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Colorectal Cancer (CRC) MATLAB Simulation Toolbox


This toolbox implements the paper

Jihyoun Jeon et al. “Evaluation of screening strategies for pre-malignant lesions using a biomathematical approach”. In: Mathematical biosciences 213.1 (2008), pp. 56–70.

which can be found on google scholar. The file tex/paper/paper.pdf explains an approximation used which decreases the computational time by two to three orders of magnitude while retaining comparable accuracy.

Overview

The repo is structured as follows

  • src: All code
  • tex: All tex related files

Installation

  • Clone the repository: git clone https://github.com/lkskstlr/msce.git
  • Add the src folder to your MATLAB path
  • Install dependencies:
    • chebfun is an excellent MATLAB package for Chebyshev polynomial approximation from Oxford's Numerical Analysis Group. It can be obtained from their website. We recommend installing through git which they call the developer option.
    • cbrewer is a MATLAB package that wraps the nice colorbrewer colors. It is used for plotting. It can be found on fileexchange.
    • export_fig is used for printing figures. The MSCE core should work without it. Find the github repo here.

Code Structure

  • src/tests contains the MATLAB unit tests which can and should be run by running src/tests/crc_run_all_tests.m.
  • The prefix crc indicates functions specific for the Colorectal Cancer paper.
  • Function Nomenclature:
    • crc_survival*.m are the survival functions for the *-stage model. They return the value.
    • crc_mksurvival*.m are the survival functions for the *-stage model. They return a chebfun approximation (accurate to nearly machine precision: 1e-15) of the survival function. crc_mklogsurvival*.m returns a chebfun for the log of the survival function.crc_mksurvival*m1.m returns a chebfun for the survival function minus 1.
    • The above holds also for the hazard functions.

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Simulation Toolbox for Multistage Clonal Expansion (MSCE) Models

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