``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...