Package: BuyseTest 3.4.0

BuyseTest: Generalized Pairwise Comparisons

Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better/worse/equivalently than a random observation drawn from the other group. Summary statistics such as the net treatment benefit, win ratio, or win odds are then deduced from these probabilities. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.

Authors:Brice Ozenne [aut, cre], Eva Cantagallo [aut], William Anderson [aut], Julien Peron [ctb], Johan Verbeeck [ctb]

BuyseTest_3.4.0.tar.gz
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BuyseTest_3.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BuyseTest/json (API)

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

Bug tracker:https://github.com/bozenne/buysetest/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • CHARM - RCT In Chronic Heart Failure Assessing an Inhibitor of the Renin-Angiotensin System.
  • EB - Rare disease trial
  • prodige - RCT In Metastatic Pancreatic Cancer Comparing Two Chemoterapy.
  • profil - N-of-1 trials with On-demand Sildenafil as a Treatment for Raynaud Phenomenon

On CRAN:

Conda:

generalized-pairwise-comparisonsnon-parametricstatisticsopenblascpp

6.19 score 8 stars 107 scripts 815 downloads 1 mentions 38 exports 100 dependencies

Last updated from:fa71668fe5. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK325
linux-devel-x86_64OK363
source / vignettesOK334
linux-release-arm64OK317
linux-release-x86_64OK282
macos-release-arm64OK367
macos-release-x86_64OK395
macos-oldrel-arm64OK267
macos-oldrel-x86_64OK623
windows-devel-arm64OK519
windows-devel-x86_64OK319
windows-release-arm64OK514
windows-release-x86_64OK284
windows-oldrel-x86_64OK321
wasm-releaseOK183

Exports:.calcIntegralCif_cpp.calcIntegralSurv_cppaucbrierBuyseMultCompBuyseTestBuyseTest.optionsBuyseTTEMcalcIntegralSurv2_cppCasinoTestcoefconfintconstStrataefronlimgetCountgetIidgetMatrixScoregetPairScoregetPseudovaluegetSurvivalGPC_cppGPC2_cppmodel.tablesnobsperformanceperformanceResampleplotpowerBuyseTestprintprodlimConditionalsensitivityshowsimBuyseTestsimCompetingRiskssummaryupdatevcovweights

Dependencies:backportsbase64encbslibcachemcheckmatecliclustercmprskcodetoolscolorspacecpp11data.tablediagramdigestdoParalleldoSNOWevaluatefarverfastmapfontawesomeforeachforeignFormulafsfuturefuture.applyggplot2glmnetglobalsgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalifecyclelistenvmagrittrMASSMatrixMatrixModelsmemoisemetsmimemultcompmvtnormnlmennetnumDerivparallellyplotrixpolsplineprodlimprogressrPublishquantregR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenriskRegressionrlangrmarkdownrmsrpartrstudioapiS7sandwichsassscalesshapesnowSparseMSQUAREMstringistringrsurvivalTH.datatimeregtinytexvctrsviridisLitewithrxfunyamlzoo

BuyseTest: overview
Performing generalized pairwise comparisons (GPC) | Getting additional inside: looking at the pair level | Dealing with missing values or/and right censoring | Simulating data using simBuyseTest | Power calculation using powerBuyseTest | Modifying default options
Rendered fromoverview.pdf.asisusingR.rsp::asis

Last update: 2026-06-01
Started: 2019-11-14

BuyseTest: paired
Paired design | Multiple cross-over design
Rendered frompaired.pdf.asisusingR.rsp::asis

Last update: 2026-05-30
Started: 2025-07-07

BuyseTest: wilcoxon test
Single Wilcoxon test | Multiple Wilcoxon tests
Rendered fromwilcoxonTest.pdf.asisusingR.rsp::asis

