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. |

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 |

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 |

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... |

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 |

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