Understanding Suppression of HIV
Add noise to viral load observations
Biphasic root function
Prepare input data
Prepare input data for non-parametric TTS calculations.
Fit model and obtain parameter estimates
Fit model and obtain parameter estimates
Compute the biphasic model curve
Calculate parameter confidence intervals
Make parameter summary table
Compute the model for a given subject's data and best-fit parameters
Evaluate error metric between data and model prediction
Evaluate error metric between data and model prediction
Non-parametric TTS function
Fit model to data using optim
Fit triphasic model to data using optim
Parametric TTS function
Extract fitted parameters
Get plotting theme
Compute the single phase model curve
Transform parameters
Compute the triphasic model curve
Time to suppression (TTS) function
Plot data
Plot model fits
Plot pairwise parameter distributions
Plot time to suppression distribution
Prune viral load data
Create data function
Simulate timepoints for subjects
Simulate timepoints for subjects according to fixed design.
Simulate vl for subjects
Single phase root function
Summarize model output
Switch names of rate parameters
Switch names of simulated rate parameters
Transform viral load data
Switch names of rate parameters
Triphasic root function
Master function
Master function for the triphasic model
Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.