docs/: Contains the latex manuscript and supplementary materials

code/: Contains all the code necessary for exactly reproducing the analyses and figures in the manuscript. The work horse behind all of the analysis is the module pihm_methods.py which provides the functions for implementing the Crofton Method, Adjei Method, and the Likelihood Method.

• All of the analyses in the manuscript can be re-run

• To run the simulations simply type the following commands at the command line

• python analysis_for_manuscript_full_likelihood.py

• python analysis_for_manuscript_hostsurvivalfxn.py

• python analysis_for_manuscript_typeIandII.py

• All figures in the plot can be remade by opening manuscript_plots.ipynb in the ipython notebook and running all the cells

• The results for table 2 are generated by analysis_for_manuscript_test_data.py

results/: Directory where the analysis results are stored