Estimating the sensitivity of wastewater metagenomic sequencing using nasal swabs

Simon Grimm, Dan Rice, Mike McLaren

Code and documentation supporting the NAO blog post Estimating the sensitivity of wastewater metagenomic sequencing using nasal swabs and its Appendix.

Reproducing the statistical analysis

To reproduce the model fits and diagnostics:

1. Clone this git repository.
2. From the R console, install the necessary R packages with: install.packages(c("tidyverse", "here", "rstan")). RStan may require additional setup; see the RStan docs.
3. Run the model-fitting script with: Rscript statistics/scripts/fit_model.R. (This script should take 5--10 minutes to run.)

The model-fitting script outputs four files (all of which are already checked into the repository):

• tables/model_diagnostics.tsv contains Stan diagnostic information, including the number of divergent transitions and the maximum rhat over all parameters.
• tables/posteriors.tsv contains posterior samples for all viruses. Note that re-running the fitting script may shuffle the order of the posterior samples in this file.
• tables/{prevalence,ra01}_posterior_summary.tsv contain posterior 15th, 50th, and 85th percentiles for prevalence and $RA_p(1%)$ for all viruses.

Publishing the appendix (NAO-internal only)

To publish an update to the appendix, make any changes, then run:

quarto publish gh-pages statistics/appendix/index.qmd

from the root of the repository.