Update README.md

README.md

@@ -34,38 +34,40 @@ Source: Webb GM, Li S, Mwakalundwa G, Folkvord JM, Greene JM, Reed JS, et al. "T
 
 The repository containts the following code (MATLAB .m functions):
 
-'N803_model_2.m' (solves ODE model)
+'N803_model_2.m' (solves ODE model for N-803 treatment of SIV)
 
 'N803_shared.m' (calls 'N803_model_2.m', but first solves for ICs and shared parameters to start from two fixed points)
 
 'N803_single.m' (calls 'N803_model_2.m', but first solves for ICs and parameters to start from one fixed point)
 
 In 'Analyzer' folder:
 
-'calibrator.m' (calibrates model parameters via multi-start local-search)
+'calibrator.m' (called by 'main.m' scripts; calibrates model parameters via multi-start local-search)
 
-'calibrator_plot.m' (plots results from calibrator.m)
+'calibrator_plot.m' (called by 'main.m' scripts; plots results from 'calibrator.m')
 
-'copyfields.m' ()
+'copyfields.m' (called by 'gridplot.m'; copies fields from one scalar structure to another) 
 
-'costFun_NLL.m' (model cost calculator: NLL,SSE,MSE w/additional options) [used with 'calibrator.m']
+'costFun_NLL.m' (called by 'main.m' scripts; model cost calculator (NLL,SSE,MSE w/additional options))
 
-'gridplot.m' ()
+'gridplot.m' (called by 'N803_plotter_2.m'; creates a grid of plots (alternative to MATLAB's 'subplot'))
 
-'linemaker.m' ()
+'linemaker.m' (called by 'gridplot.m'; plots lines to current axis, with a variety of options)
 
-'looper.m' (loops through and operates on a structure array) [used by 'calibrator.m']
+'looper.m' (called by 'calibrator.m'; loops through and operates on a structure array)
 
-'MCMCsampler.m' (performs uncertainty quantification via markov chain monte carlo) [needs result file from 'calibrator.m']
+'MCMCsampler.m' (called by 'main.m' scripts; performs uncertainty quantification via markov chain monte carlo)
 
-'parplotter.m' ()
+'parplotter.m' (called by 'N803_plotter_2_parameters.m'; plots parameter distributions)
 
-'performPT.m' (parallel tempering MCMC algorithm) [called by 'MCMCsampler.m']
+'performPT.m' (called by 'MCMCsampler.m'; parallel tempering MCMC algorithm)
+Source: https://github.com/ICB-DCM/PESTO/blob/master/private/performPT.m
 
-'prepper.m' (normalizes a data set and provides several useful outputs) [used with 'calibrator.m']
+'prepper.m' (called by 'main.m' scripts; normalizes a data set and provides several useful outputs)
 
-'sampler.m' (samples a parameter space via latin hypercube sampling) [used by 'calibrator.m']
+'sampler.m' (called by 'calibrator.m'; samples a parameter space via latin hypercube sampling)
 
-'tickmaker.m' ()
+'tickmaker.m' (called by 'N803_plotter_2.m'; creates axis tick labels)
 
-'violin.m' ()
+'violin.m' (called by 'parplotter.m'; creates violin plots)
+Source: https://github.com/bastibe/Violinplot-Matlab/blob/master/Violin.m