Update README.md

README.md

@@ -6,6 +6,7 @@ This repository contains all the code needed to replicate the following journal
 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. 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" (runs MSLS and MCMC for both cohorts with parameters shared)
@@ -15,20 +16,22 @@ To replicate the article, unzip the entire repository into a folder and run the
   5. "N803_plotter_2_parameters.m" (creates parameter violin plots)
 
 =========================
+
 The repository containts the following data (MATLAB .mat files):
 
 "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_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.
+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. 2022;96(20).
 
 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.
 
 'N803_MCMC.mat' (model parameter values, initial conditions, and outputs underlying all article figures)
 
 =========================
+
 The repository containts the following code (MATLAB .m functions):
 
 'N803_model_2.m' (solves ODE model)
@@ -39,18 +42,30 @@ The repository containts the following code (MATLAB .m functions):
 
 In 'Analyzer' folder:
 
-'calibrator.m' = calibrates model parameters via multi-start local-search
+'calibrator.m' (calibrates model parameters via multi-start local-search)
+
+'calibrator_plot.m' (plots results from calibrator.m)
+
+'copyfields.m' ()
+
+'costFun_NLL.m' (model cost calculator: NLL,SSE,MSE w/additional options) [used with 'calibrator.m']
+
+'gridplot.m' ()
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+'linemaker.m' ()
+
+'looper.m' (loops through and operates on a structure array) [used by 'calibrator.m']
 
-'calibrator_plot.m' = plots results from calibrator.m
+'MCMCsampler.m' (performs uncertainty quantification via markov chain monte carlo) [needs result file from 'calibrator.m']
 
-'costFun_NLL' = model cost calculator (NLL,SSE,MSE w/additional options) [used with 'calibrator.m']
+'parplotter.m' ()
 
-'looper.m' = loops through and operates on a structure array [used by 'calibrator.m']
+'performPT.m' (parallel tempering MCMC algorithm) [called by 'MCMCsampler.m']
 
-'MCMCsampler.m' = performs uncertainty quantification via markov chain monte carlo [needs result file from 'calibrator.m']
+'prepper.m' (normalizes a data set and provides several useful outputs) [used with 'calibrator.m']
 
-'performPT.m' = parallel tempering MCMC algorithm [called by 'MCMCsampler.m']
+'sampler.m' (samples a parameter space via latin hypercube sampling) [used by 'calibrator.m']
 
-'prepper.m' = normalizes a data set and provides several useful outputs [used with 'calibrator.m']
+'tickmaker.m' ()
 
-'sampler.m' = samples a parameter space via latin hypercube sampling [used by 'calibrator.m']
+'violin.m' ()