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ushr (version 0.1.0)

Understanding Suppression of HIV

Description

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) ; and Wu and Ding (1999) ). 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.

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Install

install.packages('ushr')

Monthly Downloads

135

Version

0.1.0

License

MIT + file LICENSE

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Repository

https://github.com/SineadMorris/ushr

Maintainer

Sinead E. Morris

Last Published

October 9th, 2019

Functions in ushr (0.1.0)

Biphasic root function

Plot time to suppression distribution

Plot model fits

Master function

Calculate parameter confidence intervals

Make parameter summary table

Get plotting theme

get_singlephase

Compute the single phase model curve

Compute the model for a given subject's data and best-fit parameters

Evaluate error metric between data and model prediction

Simulate vl for subjects

Single phase root function

summarize_model

Summarize model output

Switch names of rate parameters

Time to suppression (TTS) function

Compute the biphasic model curve

Fit model to data using optim

get_nonparametricTTS

Non-parametric TTS function

Simulate timepoints for subjects

Data from ACTG315 trial of HIV viral load in adults undergoing ART

Add noise to viral load observations

switch_simulated_params

Switch names of simulated rate parameters

Prepare input data for non-parametric TTS calculations.

Fit model and obtain parameter estimates

Prune viral load data

Extract fitted parameters

get_parametricTTS

Parametric TTS function

simulate_time_fixed

Simulate timepoints for subjects according to fixed design.

Create data function

Transform viral load data

Prepare input data

get_transformed_params

Transform parameters