Repository for the preprint "Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates" available on arXiv.
This repository contains two modules:
Analysiscontaining the functions to compute profile likelihoods and optimisations.SpheroidModelscontaining all the spheroid models used in the work.
To download, first clone this Github repo. Next, add the module folder to your LOAD_PATH:
push!(LOAD_PATH,"/path/to/repo/Module")
Next, run the following code (press ] to enter the Pkg REPL) to install all required packages and activate the project
(v1.7) pkg> activate .
(spheroid_geometry) pkg> instantiate
Code used to produce each figure in the main document and supplementary material is available in the Results/Figures folder. For example, to reproduce Figure 4, run Results/Figures/fig4.jl.
Note that, while all the computations are performed in Julia, Figure 6 is produced in MATLAB. To reproduce Figure 6, first run fig6abc.jl and fig6d.jl which produce .mat files that are read into Matlab and plotted in fig6.m.