Last update: 2026-05-30
Started: 2021-10-15

Readme and manuals

Help Manual

Help pageTopics
BuyseTest package: Generalized Pairwise ComparisonsBuyseTest-package
Substract a vector of values in each column.colCenter_cpp
Column-wise cumulative sum.colCumSum_cpp
Multiply by a vector of values in each column.colMultiply_cpp
Divide by a vector of values in each column.colScale_cpp
Substract a vector of values in each row.rowCenter_cpp
Apply cumprod in each row.rowCumProd_cpp
Row-wise cumulative sum.rowCumSum_cpp
Multiply by a vector of values in each row.rowMultiply_cpp
Dividy by a vector of values in each row.rowScale_cpp
Convert Performance Objet to data.tableas.data.table.performance
Estimation of the Area Under the ROC Curve (EXPERIMENTAL)auc
Graphical Display for GPCautoplot.S4BuyseTest
Estimation of the Brier Score (EXPERIMENTAL)brier
Adjustment for Multiple ComparisonsBuyseMultComp
Two-group GPCBuyseTest
Global options for BuyseTest packageBuyseTest.options
Class "BuyseTest.options" (global setting for the BuyseTest package)BuyseTest.options-class
Methods for the class "BuyseTest.options"alloc,BuyseTest.options-method BuyseTest.options-methods select,BuyseTest.options-method
Time to Event ModelBuyseTTEM BuyseTTEM.BuyseTTEM BuyseTTEM.formula BuyseTTEM.prodlim BuyseTTEM.survreg
Multi-group GPC (EXPERIMENTAL)CasinoTest
RCT In Chronic Heart Failure Assessing an Inhibitor of the Renin-Angiotensin System.CHARM
Extract the AUC Valuecoef.BuyseTestAuc
Extract the Brier Scorecoef.BuyseTestBrier
Extract the AUC value with its Confidence Intervalconfint.BuyseTestAuc
Extract the Brier Score with its Confidence Intervalconfint.BuyseTestBrier
Strata creationconstStrata
Rare disease trialEB
Constrained Kaplan-Meier Estimatorefronlim
Extract the Number of Favorable, Unfavorable, Neutral, Uninformative pairsgetCount getCount,S4BuyseTest-method
Extract the H-decomposition of the EstimatorgetIid getIid,S4BuyseTest-method
Extract the Score MatrixgetMatrixScore getMatrixScore,S4BuyseTest-method
Extract the Score of Each PairgetPairScore getPairScore,S4BuyseTest-method
Extract the pseudovalues of the EstimatorgetPseudovalue getPseudovalue,S4BuyseTest-method
Extract the Survival and Survival JumpsgetSurvival getSurvival,S4BuyseTest-method
Extract the idd Decomposition for the AUCiid.BuyseTestAuc
Extract the idd Decomposition for the Brier Scoreiid.BuyseTestBrier
Extract i.i.d. decomposition from a prodlim modeliid.prodlim
Inference using MOVER in match designs (EXPERIMENTAL)mover
Assess Performance of a Classifierperformance
Uncertainty About Performance of a Classifier (EXPERIMENTAL)performanceResample
Graphical Display for Sensitivity Analysisautoplot.S3sensitivity plot.S3sensitivity
Performing simulation studies with BuyseTestpowerBuyseTest
Prediction with Time to Event Modelpredict.BuyseTTEM
RCT In Metastatic Pancreatic Cancer Comparing Two Chemoterapy.prodige
Conditional survival estimator (!! Experimental !!)prodlimConditional
N-of-1 trials with On-demand Sildenafil as a Treatment for Raynaud Phenomenonprofil
Combine Resampling Results For Performance Objectsrbind.performance
Class "S4BuysePower" (output of BuyseTest)S4BuysePower-class
Extract Summary for Class "S4BuysePower"model.tables,S4BuysePower-method S4BuysePower-model.tables
Sample Size for Class "S4BuysePower"nobs,S4BuysePower-method S4BuysePower-nobs
Print Method for Class "S4BuysePower"print,S4BuysePower-method S4BuysePower-print
Show Method for Class "S4BuysePower"S4BuysePower-show show,S4BuysePower-method
Summary Method for Class "S4BuysePower"S4BuysePower-summary summary,S4BuysePower-method
Class "S4BuyseTest" (output of BuyseTest)S4BuyseTest-class
Extract Summary Statistics from GPCcoef,S4BuyseTest-method S4BuyseTest-coef
Extract Confidence Interval from GPCconfint,S4BuyseTest-method S4BuyseTest-confint
Extract Summary for Class "S4BuyseTest"model.tables,S4BuyseTest-method S4BuyseTest-model.tables
Sample Size for Class "S4BuyseTest"nobs,S4BuyseTest-method S4BuyseTest-nobs
Graphical Display for GPCplot,S4BuyseTest,ANY-method S4BuyseTest-plot
Print Method for Class "S4BuyseTest"print,S4BuyseTest-method S4BuyseTest-print
Show Method for Class "S4BuyseTest"S4BuyseTest-show show,S4BuyseTest-method
Summary Method for Class "S4BuyseTest"S4BuyseTest-summary summary,S4BuyseTest-method
Re-run two-group GPCS4BuyseTest-update update,S4BuyseTest-method
Extract Uncertainty from GPCS4BuyseTest-vcov vcov,S4BuyseTest-method
Extract Weigths from GPCS4BuyseTest-weights weights,S4BuyseTest-method
Sensitivity Analysis for the Choice of the Thresholdssensitivity sensitivity,S4BuyseTest-method
Simulation of data for the BuyseTestsimBuyseTest
Simulation of Gompertz competing risks data for the BuyseTestsimCompetingRisks
Fitted Survival Probabilities for all Stratasummary.BuyseTTEM
Summary Method for Performance Objectssummary.performance