Code and data used in the paper `An optimization framework to guide choice of thresholds for risk-based cancer screening' by Adam R Brentnall, Emma C Atakpa, Harry Hill, Ruggiero Santeramo, Celeste Damiani, Jack Cuzick, Giovanni Montana, Stephen W Duffy. The repository enables reproduction of the analysis done in the paper.
The files are organised in two directories
algorithm: python code to solve the optimisation problem, with input as described for the application in the paper.paper-analysis: R code and data files output from the algorithm, that enable the figures in the paper.
The main routines are:
- riskproto.py: python code to optimise risk groups given constraints in
config.ini, and input csv file (default isinput/input.csv) - riskproto-iterH.py: python code to optimise risk groups by looping over different values of the constraint (hard coded), given input file
The input sub-directory contains csv files for the scenarios considered in the paper.
The R script reprod-eval.R may be used to reproduce the charts presented in the paper. These scripts use data in the sub-directory data and output to the sub-directory figures.
The data sub-directory includes several csv files with the prefix output. These were obtained by running the algorithm using input files in algorithm. It also includes the data from Supplementary Table 1 (mirai-centiles.csv), and data underlying Figure 1 (histo.csv).
GNU GPL v3
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Copyright 2023, Adam Brentnall