Package: boinet 1.5.0

Yusuke Yamaguchi

boinet: Conduct Simulation Study of Bayesian Optimal Interval Design with BOIN-ET Family

Bayesian optimal interval based on both efficacy and toxicity outcomes (BOIN-ET) design is a model-assisted oncology phase I/II trial design, aiming to establish an optimal biological dose accounting for efficacy and toxicity in the framework of dose-finding. Some extensions of BOIN-ET design are also available to allow for time-to-event efficacy and toxicity outcomes based on cumulative and pending data (time-to-event BOIN-ET: TITE-BOIN-ET), ordinal graded efficacy and toxicity outcomes (generalized BOIN-ET: gBOIN-ET), and their combination (TITE-gBOIN-ET). 'boinet' is a package to implement the BOIN-ET design family and supports the conduct of simulation studies to assess operating characteristics of BOIN-ET, TITE-BOIN-ET, gBOIN-ET, and TITE-gBOIN-ET, where users can choose design parameters in flexible and straightforward ways depending on their own application.

Authors:Yusuke Yamaguchi [aut, cre], Kentaro Takeda [aut]

boinet_1.5.0.tar.gz
boinet_1.5.0.tar.gz(r-4.7-any)boinet_1.5.0.tar.gz(r-4.6-any)
boinet_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
boinet/json (API)

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.80 score 1 packages 14 scripts 323 downloads 19 exports 98 dependencies

Last updated from:d28e0e4732. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK212
source / vignettesOK229
linux-release-x86_64OK197
wasm-releaseOK179

Exports:boinetcreate_boinet_tablescreate_design_gt_tablecreate_oc_gt_tableextract_boinet_dataextract_design_summaryextract_operating_characteristicsformat_boinet_resultsfp.logitgboinetgridoptimlaunch.shinyappmulti.isoobd.selecttite.boinettite.gboinetutility.scoringutility.truncated.linearutility.weighted

Dependencies:ADGofTestaskpassbase64encbigDbitopsbslibcachemcliclustercolorspacecommonmarkcopulacpp11crosstalkcurldata.tabledigestdplyrDTevaluatefarverfastmapfontawesomefsgenericsggplot2gluegslgtgtablehighrhtmltoolshtmlwidgetshttpuvhttrIsoisobandjquerylibjsonlitejuicyjuiceknitrlabelinglaterlatticelazyevallifecyclelitedownmagrittrmarkdownMatrixmemoisemfpmimemvtnormnumDerivopensslotelpcaPPpillarpkgconfigplotlypromisespsplinepurrrR6rappdirsRColorBrewerRcppreactablereactRrhandsontablerlangrmarkdownS7sassscalesshinyshinyBSshinydashboardsourcetoolsstablediststringistringrsurvivalsystibbletidyrtidyselecttinytexutf8V8vctrsviridisLitewithrxfunxml2xtableyaml

Complete Quarto Workflow for BOIN-ET Reports
Overview | Helper Functions for Reports | Mock Data for Demonstration | Complete Quarto Document Template | Basic Template Structure | Example Report Sections | Dose Selection Visualization | Risk-Benefit Analysis | Parameterized Reports | Setting Up Parameters | Batch Report Generation | Conditional Content | Best Practices for Quarto Reports | 1. Document Structure | 2. Chunk Management | 3. Reproducible Workflows | 4. Output Formatting | Template Library | Clinical Protocol Report Template | Regulatory Submission Template | Troubleshooting Common Issues | Package Availability Issues | Memory and Performance Issues | Conclusion
Rendered fromquarto_workflow_vignette.rmdusingknitr::rmarkdown

Last update: 2025-06-05
Started: 2025-06-05

Creating Publication-Ready Tables with gt Integration
Overview | Key Features | Mock Data Setup | Helper Functions for Table Creation | Basic Table Creation | Operating Characteristics Table | Design Parameters Table | Custom Table Styling | Enhanced Operating Characteristics Table | Professional Clinical Table | Scenario Comparison | Multiple Design Comparison | Advanced Formatting | Design Parameters with Categories | Saving Tables | Export Options | Integration Tips | Best Practices for Clinical Tables | Troubleshooting | Common Issues and Solutions | Conclusion
Rendered fromgt_integration_vignette.rmdusingknitr::rmarkdown

Last update: 2025-06-05
Started: 2025-06-05

Result Formatting with Enhanced boinet Package
Overview | Key Approach | Basic Workflow | Step 1: Run Simulation | Step 2: Extract and Format Data | Manual Data Extraction | Working with Different Design Types | Custom Analysis Examples | Dose Selection Analysis | Safety Analysis | Efficacy-Toxicity Trade-off | Creating Visualizations | Creating Summary Tables | Operating Characteristics Table | Design Parameters Table | Enhanced Summary Output | Exporting Data | Best Practices | 1. Consistent Workflow | 2. Data Validation | 3. Reproducible Analysis | 4. Custom Utility Functions | Advanced Analysis Examples | Sensitivity Analysis | Comparative Analysis Framework | Conclusion
Rendered fromresult_formatting_vignette.rmdusingknitr::rmarkdown

Last update: 2025-06-05
Started: 2025-06-05

Readme and manuals

Help Manual

Help pageTopics
BOIN-ET: Bayesian Optimal Interval Design for Dose-Finding Based on Efficacy and Toxicityboinet
Create Report-Ready Tables from BOIN-ET Resultscreate_boinet_tables
Create GT Table for Design Parameterscreate_design_gt_table
Create GT Table for Operating Characteristicscreate_oc_gt_table
Extract Tidy Data from BOIN-ET Resultsextract_boinet_data
Extract Design Parameters Summaryextract_design_summary
Extract Operating Characteristics in Tidy Formatextract_operating_characteristics
Format BOIN-ET Results for Reportingformat_boinet_results
Fractional Polynomial Logistic Regression for Dose-Efficacy Modelingfp.logit
gBOIN-ET: Generalized Bayesian Optimal Interval Design for Ordinal Graded Outcomesgboinet
Grid Search Optimization for BOIN-ET Design Boundariesgridoptim
Launch the Shiny Applaunch.shinyapp
Model Averaging of Multiple Unimodal Isotonic Regressionmulti.iso
Optimal Biological Dose Selectionobd.select
Print boinetprint.boinet
Print gboinetprint.gboinet
Print tite.boinetprint.tite.boinet
Print tite.gboinetprint.tite.gboinet
Summary method for boinet objectssummary.boinet
Summary method for gboinet objectssummary.gboinet
Summary method for tite.boinet objectssummary.tite.boinet
Summary method for tite.gboinet objectssummary.tite.gboinet
TITE-BOIN-ET: Time-to-Event Bayesian Optimal Interval Designtite.boinet
TITE-gBOIN-ET: Time-to-Event Generalized BOIN Design for Ordinal Graded Outcomestite.gboinet
Discrete Scoring Utility Function for Toxicity-Efficacy Trade-offsutility.scoring
Truncated Linear Utility Function for Toxicity-Efficacy Trade-offsutility.truncated.linear
Weighted Utility Function for Toxicity-Efficacy Trade-offutility.weighted