This repository is the culmination of the work done in Carr et al. (2021). In Data you will find the data used in this project from raw to processed. In R and MATLAB you will find the code (in the respective languages) used to simulate the collective cell spreading experiment from the Simpson et al. (2018) model, the Sequential Monte Carlo Approximate Bayesian Computation (SMC-ABC) algorithm used to estimate the model parameters, and any other helper functions. In Plot Functions (R) you will find the R script used to produce the figures in Carr et al. (2021). Finally, in Computational Efficiency (R) you will find an R script which computes the computational cost of simulating the Rcpp version of the model.

References

Carr, M. J., Simpson, M. J. & Drovandi, C. (2021). Estimating parameters of a stochastic cell invasion model with fluorescent cell cycle labelling using Approximate Bayesian Computation. bioarXiv, doi: https://doi.org/10.1101/2021.04.20.440712

Simpson, M. J., Jin, W., Vittadello, S. T., Tambyah, T. A., Ryan, J. M., Gunasingh, G., Haass, N. K. & McCue, S. W. (2018). Stochastic models of cell invasion with fluorescent cell cycle indicators. PhysicaA: Statistical Mechanics and its Applications,510, 375–386.