From 533bc3890ffb5499f463112bacae269496d6bd5c Mon Sep 17 00:00:00 2001 From: "Cody, Jonathan William" Date: Tue, 27 Dec 2022 10:23:56 -0600 Subject: [PATCH] Update README.md --- README.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/README.md b/README.md index 0d6970d..4651b31 100644 --- a/README.md +++ b/README.md @@ -10,3 +10,21 @@ ODE model of viral and immune dynamics in response to treatment of SIV with IL-1 'N803_shared_noN.m' = repeat of 'N803_shared.m' without non-SIV-specific CD8+ T cells 'N803_single.m' = calls 'N803_model_2.m', but first solves for ICs and parameters to start from one fixed point + +'Analyzer' folder: + + -> 'calibrator.m' = calibrates model parameters via multi-start local-search + + -> 'calibrator_plot.m' = plots results from 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']