concRt

This package allows users to generate posterior estimates of the effective reproduction number from RNA concentrations and case counts and allows the user to fit the four models described in "Semiparametric Inference of Effective Reproduction Number Dynamics from Wastewater Pathogen RNA Concentrations."

Required Installation Steps

To install the package type ] to activate pkg, then use the command

add https://github.com/igoldsteinh/concRt.jl

Example usage

using concRt

data = [7.746720258212705, 8.480719432981955, 8.326951744058404, 7.7084576380183, 9.522542336229806, 8.22919522225484, 7.906042278483086, 8.016161975227881, 8.055971726781609, 8.819137047777467, 8.179845943869427, 9.279987578665471, 10.493308139257781, 10.498784254098249]
obstimes = [1.0, 3.0, 5.0, 7.0, 9.0, 11.0, 13.0, 15.0, 17.0, 19.0, 21.0, 23.0, 25.0, 27.0]
param_change_times = [7.0, 14.0, 21.0]
priors_only = false
n_samples::Int64 = 10
n_chains::Int64 = 1

posterior_samples_eirr <- fit_eirrc(data, 
                               obstimes, 
                               param_change_times, 
                               priors_only, 
                               n_samples, 
                               n_chains, 
                               seed)