# Estimate the Effective Reproductive Number with Trend Filtering

## Documentation for package ‘rtestim’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cancovid | Canadian Incident COVID-19 Cases
confband | Add confidence bands to estimated Rt or incidence curves
configure_rt_admm | Rt estimation algorithm configuration
cv_estimate_rt | Leave-kth-out cross validation for choosing a optimal parameter lambda
delay_calculator | Calculate the total infectiousness at each observed time point.
discretize_gamma | Compute the discretized density function for gamma distribution
estimate_rt | Estimate Rt using smoothness-penalized Poisson likelihood
fitted.cv_poisson_rt | Fitted cv_poisson_rt
interpolate_rt | Interpolate (or extrapolate) Rt estimates to intermediate design points
interpolate_rt.cv_poisson_rt | Interpolate (or extrapolate) Rt estimates to intermediate design points
interpolate_rt.poisson_rt | Interpolate (or extrapolate) Rt estimates to intermediate design points
plot.cv_poisson_rt | Plot cv_poisson_rt
plot.poisson_rt | Plot estimated Rt values from a 'poisson_rt' object
plot.rt_confidence_band | Plot estimated confidence bands for an estimate of Rt
predict.cv_poisson_rt | Predict observed data using estimated Rt
predict.poisson_rt | Predict observed data using estimated Rt