Resubmission v1

Response to first round of reviewer comments, PLoS Pathogens.

Initial_submission

Code for initial submission to PLoS Pathogens.

Identical to v1.3. Drafting new release to address corrupted DOI assignment in Zenodo.

Initial_submission

Contains code for initial submission to PLoS Pathogens. Updated July 5, 2019.

v1.3 removes manuscript draft files, which are unrelated to data analysis.

Initial_submission

Code for initial submission to PLoS Pathogens. Created July 5, 2019.

v1.1 adds a license, removes junk files and converts all figures (previously in .pdf format) to .tiff, in compliance with PLoS submission guidelines.

First release

For manuscript initial submission, 3 July 2019.