RSV Transmission model

THIS CODE HAS BEEN SUPERSEEDED

The fitting part of the code has an R implementation: dchodge/rsv_model_R_fit The intevention part of the code has an R implementaiton here: dchodge/rsv_model_R_custom

David Hodgson's RSV transmission model

This is the c++ code is used to determine the cost-effectiveness of different intervention programmes agaisnt RSV infection in England. The model comprises three main parts:

1. A code to calibrate the dynamic transmission model to RSV positive samples using a parallel tempering MCMC method
2. Codes to evaluate the impact of the intervention prgorammes at preventing outcomes, including symptomatic infections, hospitalised cases, deaths, GP consultations, and bed days.
3. A cost-effectiveness analysis to convert the outcomes averted into QALY loss and costs.

LICENSE

Copyright (C) 2019 David Hodgson

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Installation

A c++14 compliant complier is required

Dependencies

A header folder should be made and the following header-only packages should be placed there:

• Ascent https://github.com/AnyarInc/Ascent
• Eigen http://eigen.tuxfamily.org/index.php?title=Main_Page

Boost is also required, and the boost_random package should be linked.

Outline of .cpp and .h files in src folder

Main.cpp

This section outlines the five main functions;

FUNC1: parallel_temp_mcmc -> Run the MCMC parallel tempering algorithm FUNC2:"posterior_inc -> Determine incidence from posterior samples FUNC3:"find_optimal_week" -> Determine the optimal month for seasonal programmes to begin FUNC5a:"intervention_p" -> Run the simualtions for the 14 intervention progammes FUNC5b:"intervention_p_SA" -> Run the simualtions for the sensitivtiy analysis

I comment out the functions I don't want and run then build and run. Probably very easy to make an interface for this.

pre.h

A few type defs, probability distributions functions, and global functions are defined here

epmgp.h

This is just a c++ versions of a script outlined here >>> https://github.com/cunni/epmgp. It just helps evaluated a point x in a multivariate truncated normal distribution with support: a<x<b, mean: mu, and covariance matrix Sigma.

mcmc.h

Code for the adaptive parallel tempering mcmc methods >> https://arxiv.org/abs/1205.1076. amh namespace refers to metropolis hasting on each of the chains, mhp namespace refers to parameters relevant to all the chains

model.h

Priors, ODES, likelihood, data import for the calibration dynamic transmission model. all data is in the inputs folder.

outcomes.h

Code used to determine the probabilities of each outcome.

interventions.h

Code outlining the characteristics of each of the intervention programmes, generating the dynamic calendar, and the ODEs for the augmented model

writing.h

Formating the vectors into a exportable format (see outputs folder)

cea.h

code for converting the outcomes averted into QALY and costs