Man pages for SC-COSMO/sccosmomcma
Stanford-CIDE COronavirus Simulation MOdel (SC-COSMO) for Mexico City Metropolitan Area Analysis
| acor2cov | Covariance matrix from autocorrelation coefficients and... |
| add_intervention | Building list of interventions to be simulated in the... |
| add_list_periods | Helper function add lists of periods into single containing... |
| add_period | Helper function add periods together into a list containing... |
| aggregate_pop_ages | Aggregate population ages into age groups of interest |
| calc_basic_reproduction_number_kr | Calculate basic reproduction number according to Keeling &... |
| calc_deathsdx_totals | Total Covid-19 deaths from diagnosed infections |
| calc_deaths_totals | Total Covid-19 deaths |
| calc_dxcum_totals | Total cumulative diagnosed infections (E and I) |
| calc_dx_hosp | Total Prevalent DX hospitalizations |
| calc_dx_hosp_icu | Total Prevalent DX ICU hospitalizations |
| calc_dx_hosp_nonicu | Total Prevalent DX Non-ICU hospitalizations |
| calc_dx_inchosp | Total Incident DX hospitalizations |
| calc_dx_inchosp_icu | Total Incident DX ICU hospitalizations |
| calc_dx_inchosp_nonicu | Total Incident DX Non-ICU hospitalizations |
| calc_dxinc_totals | Total incident diagnosed infections (E and I) |
| calc_dx_totals | Total diagnosed infections (E and I) |
| calc_expinf_totals | Total infections (E and I) |
| calc_idxcum_totals | Total cumulative diagnosed infectious infections |
| calc_idxinc_totals | Total incident diagnosed infectious infections |
| calc_idx_totals | Total diagnosed infections |
| calc_incdeathsdx_totals | Total Incident Covid-19 deaths from diagnosed infections |
| calc_infcum_totals | Total cumulative infections |
| calc_infinc_totals | Total incident infections |
| calc_inf_totals | Total infections |
| calc_popsize_totals | Total population |
| calc_rec_totals | Total Recovered |
| calc_reproduction_number_wt | Estimate the time dependent reproduction number according to... |
| calc_sx_totals | Total symptomatic infections (E and I) |
| calibration_out | Generate model outputs for calibration from a parameter set |
| compute_inflows | Compute inflows considering competing risks using convolution... |
| cosmo | The Stanford-CIDE COronavirus Simulation MOdel (SC-COSMO) |
| cosmo_dXdt | Derivatives of the Stanford-CIDE COronavirus Simulation MOdel... |
| cosmo_dXdt_comp | Compiled Stanford-CIDE COronavirus Simulation MOdel... |
| gen_all_betas | Efficiency by precomputing beta component of force of... |
| gen_all_intervention_effects | Efficiency by precomputing intervention effects at each time... |
| gen_all_waifws | Efficiency by precomputing WAIFW matrices at each time step... |
| general_logit | Generalized logistic function |
| gen_hh_n | Generate household possibilities |
| gen_hosp_targets | Generate hospitalization targets. |
| gen_household_matrices_mc_seir | Generate household matrices |
| gen_household_transmission_mc_seir | Generate household transmission |
| gen_targets | Generate calibration targets |
| gen_time_varying | Helper function for creating time-varying vector of values |
| get_betas | Computing force of infection at each time step for the... |
| get_bounds | Get bounds for parameters to calibrate |
| get_case_detection | Case detection parameters |
| get_cfr | Proportion (age-specific) of detected cases that die |
| get_const_multiage_list | Helper convenience function that defines age-specific lists... |
| get_contact_matrices_world | Get contact matrices |
| get_contact_matrix | Get contact matrix main function |
| get_countrycode | Get a three letter code for a country's name |
| get_cum_mort_risk | Generate cumulative mortality risk |
| get_densities | Get population density |
| get_densities_mx | Get population density for Mexico subnational regions |
| get_fipscodes_mx | Get FIPS codes for Mexican states |
| get_gamma_params | Get parameters for gamma distribution |
| get_hosp_bounds | Get bounds for hospitalization parameters to calibrate |
| get_idx_scale_factor | Get reduction factor on transmission from detected infectious... |
| get_ifr | Get the fraction of undetected cases that die |
| get_intervention_effects | Gets correct intervention effect multipliers for the... |
| get_lifetables | Get lifetables |
| get_lifetables_mx | Get lifetables for MX states |
| get_MCMA_prop_hosp | Generate hospitalization proportions. |
| get_non_const_multiage_list | Helper convenience function that defines age-specific lists... |
| get_os | Get operating system |
| get_parameters | Get time-varying parameters for the Stanford-CIDE COronavirus... |
