Dawson et al.2021_Inferring environmental transmission using phylodynamics: A case-study using simulated evolution of an enteric pathogen

Published: 17-05-2021| Version 2 | DOI: 10.17632/tbwx3fdmym.2
Contributors:
Daniel Dawson,
Cristina Lanzas,
David Rasmussen,
Xinxia Peng

Description

This dataset is associated with a manuscript entitled "Inferring environmental transmission using phylodynamics: A case-study using simulated evolution of an enteric pathogen" by Dawson et al., published by the Journal of the Royal Society Interface in 2021. This dataset contains the scripts and data necessary to reproduce the results presented in that manuscript. The included "Readme" file explains the contents of the dataset in greater detail.

Files

Steps to reproduce

This research conducted to produce this dataset and the manuscript that corresponds to it was conducted at North Carolina State University. All computational work was done using either program R, BEAST2, or Python. Most R scripts here were developed by the corresponding author, Daniel Dawson. The R script SeedyEnvModel_Transmission_Scenarios_Manuscript.R was developed by modifying the SEEDY model by Worby and Read (2015) and included in the seedy package or R. Two Python scripts included here were modified versions of scripts provided with the SCOTTI algorithm.