ern2.1.2 package

Infer daily counts from aggregates

Attach start date from first observation for aggregated data from time...

Attach internal time index column

Attach time index (number of days) column. Exclude first day since we ...

Check the format of input clinical data

Check if input data is already daily

Check distributions

Check that deconvolution inputs are compatible

Check parameters for daily data inference check

Check parameters for daily data inference

Check parameters for Rt calculation

Check parameters for smoothing

Correct underreporting by scaling up

Wrapper for deconvolution with a given distribution

Deconvoluting Wastewater Data to Incidence

Richardson-Lucy Deconvolution.

Define a family of distributions.

Draw from gamma for a parameter specified in a distribution family lis...

Estimate the effective reproduction from clinical report data

Ensemble estimate of Rt

A single realization of the Rt estimate

Estimate the effective reproduction from wastewater concentration data...

Extract MCMC chains from a JAGS object

Fit JAGS model to aggregated data

Get a discretized, truncated version of a distribution

Retrieve realizations for aggregated to daily inference

Get dates for which to use (trust) inferred daily reports

Helper function. Converts wastewater to Rt after sampling one fecal sh...

Estimate Rt using EpiEstim

Daily incidence from linear interpolation

Replace NAs with 0s in vector

Diagnostic plot for R estimation from clinical report data

Diagnostic plot for R estimation from wastewater data

Plot a distribution

Plot the Gelman Rubin statistic for all parameters.

Plot MCMC traces

Infer incidence from reports via a series of deconvolutions

Reshape JAGS fit object

Sample parameters for a single distribution from a family of distribut...

Sample from a distribution (currently only implemented for a uniform d...

Smooth realizations from estimating daily reports

Smooth wastewater data (using pre-processed wastewater)

Summarise observations by date for several ensembles

Summarise observations by date for raw iterations from an ensemble

Summarise daily inferred reports based on original reporting schedule ...