Man pages for rplzzz/CovMitigation
COVID-19 infection model for Virginia

bayesian_filterProject infection in a single county using a Bayesian filter
calc_nhospCalculate the expected number of hospitalizations for a model
census_model_outputCompute input for the hospital census model from a filter...
coefsCaclulate model coefficients from parameters
complete_paramsAdd default parameters for parameters not overridden in the...
CovMitigationCovMitigation: Data and modeling for UVAHS epidemic response
cutdateConvert vector of dates into a factor of date ranges
ensemble_devianceCompute the deviance for models in an ensemble.
extend_filter_modelExtend a filter model with new data.
fetch_vdh_cov19Download latest COVID-19 data from Virginia Department of...
filter_fit_localityRun the filter model for a single locality
filter_model_comparison_plotCompare filter model fits in various localities
filter_model_diagnositc_plotsGenerate diagnostic plots for filter models
filter_model_ensemble_plotPlot traces for ensemble members in a filter model fit
fit_filterFit a Bayesian filter over time
fsymptoFind the symptomatic infection fraction
gen_likelihoodPrepare a likelihood function for use in Bayesian calibration
gen_parm_vecGenerate a vector of parameters for the posterior PDF
gen_postPrepare a posterior log-pdf function for use in Bayesian...
gen_priorGenerate a log prior function
gen_simobs_likelihoodGenerate a likelihood function for single-county simulated...
gen_simobs_posteriorGenerate log-posterior function for filter model
get_obsdataPrepare the observed data for use in the likelihood function
getparamGet a time variable parameter from a table of step-changes
growth_categoriesCounty growth categories
initialize_parmsetRun compartment model from an initial state
is.ScenarioTest whether an object is a scenario
llanalysisFunctions for analyzing data contributions to the likelihood
localbetaCalculate the local value of beta from population density
locality_startdateCompute start of the infection for a locality.
localize_scenarioSpecialize a scenario to a locality
local_mobilityExtract the mobility table for a specified locality.
losigCompute a sigmoid function of the log-odds of a probability
marketFractionFinalMarket fractions for Virginia localities
mask_indicatorIndicator function for mask use requirement
mobility_adjustCompute transmissibility adjustment for mobility
namebackupFind a name for a backup file
nhosp_likelihoodCalculate the likelihood adjustment for number of hospital...
padjustAdjust probabilities by a bias factor
parametersModel parameters and hyperparameters
pdistHelper functions for creating parameter distributions
plt_modobsPlot model predictions against data observations
plt_projectionsPlot model projections for comparison
project_filter_modelContinue a run from a fitted filter model.
qpriorEvaluate the quantile for the multidimensional df defined by...
run_mcRun a Monte Carlo simulation of a scenario
run_parmsRun the scenario for a vector of likelihood parameters
run_parmsetRun the compartment model for a single set of parameters
run_scenarioRun a single hospital census scenario
run_single_countyRun the hospital census model for a single locality
sampleCountiesMarket fraction and FIPS code for Virginia localities with...
ScenarioConstruct a scenario structure
scenario_change_timesFind the times at which a scenario's parameters change
scenario_parm_valueCompute parameter value by time for a local scenario
seir_equationsDifferential equations for the SEIR model
simobsCreate simulated observations from a scenario run
update_filter_modelsUpdate all saved filter models
uva_covid_countCounts of various categories of COVID cases
va_county_first_caseDate of first report for VA counties
validate_paramsCheck that a parameter vector has no unknown parameters
vaMyAgeBandsCensus data for Virginia localities
vintage_plotPlot uncertainty ranges by vintage
wkaggAggregate model output to weekly resolution
rplzzz/CovMitigation documentation built on Jan. 27, 2021, 8:09 p.m.