willgreen236 / cttrajectories_b117

Data and code associated with "Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2"

S.M. Kissler*, J.R. Fauver*, C. Mack*, C. Tai, M. Breban, A. Watkins, R.M. Samant, D.J. Anderson, D.D. Ho, N. Grubaugh+, Y.H. Grad+

* denotes equal contribution

+ denotes co-senior author

Correspondence: [email protected]

run_analysis.R is the main analysis file. It calls all other functions in the proper order. It calls data from the data/ directory, saves key figures into the figures/ directory, and saves the fitted distributions into the output/ directory.

ct_dat_refined.csv is the main data file. It contains a person ID, a diagnosis of novel/persistent infection, the B.1.1.7 status (Yes/No), the Test Date Index (days from that person's minimum recorded Ct value), and a clean Person ID column running from 1 to 65.

fit_posteriors.R runs the MCMC sampling scheme to fit the viral trajectory parameters.

fit_posteriors_b117.R contains the Stan program for fitting the viral trajectory parameters.

fit_posteriors_preamble.R defines key data structures for fitting the viral trajectories.

make_figures.R generates the figures from the manuscript.

save_figures.R writes the figures to .pdf. The directory for saving the figures is speified in run_analysis.R (default is the figures/ directory).

set_global_pars.R defines parameters needed throughout the code (currently just the PCR limit of detection).

summarise_dists.R conveniently summarizes the mean posterior viral trajectory distributions.

utils.R contains key functions needed for the analysis.

All code is available under the GNU General Public License, version 3, included in this repository under the following terms:

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/>.