| get_population_ages | Get population and age structure |
| get_population_ages_mx | Get population and age structure for MX subnational regions |
| get_population_birth | Get crude birth rates |
| get_population_birth_mx | Get crude birth rates for MX states |
| get_projection_scenarios | Generates interventions input list for performing projections... |
| get_prop_hosp | Get proportion of cases that go into hospitalization over... |
| get_screen_detection | Get screen detection parameters for the Stanford-CIDE... |
| get_waifw | Gets correct mixing matrices for the Stanford-CIDE... |
| hosp_acor2cov | Covariance matrix from autocorrelation coefficients and... |
| hosp_calibration_out | Generate model outputs for calibration from a hospitalization... |
| hosp_likelihood | Likelihood |
| hosp_log_lik | Log-likelihood function for a hospitalization parameter set |
| hosp_log_lik_opt | Log-likelihood function for a hospitalization parameter set |
| hosp_log_lik_par | Parallel evaluation of log-likelihood function for a sets of... |
| hosp_log_post | Evaluate log-posterior of calibrated hospitalization... |
| hosp_log_post_opt | Evaluate log-posterior of calibrated hospitalization... |
| hosp_log_prior | Evaluate log-prior of calibrated hospitalization parameters |
| hosp_log_prior_opt | Evaluate log-prior of calibrated hospitalization parameters... |
| hosp_posterior | Evaluate posterior of calibrated hospitalization parameters |
| hosp_prior | Evaluate prior of calibrated hospitalization parameters |
| hosp_sample_prior | Sample from prior distributions of calibrated parameters |
| likelihood | Likelihood |
| load_all_params | Load all parameters |
| load_params_init | Base-case initial parameter set |
| log_lik | Log-likelihood function for a parameter set |
| log_lik_opt | Log-likelihood function for a parameter set |
| log_lik_par | Parallel evaluation of log-likelihood function for a sets of... |
| log_post | Evaluate log-posterior of calibrated parameters |
| log_post_opt | Evaluate log-posterior of calibrated parameters for... |
| log_prior | Evaluate log-prior of calibrated parameters |
| log_prior_opt | Evaluate log-prior of calibrated parameters for OPTIMIZATION... |
| make_intervention | Constructing intervention descriptions for each intervention... |
| make_period | Helper function to define a time chunk for a time varying... |
| m_general_logit | Generalized logistic function (matrix version) |
| number_ticks | Number of ticks for 'ggplot2' plots |
| obtain_init_pop | Obtain initial population |
| obtain_setting_data | Obtain initial population |
| plot_cosmo_data | Plot COSMO data |
| plot_deathsdx_totals | Plot total Covid-19 deaths |
| plot_deaths_totals | Plot total Covid-19 deaths |
| plot_dxcum_totals | Plot total cumulative diagnosed infections (E and I) |
| plot_dxinc_totals | Plot total incident diagnosed cases (E and I) |
| plot_dx_totals | Plot total diagnosed infections (E and I) |
| plot_expinf_totals | Plot total infections (E and I) |
| plot_hosp_prop | Plot proportion of incident detected cases hospitalized |
| plot_hosp_targets | Plot hospitalization targets |
| plot_idxcum_totals | Plot total cumulative diagnosed infectious infections |
| plot_idxinc_totals | Plot total incident diagnosed infectious infections |
| plot_idx_totals | Plot total diagnosed infections |
| plot_incdeathsdx_totals | Plot total incident Covid-19 deaths from diagnosed infections |
| plot_infcum_totals | Plot total cumulative infections |
| plot_infinc_totals | Plot total incident infections |
| plot_inf_totals | Plot total infections |
| plot_model_out_vs_targets | Plot Targets |
| plot_mort_risk | Plot expected cumulative mortality risk |
| plot_popsize_totals | Plot total population |
| plot_rec_totals | Plot total recovered |
| plot_sx_totals | Plot total symptomatic infections |
| plot_targets | Plot Targets |
| posterior | Evaluate posterior of calibrated parameters |
| prep_dx_hosp_calib | Produce hospitalization occupation over time |
| prep_dx_hospitalizations | Produce hospitalization occupation over time |
| prior | Evaluate prior of calibrated parameters |
| project_epi_out | Calculate epidemiological outcomes projections from SC-COSMO |
| project_interventions_probabilistic | Probabilistic projections of interventions |
| sample.prior | Sample from prior distributions of calibrated parameters |
| sccosmo | 'sccosmo' package |
| summarise_data | Summarize posterior output |
| update_param_list | Update parameters |
| validate_out | Generate outputs for validation |
| wrangle_contact_matrix | Get wrangle contact matrix |
