Short_term_sub_model

This directory contains all of the code necessary to estimate the parameters of the sub-model of the short-term titer dynamics, to simulate the dynamics from the best-fit sub-model parameters, and to perform model validation. Please refer to the Introductory page for a step-by-step overview of the manuscript analysis. Briefly, the worfklow for this directory is as follows:

1. Estimate the parameters that guide the short-term post-infection titer dynamics (using the code in the Inference subdirectory).

2. Analyze the inference results and calculate the parameter MLEs/95% CIs (using the code in the Results_analysis subdirectory). After you have estimated all of the fitted parameters, create a .rda file containing a named vector of all parameters for the model simulations (step 3).

3. Simulate the dynamics from the best-fit model parameters and generate the output plots (using code in the Simulations subdirectory). The output plots will save as .pdf files in the Output_plots subdirectory.