analyses/scripts/R-scripts/Models/README.md

In thednainus/senegalHIVmodel: Analysis of HIV data from Senegal

Directories are organized by (1) analyses by subtype (subtype C and CRF 02_AG) and (2) analyses for subtypes combined (including subtypes B, C and CRF 02_AG). In each directory will you find one the following files summarized below. In the OSG directory will you find the scripts used in the Open Scince Grid computer resources.

Summary of each file

1.model.R

Mathematical model for the Senegal HIV dynamics

2.load_data.R

Load the necessary data for the phylodynamic analysis

3.mcmc.R

Source the files "1.model.R" and "2.load_data.R". Perform the MCMC using the BayesianTools R package

4.mcmc_zMatrix.R

Source the files "1.model.R" and "2.load_data.R". Perform the MCMC using the BayesianTools R package. The difference here is that it uses a previous run to generate values for a z-matrix. This previous run was generated using script 3.mcmc.R. For more information see https://github.com/florianhartig/BayesianTools/issues/79

thednainus/senegalHIVmodel documentation built on Oct. 14, 2024, 5:46 a.m.