Update README.md

README.md

@@ -1,19 +1,23 @@
 # N-803_SIV_Model
 Jonathan W. Cody
 
-This repository contains all the code needed to replicate the following journal article, submitted to PLoS Computational Biology. MATLAB R2018b or later is required.
-
+This repository contains all the code needed to replicate the following article. MATLAB R2018b or later is required.
 Cody JW, Ellis-Connell AL, O’Connor SL, Pienaar E. "Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load."
 
 =========================
 
-To replicate the article, unzip the entire repository into a folder and run the code in the following order below. Results of step #3 are included in the repository in the file 'N803_ForPlots.mat', which allows you to skip to plotting (steps #4,5). 
+To replicate the article, unzip the entire repository into a folder and run the code in the following order below. Results of step #3 are included in the repository in the file 'N803_ForPlots.mat', which allows you to skip to plotting (steps #4,5). To replicate only the MAIN TEXT results, perform steps #1,3,4, but first edit 'N803_collector_2.m' and 'N803_plotter_2.m' (see those scripts for instructions).
 
-  1. "main_shared_2_calibration" (runs MSLS and MCMC for both cohorts with shared constants)
-  2. "main_singles_calibration_2022_09_25.m" (repeat with parameters not shared)
-  3. "N803_collector_2.m" (stores model outputs, parameters, and initial conditions from thinned MCMC sample)
-  4. "N803_plotter_2.m" (creates all time-course plots)
-  5. "N803_plotter_2_violin.m" (creates violin plots)
+  1. 'main_shared_2_calibration.m' (runs MSLS and MCMC for both cohorts with shared constants)
+  2. supplemental calibrations:
+     -> 'main_shared_2A_calibration.m'
+     -> 'main_shared_2B_calibration.m'
+     -> 'main_shared_2C_calibration.m'
+     -> 'main_shared_2D_calibration.m'
+     -> 'main_single_2_calibration.m'
+  3. 'N803_collector_2.m' (stores model outputs, parameters, and initial conditions from thinned MCMC sample)
+  4. 'N803_plotter_2.m' (creates all time-course plots)
+  5. 'N803_plotter_2_violin.m' (creates violin plots)
 
 =========================
 
@@ -34,42 +38,37 @@ 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):
+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_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)
+'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
-
+    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
+    Source: https://github.com/bastibe/Violinplot-Matlab/blob/master/Violin.m