcalib_2021Nov01.rda ├── ONcalib_2021Nov08.rda ├── ONcalib_2021Nov15.rda ├── ONcalib_2021Nov22.rda ├── ONcalib_2021Nov29.rda ├── ONcalib_2021Oct04.rda ├── ONcalib_2021Oct18.rda ├── ONcalib_2021Oct25.rda ├── ONcalib_2021Sep06.rda ├── ONcalib_2021Sep13.rda ├── ONcalib_2021Sep20.rda ├── ONcalib_2021Sep27.rda ├── ONcalib_2022Apr04.rda ├── ONcalib_2022Apr11.rda ├── ONcalib_2022Apr18.rda ├── ONcalib_2022Apr25.rda ├── ONcalib_2022Feb07.rda ├── ONcalib_2022Feb14.rda ├── ONcalib_2022Feb21.rda ├── ONcalib_2022Feb28.rda ├── ONcalib_2022Jan03.rda ├── ONcalib_2022Jan10.rda ├── ONcalib_2022Jan17.rda ├── ONcalib_2022Jan24.rda ├── ONcalib_2022Jan31.rda ├── ONcalib_2022Mar07.rda ├── ONcalib_2022Mar14.rda ├── ONcalib_2022Mar21.rda ├── ONcalib_2022Mar28.rda ├── ONcalib_2022May02.rda ├── ONcalib_2022May09.rda ├── ONcalib_2022May16.rda ├── prediction_2021Aug02.png ├── prediction_2021Aug09.png ├── prediction_2021Aug16.png ├── prediction_2021Aug23.png ├── prediction_2021Aug30.png ├── prediction_2021Dec06.png ├── prediction_2021Dec13.png ├── prediction_2021Dec20.png ├── prediction_2021Dec27.png ├── prediction_2021Jul07.png ├── prediction_2021Jul08.png ├── prediction_2021Jul13.png ├── prediction_2021Jul16.png ├── prediction_2021Jul19.png ├── prediction_2021Jul26.png ├── prediction_2021Nov01.png ├── prediction_2021Nov08.png ├── prediction_2021Nov15.png ├── prediction_2021Nov22.png ├── prediction_2021Nov29.png ├── prediction_2021Oct04.png 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