jwatowatson / platcov-remdesivir-regeneron

Analysis of casirivimab/imdevimab and remdesivir arms of the PLATCOV study

PLATCOV-Remdesivir-Regeneron

``Clinical antiviral efficacy of remdesivir and casirivimab/imdevimab against the SARS-CoV-2 Delta and Omicron variants''

This repository provides code and data for the analysis of the casirivimab/imdevimab (Regeneron monoclonal antibody) and remdesivir arms of the PLATCOV trial.

The repository is structured as follows:

• Paper2_analysis.csv is the dataset
• Full_Analysis.Rmd is an RMarkdown file which sets up all analyses and generates all plots
• run_models_local.R runs all models (run_models.R is written for remote cluster)
• The folder Stan_models contains stan code for the linear and nonlinear regression models
• functions.R has a bunch of useful functions for making the stan datasets and plotting output.

All the analyses are done in the RMarkdown file Full_Analysis.Rmd. There are 7 datasets used (see Supplementary Materials of the paper), and 5 models fitted per data set (total of 35 model fits).

The statistical analysis plan used to guide the analyses is given in PLATCOV_SAP_v2.2_21092022.pdf.

The following R packages are needed:

• rstan (compile and fit stan models)
• loo (model comparison)
• RColorBrewer (nice colors)
• brms (sanity check handwritten stan models)
• plotrix (gap plots)

Analysis is still work in progress - drop me a message at jwatowatson at gmail dot com if you spot any errors...