R: Understanding Suppression of HIV

# Understanding Suppression of HIV

## Documentation for package ‘ushr’ version 0.2.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

actg315raw | Data from ACTG315 trial of HIV viral load in adults undergoing ART
add_noise | Add noise to viral load observations
biphasic_root | Biphasic root function
filter_data | Prepare input data
filter_dataTTS | Prepare input data for non-parametric TTS calculations.
fit_model | Fit model and obtain parameter estimates
fit_model_triphasic | Fit model and obtain parameter estimates
get_biphasic | Compute the biphasic model curve
get_CI | Calculate parameter confidence intervals
get_CItable | Make parameter summary table
get_curve | Compute the model for a given subject's data and best-fit parameters
get_error | Evaluate error metric between data and model prediction
get_error_triphasic | Evaluate error metric between data and model prediction
get_nonparametricTTS | Non-parametric TTS function
get_optim_fit | Fit model to data using optim
get_optim_fit_triphasic | Fit triphasic model to data using optim
get_parametricTTS | Parametric TTS function
get_params | Extract fitted parameters
get_plottheme | Get plotting theme
get_singlephase | Compute the single phase model curve
get_transformed_params | Transform parameters
get_triphasic | Compute the triphasic model curve
get_TTS | Time to suppression (TTS) function
plot_data | Plot data
plot_model | Plot model fits
plot_pairs | Plot pairwise parameter distributions
plot_TTS | Plot time to suppression distribution
remove_vl0 | Prune viral load data
simulate_data | Create data function
simulate_time | Simulate timepoints for subjects
simulate_time_fixed | Simulate timepoints for subjects according to fixed design.
simulate_vl | Simulate vl for subjects
single_root | Single phase root function
summarize_model | Summarize model output
switch_params | Switch names of rate parameters
switch_simulated_params | Switch names of simulated rate parameters
transformVL | Transform viral load data
triphasic_root | Triphasic root function
tri_switch_params | Switch names of rate parameters
ushr | Master function
ushr_triphasic | Master function for the triphasic model