diff --git a/README.md b/README.md index c0cece5..c9d919b 100644 --- a/README.md +++ b/README.md @@ -41,34 +41,57 @@ Source: Webb GM, Li S, Mwakalundwa G, Folkvord JM, Greene JM, Reed JS, et al. "T In addition to the MATLAB scripts referenced above, this repository contains the following functions: 'N803_model_2.m' (solves ODE model for N-803 treatment of SIV) + 'N803_model_2A.m' (solves ODEs for alternative model A) + 'N803_model_2B.m' (solves ODEs for alternative model B) + 'N803_model_2C.m' (solves ODEs for alternative model C) + 'N803_model_2D.m' (solves ODEs for alternative model D) + 'N803_model_2_naive.m' (solves ODE model for N-803 given to SIV-naive NHP) 'N803_shared_2.m' (calls 'N803_model_2.m', but first solves for ICs and shared parameters to start from two fixed points) + 'N803_shared_2A.m' (calls 'N803_model_2A.m', but first solves for ICs and shared parameters to start from two fixed points) + 'N803_shared_2B.m' (calls 'N803_model_2B.m', but first solves for ICs and shared parameters to start from two fixed points) + 'N803_shared_2C.m' (calls 'N803_model_2C.m', but first solves for ICs and shared parameters to start from two fixed points) + 'N803_shared_2D.m' (calls 'N803_model_2D.m', but first solves for ICs and shared parameters to start from two fixed points) + 'N803_single_2.m' (calls 'N803_model_2.m', but first solves for ICs and parameters to start from one fixed point) In 'Analyzer' folder: 'calibrator.m' (called by 'main.m' scripts; calibrates model parameters via multi-start local-search) + 'calibrator_plot.m' (called by 'main.m' scripts; plots results from 'calibrator.m') + 'copyfields.m' (called by 'gridplot.m'; copies fields from one scalar structure to another) + 'costFun_NLL.m' (called by 'main.m' scripts; model cost calculator (NLL,SSE,MSE w/additional options)) + 'gridplot.m' (called by 'N803_plotter_2.m'; creates a grid of plots (alternative to MATLAB's 'subplot')) + 'linemaker.m' (called by 'gridplot.m'; plots lines to current axis, with a variety of options) + 'looper.m' (called by 'calibrator.m'; loops through and operates on a structure array) + 'MCMCsampler.m' (called by 'main.m' scripts; performs uncertainty quantification via markov chain monte carlo) + 'parplotter.m' (called by 'N803_plotter_2_parameters.m'; plots parameter distributions) + 'performPT.m' (called by 'MCMCsampler.m'; parallel tempering MCMC algorithm) Source: https://github.com/ICB-DCM/PESTO/blob/master/private/performPT.m + 'prepper.m' (called by 'main.m' scripts; normalizes a data set and provides several useful outputs) + 'sampler.m' (called by 'calibrator.m'; samples a parameter space via latin hypercube sampling) + 'tickmaker.m' (called by 'N803_plotter_2.m'; creates axis tick labels) + 'violin.m' (called by 'parplotter.m'; creates violin plots) Source: https://github.com/bastibe/Violinplot-Matlab/blob/master/Violin.m