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ushr (version 0.2.3)

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

113

Version

0.2.3

License

MIT + file LICENSE

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Repository

https://github.com/SineadMorris/ushr

Maintainer

Sinead E. Morris

Last Published

April 21st, 2020

Functions in ushr (0.2.3)

Extract fitted parameters

Simulate timepoints for subjects

get_nonparametricTTS

Non-parametric TTS function

Create data function

Compute the biphasic model curve

Fit model to data using optim

get_transformed_params

Transform parameters

Transform viral load data

get_singlephase

Compute the single phase model curve

Get plotting theme

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

Fit model and obtain parameter estimates

Plot model fits

Simulate vl for subjects

simulate_time_fixed

Simulate timepoints for subjects according to fixed design.

Master function for the triphasic model

tri_switch_params

Switch names of rate parameters

Evaluate error metric between data and model prediction

get_error_triphasic

Evaluate error metric between data and model prediction

Compute the triphasic model curve

get_optim_fit_triphasic

Fit triphasic model to data using optim

Plot time to suppression distribution

get_parametricTTS

Parametric TTS function

Single phase root function

Plot pairwise parameter distributions

Master function

Prune viral load data

Triphasic root function

switch_simulated_params

Switch names of simulated rate parameters

Switch names of rate parameters

summarize_model

Summarize model output

Prepare input data

Prepare input data for non-parametric TTS calculations.

Biphasic root function

Time to suppression (TTS) function

fit_model_triphasic

Fit model and obtain parameter estimates

Make parameter summary table

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

Add noise to viral load observations

Calculate parameter confidence intervals