Understanding Suppression of HIV

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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