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Understanding Suppression of HIV

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.

Functions in ushr

Name Description
biphasic_root Biphasic root function
plot_TTS Plot time to suppression distribution
plot_model Plot model fits
plot_data Plot data
ushr Master function
get_CI Calculate parameter confidence intervals
get_CItable Make parameter summary table
get_plottheme Get plotting theme
get_singlephase Compute the single phase model curve
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
simulate_vl Simulate vl for subjects
single_root Single phase root function
summarize_model Summarize model output
switch_params Switch names of rate parameters
get_TTS Time to suppression (TTS) function
get_biphasic Compute the biphasic model curve
get_optim_fit Fit model to data using optim
get_nonparametricTTS Non-parametric TTS function
simulate_time Simulate timepoints for subjects
actg315raw Data from ACTG315 trial of HIV viral load in adults undergoing ART
add_noise Add noise to viral load observations
switch_simulated_params Switch names of simulated rate parameters
filter_dataTTS Prepare input data for non-parametric TTS calculations.
fit_model Fit model and obtain parameter estimates
remove_vl0 Prune viral load data
get_params Extract fitted parameters
get_parametricTTS Parametric TTS function
simulate_time_fixed Simulate timepoints for subjects according to fixed design.
simulate_data Create data function
transformVL Transform viral load data
filter_data Prepare input data
get_transformed_params Transform parameters
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Vignettes of ushr

Name
HIV.bib
Vignette.Rmd
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Details

Type Package
Date 2019-09-26
License MIT + file LICENSE
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
VignetteBuilder knitr
URL https://github.com/SineadMorris/ushr
NeedsCompilation no
Packaged 2019-10-08 01:42:18 UTC; sineadmorris
Repository CRAN
Date/Publication 2019-10-09 15:00:02 UTC

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