Implements Empirical Bayes Incidence Curves

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Documentation for package ‘incidental’ version 0.1

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

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compute_expected_cases	Compute expected cases
compute_log_incidence	Compute log likelihood of incidence model
covid_delay_dist	Delay distribution from COVID-19 pandemic.
covid_new_york_city	New York City data from the COVID-19 pandemic.
data_check	Input data check
data_processing	Data processing wrapper
diff_trans	Transpose of the 1st difference operator
fit_incidence	Fit incidence curve to reported data
front_zero_pad	Pad reported data with zeros in front
incidence_to_df	Export incidence model to data frame
init_params	Initialize spline parameters (beta)
make_ar_extrap_samps	Make AR samples for extrapolation past end point
make_likelihood_matrix	Make delay likelihood matrix
make_spline_basis	Create spline basis matrix
marg_loglike_poisson	Marginal log likelihood This function computes the marginal probability of Pr(reported | beta). Note that lnPmat must be zero padded enough (or censored) to match the length of reported cases vector.
marg_loglike_poisson_fisher	Marginal log likelihood Fisher information matrix
marg_loglike_poisson_grad	Marginal log likelihood gradient
plot.incidence_spline_model	Plot model from fit_incidence
poisson_objective	Poisson objective function
poisson_objective_grad	Poisson objective function gradient
poisson_objective_post_cov_approx	Compute Fisher information matrix for Poisson objective
regfun	Beta regularization function
regfun_grad	Beta regularization function gradient
regfun_hess	Beta regularization function Hessian
sample_laplace_log_incidence_poisson	Generate Laplace samples of incidence
scan_spline_dof	Scan spline degrees of freedom
scan_spline_lam	Scan spline regularization parameter
spanish_flu	Daily flu mortality from 1918 flu pandemic.
spanish_flu_delay_dist	Delay distribution from 1918 flu pandemic.
train_and_validate	Train and validate model on reported data
train_val_split	Split reported case data