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BuyseTest (version 3.1.0)

Generalized Pairwise Comparisons

Description

Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) for complete observations, and extended in Peron (2018) 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 ), 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.

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Version

Install

install.packages('BuyseTest')

Monthly Downloads

865

Version

3.1.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/bozenne/BuyseTest

Maintainer

Brice Ozenne

Last Published

March 4th, 2025

Functions in BuyseTest (3.1.0)

Adjustment for Multiple Comparisons

BuyseTest.options-methods

Methods for the class "BuyseTest.options"

Time to Event Model

BuyseTest.options

Global options for BuyseTest package

C++ function performing the pairwise comparison over several endpoints.

S4BuysePower-class

Class "S4BuysePower" (output of BuyseTest)

Multi-group GPC (EXPERIMENTAL)

S4BuyseTest-class

Class "S4BuyseTest" (output of BuyseTest)

S4BuyseTest-confint

Extract Confidence Interval from GPC

S4BuysePower-nobs

Sample Size for Class "S4BuysePower"

S4BuysePower-model.tables

Extract Summary for Class "S4BuysePower"

S4BuyseTest-nobs

Sample Size for Class "S4BuyseTest"

S4BuyseTest-model.tables

Extract Summary for Class "S4BuyseTest"

autoplot.S4BuyseTest

Graphical Display for GPC

S4BuyseTest-coef

Extract Summary Statistics from GPC

S4BuyseTest-print

Print Method for Class "S4BuyseTest"

S4BuysePower-show

Show Method for Class "S4BuysePower"

Estimation of the Area Under the ROC Curve (EXPERIMENTAL)

S4BuysePower-print

Print Method for Class "S4BuysePower"

S4BuysePower-summary

Summary Method for Class "S4BuysePower"

coef.BuyseTestAuc

Extract the AUC Value

Strata creation

S4BuyseTest-plot

Graphical Display for GPC

Substract a vector of values in each row

Divide by a vector of values in each column

.rowCumProd_cpp

Apply cumprod in each row

coef.BuyseTestBrier

Extract the Brier Score

RCT In Chronic Heart Failure Assessing an Inhibitor of the Renin-Angiotensin System.

.calcIntegralCif_cpp

C++ Function Computing the Integral Terms for the Peron Method in the presence of competing risks (CR).

.calcIntegralSurv_cpp

C++ Function Computing the Integral Terms for the Peron Method in the survival case.

Estimation of the Brier Score (EXPERIMENTAL)

.colMultiply_cpp

Multiply by a vector of values in each column

Dividy by a vector of values in each row

Constrained Kaplan-Meier Estimator

calcIntegralSurv2_cpp

C++ Function pre-computing the Integral Terms for the Peron Method in the survival case.

plot.S3sensitivity

Graphical Display for Sensitivity Analysis

as.data.table.performance

Convert Performance Objet to data.table

Rare disease trial

Extract the H-decomposition of the Estimator

RCT In Metastatic Pancreatic Cancer Comparing Two Chemoterapy.

Substract a vector of values in each column

S4BuyseTest-summary

Summary Method for Class "S4BuyseTest"

confint.BuyseTestAuc

Extract the AUC value with its Confidence Interval

Extract the Number of Favorable, Unfavorable, Neutral, Uninformative pairs

Row-wise cumulative sum

simCompetingRisks

Simulation of Gompertz competing risks data for the BuyseTest

Performing simulation studies with BuyseTest

Simulation of data for the BuyseTest

.rowMultiply_cpp

Multiply by a vector of values in each row

Sensitivity Analysis for the Choice of the Thresholds

Column-wise cumulative sum

Assess Performance of a Classifier

iid.BuyseTestBrier

Extract the idd Decomposition for the Brier Score

Extract i.i.d. decomposition from a prodlim model

iid.BuyseTestAuc

Extract the idd Decomposition for the AUC

rbind.performance

Combine Resampling Results For Performance Objects

summary.performance

Summary Method for Performance Objects

Check Arguments of a function.

predict.BuyseTTEM

Prediction with Time to Event Model

performanceResample

Uncertainty About Performance of a Classifier (EXPERIMENTAL)

Extract the Survival and Survival Jumps

Extract the pseudovalues of the Estimator

confint.BuyseTestBrier

Extract the Brier Score with its Confidence Interval

Extract the Score of Each Pair

BuyseTest.options-class

Class "BuyseTest.options" (global setting for the BuyseTest package)

BuyseTest-package

BuyseTest package: Generalized Pairwise Comparisons