Code and data used to generate figures / datatables associated with the India hospital wastewater paper:
Talat A., Blake K.S., Dantas G., Khan A.U. Metagenomic insight into microbiome and antibiotic resistance genes of high clinical concern in urban and rural hospital wastewater of Northern India origin: a major reservoir of antimicrobial resistance. Microbiology Spectrum. 2023 Feb 14;e0410222. doi: 10.1128/spectrum.04102-22. PMID: 36786639. LINK
Each .Rmd file can be exported as an .html report by pressing the Knit button in RStudio.
By default, export directory structure (under /reports) is not created, and plots/datatables are NOT exported. The code for this is commented-out in _common.R and all .Rmd files. Remove the comments where indicated to export these as .pdf/.csv.