Update README.md

README.md

@@ -3,41 +3,54 @@ Jonathan W. Cody
 
 This repository contains all the code needed to replicate the following journal article, soon to be submitted to PLoS Computational Biology. MATLAB R2018b or later is required.
 
-"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"
-Article Authors: Jonathan W. Cody, Amy L. Ellis-Connell, Shelby L. O’Connor, Elsje Pienaar
+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:
+=========================
+To replicate the article, unzip the entire repository into a folder and run the code in the following order below. Steps #1,2 are lengthy (~1 week each). Results of step #3 are included in the repository in the file 'N803_MCMC.mat', which allows you to skip to plotting (steps #4,5). 
 
-  1. "main_shared_calibration_2022_08_18.m"
-  2. "main_singles_calibration_2022_09_25.m"
-  3. "N803_collector_2.m"
-  4. "N803_plotter_2.m"
-  5. "N803_plotter_2_parameters.m"
-
-The following is list of files (INCOMPLETE)
+  1. "main_shared_calibration_2022_08_18.m" (runs MSLS and MCMC for both cohorts with parameters shared)
+  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_parameters.m" (creates parameter violin plots)
 
-'N803_model_1.m' = single-compartment model for article 1
+=========================
+The repository containts the following data (MATLAB .mat files):
 
-'N803_model_2.m' = single-compartment model for article 2
+"N803_DataSet_1.mat" (Cohort 1 calibration data)
+Source: Ellis-Connell AL, Balgeman AJ, Zarbock KR, Barry G, Weiler A, Egan JO, et al. "ALT-803 Transiently Reduces Simian Immunodeficiency Virus Replication in the Absence of Antiretroviral Treatment." Journal of virology. 2018;92(3).
 
-'N803_shared.m' = calls 'N803_model_2.m', but first solves for ICs and shared parameters to start from two fixed points
+"N803_DataSet_2.mat" (Cohort 2 calibration data, validation data)
+Source: Ellis-Connell AL, Balgeman AJ, Harwood OE, Moriarty RV, Safrit JT, Weiler AM, et al. "Control of Simian Immunodeficiency Virus Infection in Prophylactically Vaccinated, Antiretroviral Treatment-Naive Macaques Is Required for the Most Efficacious CD8 T Cell Response during Treatment with the Interleukin-15 Superagonist N-803." Journal of virology.
 
-'N803_single.m' = calls 'N803_model_2.m', but first solves for ICs and parameters to start from one fixed point
+Webb_DataSet.mat" (validation data)
+Source: Webb GM, Li S, Mwakalundwa G, Folkvord JM, Greene JM, Reed JS, et al. "The human IL-15 superagonist ALT-803 directs SIV-specific CD8(+) T cells into B-cell follicles." Blood advances. 2018;2(2):76-84.
 
-'Analyzer' folder:
+'N803_MCMC.mat' (model parameter values, initial conditions, and outputs underlying all article figures)
 
-  -> 'calibrator.m' = calibrates model parameters via multi-start local-search
+=========================
+The repository containts the following code (MATLAB .m functions):
 
-  -> 'calibrator_plot.m' = plots results from calibrator.m
+'N803_model_2.m' (solves ODE model)
 
-  -> 'costFun_NLL' = model cost calculator (NLL,SSE,MSE w/additional options) [used with 'calibrator.m']
+'N803_shared.m' (calls 'N803_model_2.m', but first solves for ICs and shared parameters to start from two fixed points)
 
-  -> 'looper.m' = loops through and operates on a structure array [used by 'calibrator.m']
+'N803_single.m' (calls 'N803_model_2.m', but first solves for ICs and parameters to start from one fixed point)
 
-  -> 'MCMCsampler.m' = performs uncertainty quantification via markov chain monte carlo [needs result file from 'calibrator.m']
+In 'Analyzer' folder:
 
-  -> 'performPT.m' = parallel tempering MCMC algorithm [called by 'MCMCsampler.m']
+'calibrator.m' = calibrates model parameters via multi-start local-search
 
-  -> 'prepper.m' = normalizes a data set and provides several useful outputs [used with 'calibrator.m']
+'calibrator_plot.m' = plots results from calibrator.m
 
-  -> 'sampler.m' = samples a parameter space via latin hypercube sampling [used by 'calibrator.m']
+'costFun_NLL' = model cost calculator (NLL,SSE,MSE w/additional options) [used with 'calibrator.m']
+
+'looper.m' = loops through and operates on a structure array [used by 'calibrator.m']
+
+'MCMCsampler.m' = performs uncertainty quantification via markov chain monte carlo [needs result file from 'calibrator.m']
+
+'performPT.m' = parallel tempering MCMC algorithm [called by 'MCMCsampler.m']
+
+'prepper.m' = normalizes a data set and provides several useful outputs [used with 'calibrator.m']
+
+'sampler.m' = samples a parameter space via latin hypercube sampling [used by 'calibrator.m']