Files to generate the results that are plotted in Figure 7H OF THE MANUSCRIPT in "Vaccine-primed subcapsular sinus macrophages promote germinal centre re-entry by memory B cells" by Rama Dhenni et al.

In order to generate the results, the following files are needed
1. script_fig_7h.R-> this is the main script to produce the modeling results as in Fig 7H in the manuscript. The script will produce a .csv file (Results.csv) containing the population estimates of the antibody for ancestral, delta, and BA1 variant. 
2. data_all_mixed_model.txt -> raw dataset of antibody titers, with the following columns:
	a. id-> unique identifier for each subject
	b. Variant -> Categorical variable (indicator for ancestral, delta, or BA1 variant)
	c. Time -> days post boost
	d. Cens -> censoring indicator, this will be 1 if the raw neutralization antibody level is less than 28.7257
	e. Y-> log-transformed neutralization antibody level (log10)
3. model_peak.txt -> model formula, as described in the methods section of the paper "Estimating growth and decay of neutralizing antibody titres"
4. model_dv_ga.mlxproperties -> MONOLIX model file
5. model_dv_ga.mlxtran -> MONOLIX model file

In order to run the script, the package MONOLIX needs to be installed (in R). Note that the MONOLIX pacgkage requires a licence, which can be obtained from here: https://lixoft.com/downloads/#RequestLicense

Running script_fig_7h.R will generate the file below that can be used to plot Figure 7H
6. Results.csv -> population estimates of the antibody level for ancestral, delta, and BA1 variant 

MONOLIX and R installation guides below: 
https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/