This directory contains a script to produce each manuscript figure. The scripts map to manuscript figures as follows:
- Figure 1A, Figure 2, Figure S1: figure comparing APD to observed time (Figure 1A) and overlaid with inferred model APD slopes (Figure 2); also a figure showing credible intervals for inferred APD slopes (Figure S1)
- Figure 3: figure comparing median APD slopes with set-point viral load
- Figure 5: figure showing mean absolute error by sequencing region, comparison of true time since infection and model-derived time since infection, and mean residual versus true time since infection
- Figure 7: figure showing mean absolute error by sequencing region using the testing dataset
- Figure S2: figure comparing median APD slopes with rate of CD4 decline
- Figure S3: figure showing histograms for various model posterior predictive checks
- Figure S4: comparison of the model prediction errors for the training data set when drawing observations from a Laplace distribution and a Normal distribution within the infant-trained hierarchical model formulation
- Figure S5 and Figure S6: distribution of APD measures for the three gene-regions for each data set