Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection
This repository contains three folders named figure_codes, figure_data_files, and monolix_files which can be used to generate the figures in the manuscript. The julia_packages.txt file lists all the packages used in Julia 1.7.3 to perform the calculations. A description of the files in the individual folders is given below:
These files fit the best-fit model of our study to the longitudinal data and infer the parameter values. The file masterfile_model_1.mlxtran is the Monolix file that should be run to obtain these estimates. While modelFile_model_1.txt codes the model, the master_data_RNA_DNA_p27_kE0.csv is the raw longitudinal data file; both files are formatted as per the requirement of Monolix. Finally, the nohup.txt is the output obtained by running the .mlxtran file.
This folder contains all the .xlsx and .csv files required to plot the figures. The names of the files are self-explanatory: files with the suffix parameters_ have the parameter values estimated for different models employed in the study; the master_data_ suffix refers to files with the raw longitudinal data--both in vivo and ex vivo models; and the modified_DNA_post_peak.xlsx is the SIV DNA data without the measurements before the peak in the data.
This folder contains the Julia files that can be run to reproduce the figures; names are self-explanatory.