Repository containing the code and methods for Bosch & DeJesus et al. 2021
Below is a short legend describing the main files, followed by example running the code:
R code with functions useful for running the vulnerability analysis.
R code with functions useful for plotting vulnerability results
R code for running vulnerability analysis in paralell.
Stan code for the vulnerability model.
R code for creating plots of vulnerability results in parallel.
To run the actual analysis with example parameters simply run:
Rscript gene_vul_analysis_parellel.R
Alternatively, users can provide three parameters:
- desired_strain (label to describe strain being analyzed, helpful to distinguish results)
- label (general label to distinguish results)
- data_path (path to the CSV formatted file with passaging data)
Rscript gene_vul_analysis_parellel.R H37Rv test example_H37Rv_data.txt
Similarly, users can create plots of the results by running the following command:
Rscript gene_vul_plots_parallel.R
Alternatively users can provide four parameters:
- desired_strain (label to describe strain being analyzed, helpful to distinguish results)
- label (general label to distinguish results)
- data_path (path to the CSV formatted file with passaging data)
- results path (path to the directory containing the resuls from the analysis.)
Rscript gene_vul_plots_parallel.R H37Rv test example_H37Rv_data.txt data/H37Rv/test/