Package: ushr 0.2.3

Sinead E. Morris

ushr: 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.

Authors:Sinead E. Morris [aut, cre], Luise Dziobek-Garrett [ctb], Andrew Yates [ctb]

ushr_0.2.3.tar.gz
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ushr.pdf |ushr.html✨
ushr/json (API)
NEWS

# Install 'ushr' in R:
install.packages('ushr', repos = c('https://sineadmorris.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sineadmorris/ushr/issues

Datasets:
  • actg315raw - Data from ACTG315 trial of HIV viral load in adults undergoing ART

On CRAN:

Conda:

arthivmodeling-tools

4.04 score 2 stars 11 scripts 140 downloads 1 mentions 20 exports 36 dependencies

Last updated 5 years agofrom:5f51b056c7. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winOKMar 29 2025
R-4.5-macOKMar 29 2025
R-4.5-linuxOKMar 29 2025
R-4.4-winOKMar 29 2025
R-4.4-macOKMar 29 2025
R-4.4-linuxOKMar 29 2025
R-4.3-winOKMar 29 2025
R-4.3-macOKMar 29 2025

Exports:biphasic_rootfilter_datafilter_dataTTSget_biphasicget_curveget_nonparametricTTSget_parametricTTSget_singlephaseget_triphasicget_TTSplot_dataplot_modelplot_pairsplot_TTSsimulate_datasingle_rootsummarize_modeltriphasic_rootushrushr_triphasic

Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

ushr: understanding suppression of HIV in R

Sinead E. Morris

Rendered fromVignette.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2020-04-21
Started: 2019-09-27

Readme and manuals

Help Manual

Help pageTopics
Data from ACTG315 trial of HIV viral load in adults undergoing ARTactg315raw
Add noise to viral load observationsadd_noise
Biphasic root functionbiphasic_root
Prepare input datafilter_data
Prepare input data for non-parametric TTS calculations.filter_dataTTS
Fit model and obtain parameter estimatesfit_model
Fit model and obtain parameter estimatesfit_model_triphasic
Compute the biphasic model curveget_biphasic
Calculate parameter confidence intervalsget_CI
Make parameter summary tableget_CItable
Compute the model for a given subject's data and best-fit parametersget_curve
Evaluate error metric between data and model predictionget_error
Evaluate error metric between data and model predictionget_error_triphasic
Non-parametric TTS functionget_nonparametricTTS
Fit model to data using optimget_optim_fit
Fit triphasic model to data using optimget_optim_fit_triphasic
Parametric TTS functionget_parametricTTS
Extract fitted parametersget_params
Get plotting themeget_plottheme
Compute the single phase model curveget_singlephase
Transform parametersget_transformed_params
Compute the triphasic model curveget_triphasic
Time to suppression (TTS) functionget_TTS
Plot dataplot_data
Plot model fitsplot_model
Plot pairwise parameter distributionsplot_pairs
Plot time to suppression distributionplot_TTS
Prune viral load dataremove_vl0
Create data functionsimulate_data
Simulate timepoints for subjectssimulate_time
Simulate timepoints for subjects according to fixed design.simulate_time_fixed
Simulate vl for subjectssimulate_vl
Single phase root functionsingle_root
Summarize model outputsummarize_model
Switch names of rate parametersswitch_params
Switch names of simulated rate parametersswitch_simulated_params
Transform viral load datatransformVL
Switch names of rate parameterstri_switch_params
Triphasic root functiontriphasic_root
Master functionushr
Master function for the triphasic modelushr_triphasic