Man pages for rplzzz/CovMitigation
COVID-19 infection model for Virginia
| bayesian_filter | Project infection in a single county using a Bayesian filter |
| calc_nhosp | Calculate the expected number of hospitalizations for a model |
| census_model_output | Compute input for the hospital census model from a filter... |
| coefs | Caclulate model coefficients from parameters |
| complete_params | Add default parameters for parameters not overridden in the... |
| CovMitigation | CovMitigation: Data and modeling for UVAHS epidemic response |
| cutdate | Convert vector of dates into a factor of date ranges |
| ensemble_deviance | Compute the deviance for models in an ensemble. |
| ensemble_eval | Evaluate ensemble members according to their agreement with... |
| extend_filter_model | Extend a filter model with new data. |
| fetch_vdh_cov19 | Download latest COVID-19 data from Virginia Department of... |
| filter_fit_locality | Run the filter model for a single locality |
| filter_model_comparison_plot | Compare filter model fits in various localities |
| filter_model_diagnositc_plots | Generate diagnostic plots for filter models |
| filter_model_ensemble_plot | Plot traces for ensemble members in a filter model fit |
| fit_filter | Fit a Bayesian filter over time |
| fsympto | Find the symptomatic infection fraction |
| gen_likelihood | Prepare a likelihood function for use in Bayesian calibration |
| gen_parm_vec | Generate a vector of parameters for the posterior PDF |
| gen_post | Prepare a posterior log-pdf function for use in Bayesian... |
| gen_prior | Generate a log prior function |
| gen_simobs_likelihood | Generate a likelihood function for single-county simulated... |
| gen_simobs_posterior | Generate log-posterior function for filter model |
| get_obsdata | Prepare the observed data for use in the likelihood function |
| getparam | Get a time variable parameter from a table of step-changes |
| growth_categories | County growth categories |
| hospitalizations | Weekly UVAHS Covid admissions by date and locality of origin |
| initialize_parmset | Run compartment model from an initial state |
| is.Scenario | Test whether an object is a scenario |
| llanalysis | Functions for analyzing data contributions to the likelihood |
| localbeta | Calculate the local value of beta from population density |
| locality_startdate | Compute start of the infection for a locality. |
| localize_scenario | Specialize a scenario to a locality |
| local_mobility | Extract the mobility table for a specified locality. |
| losig | Compute a sigmoid function of the log-odds of a probability |
| marketFractionFinal | Market fractions for Virginia localities |
| mask_indicator | Indicator function for mask use requirement |
| mobility_adjust | Compute transmissibility adjustment for mobility |
| namebackup | Find a name for a backup file |
| newsympto | Calculate incidence of symptomatic cases |
| nhosp_likelihood | Calculate the likelihood adjustment for number of hospital... |
| padjust | Adjust probabilities by a bias factor |
| parameters | Model parameters and hyperparameters |
| pdist | Helper functions for creating parameter distributions |
| plt_modobs | Plot model predictions against data observations |
| plt_projections | Plot model projections for comparison |
| project_filter_model | Continue a run from a fitted filter model. |
| qprior | Evaluate the quantile for the multidimensional df defined by... |
| refresh_ensemble | Refresh a model ensemble by replacing low performing members. |
| run_mc | Run a Monte Carlo simulation of a scenario |
| run_parms | Run the scenario for a vector of likelihood parameters |
| run_parmset | Run the compartment model for a single set of parameters |
| run_scenario | Run a single hospital census scenario |
| run_single_county | Run the hospital census model for a single locality |
| sampleCounties | Market fraction and FIPS code for Virginia localities with... |
| Scenario | Construct a scenario structure |
| scenario_change_times | Find the times at which a scenario's parameters change |
| scenario_parm_value | Compute parameter value by time for a local scenario |
| seir_equations | Differential equations for the SEIR model |
| simobs | Create simulated observations from a scenario run |
| update_filter_models | Update all saved filter models |
| uva_covid_count | Counts of various categories of COVID cases |
| va_county_first_case | Date of first report for VA counties |
| validate_params | Check that a parameter vector has no unknown parameters |
| vaMyAgeBands | Census data for Virginia localities |
| vintage_plot | Plot uncertainty ranges by vintage |
| wkagg | Aggregate model output to weekly resolution |
