incidental0.1 package

Compute expected cases

Compute log likelihood of incidence model

Input data check

Data processing wrapper

Transpose of the 1st difference operator

Fit incidence curve to reported data

Pad reported data with zeros in front

Export incidence model to data frame

incidental: A package for computing incidence curves from delayed case...

Initialize spline parameters (beta)

Make AR samples for extrapolation past end point

Make delay likelihood matrix

Create spline basis matrix

Marginal log likelihood This function computes the marginal probabilit...

Marginal log likelihood Fisher information matrix

Marginal log likelihood gradient

Plot model from fit_incidence

Poisson objective function

Poisson objective function gradient

Compute Fisher information matrix for Poisson objective

Beta regularization function

Beta regularization function gradient

Beta regularization function Hessian

Generate Laplace samples of incidence

Scan spline degrees of freedom

Scan spline regularization parameter

Daily flu mortality from 1918 flu pandemic.

Delay distribution from 1918 flu pandemic.

Train and validate model on reported data

Split reported case data