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BuyseTest (version 3.0.2)

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 than a random observation drawn from the other group (Mann-Whitney parameter). The net benefit and win ratio statistics, i.e. the difference and ratio between the probabilities relative to the intervention and control groups, can then also be estimated. 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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Install

install.packages('BuyseTest')

Monthly Downloads

865

Version

3.0.2

License

GPL-3

Issues

Pull Requests

Stars

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Maintainer

Brice Ozenne

Last Published

January 23rd, 2024

Functions in BuyseTest (3.0.2)

CasinoTest

Multi-group GPC (EXPERIMENTAL)
S4BuyseTest-confint

Extract Confidence Interval from GPC
S4BuysePower-summary

Summary Method for Class "S4BuysePower"
S4BuysePower-print

Print Method for Class "S4BuysePower"
getIid

Extract the H-decomposition of the Estimator
getPairScore

Extract the Score of Each Pair
S4BuyseTest-coef

Extract Summary Statistics from GPC
S4BuyseTest-class

Class "S4BuyseTest" (output of BuyseTest)
getCount

Extract the Number of Favorable, Unfavorable, Neutral, Uninformative pairs
S4BuyseTest-model.tables

Extract Summary for Class "S4BuyseTest"
S4BuyseTest-nobs

Sample Size for Class "S4BuyseTest"
sensitivity

Sensitivity Analysis for the Choice of the Thresholds
S4BuysePower-model.tables

Extract Summary for Class "S4BuysePower"
getPseudovalue

Extract the pseudovalues of the Estimator
getSurvival

Extract the Survival and Survival Jumps
S4BuysePower-nobs

Sample Size for Class "S4BuysePower"
brier

Estimation of the Brier Score (EXPERIMENTAL)
constStrata

Strata creation
as.data.table.performance

Convert Performance Objet to data.table
S4BuyseTest-summary

Summary Method for Class "S4BuyseTest"
.calcIntegralCif_cpp

C++ Function Computing the Integral Terms for the Peron Method in the presence of competing risks (CR).
S4BuyseTest-plot

Graphical Display for GPC
.rowScale_cpp

Dividy by a vector of values in each row
.rowMultiply_cpp

Multiply by a vector of values in each row
S4BuysePower-show

Show Method for Class "S4BuysePower"
auc

Estimation of the Area Under the ROC Curve (EXPERIMENTAL)
confint.BuyseTestAuc

Extract the AUC value with its Confidence Interval
calcIntegralSurv2_cpp

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

Extract the Brier Score with its Confidence Interval
S4BuyseTest-print

Print Method for Class "S4BuyseTest"
coef.BuyseTestAuc

Extract the AUC Value
.colCumSum_cpp

Column-wise cumulative sum
coef.BuyseTestBrier

Extract the Brier Score
iid.BuyseTestAuc

Extract the idd Decomposition for the AUC
.colScale_cpp

Divide by a vector of values in each column
autoplot.S4BuyseTest

Graphical Display for GPC
.calcIntegralSurv_cpp

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

Substract a vector of values in each row
summary.performance

Summary Method for Performance Objects
.rowCumProd_cpp

Apply cumprod in each row
iid.prodlim

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

Simulation of Gompertz competing risks data for the BuyseTest
.colCenter_cpp

Substract a vector of values in each column
performance

Assess Performance of a Classifier
performanceResample

Uncertainty About Performance of a Classifier (EXPERIMENTAL)
powerBuyseTest

Performing simulation studies with BuyseTest
rbind.performance

Combine Resampling Results For Performance Objects
.rowCumSum_cpp

Row-wise cumulative sum
.colMultiply_cpp

Multiply by a vector of values in each column
iid.BuyseTestBrier

Extract the idd Decomposition for the Brier Score
plot.S3sensitivity

Graphical Display for Sensitivity Analysis
simBuyseTest

Simulation of data for the BuyseTest
predict.BuyseTTEM

Prediction with Time to Event Model
validFCTs

Check Arguments of a function.
BuyseTest.options-class

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

BuyseTest package: Generalized Pairwise Comparisons
BuyseTest.options-methods

Methods for the class "BuyseTest.options"
BuyseTest

Two-group GPC
S4BuysePower-class

Class "S4BuysePower" (output of BuyseTest)
BuyseTest.options

Global options for BuyseTest package
GPC_cpp

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

Adjustment for Multiple Comparisons
BuyseTTEM

Time to Event Model