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BuyseTest (version 3.0.5)

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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Install

install.packages('BuyseTest')

Monthly Downloads

831

Version

3.0.5

License

GPL-3

Issues

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Repository

https://github.com/bozenne/BuyseTest

Maintainer

Last Published

October 13th, 2024

Functions in BuyseTest (3.0.5)

S4BuysePower-model.tables

Extract Summary for Class "S4BuysePower"

S4BuysePower-print

Print Method for Class "S4BuysePower"

S4BuysePower-nobs

Sample Size for Class "S4BuysePower"

S4BuyseTest-class

Class "S4BuyseTest" (output of BuyseTest)

S4BuyseTest-coef

Extract Summary Statistics from GPC

Extract the H-decomposition of the Estimator

S4BuysePower-summary

Summary Method for Class "S4BuysePower"

Extract the Score of Each Pair

S4BuyseTest-model.tables

Extract Summary for Class "S4BuyseTest"

Sensitivity Analysis for the Choice of the Thresholds

as.data.table.performance

Convert Performance Objet to data.table

S4BuyseTest-nobs

Sample Size for Class "S4BuyseTest"

S4BuyseTest-plot

Graphical Display for GPC

S4BuyseTest-summary

Summary Method for Class "S4BuyseTest"

S4BuyseTest-print

Print Method for Class "S4BuyseTest"

S4BuysePower-show

Show Method for Class "S4BuysePower"

S4BuyseTest-confint

Extract Confidence Interval from GPC

Extract the pseudovalues of the Estimator

Estimation of the Area Under the ROC Curve (EXPERIMENTAL)

coef.BuyseTestAuc

Extract the AUC Value

Strata creation

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

confint.BuyseTestAuc

Extract the AUC value with its Confidence Interval

Extract the Survival and Survival Jumps

Divide by a vector of values in each column

autoplot.S4BuyseTest

Graphical Display for GPC

performanceResample

Uncertainty About Performance of a Classifier (EXPERIMENTAL)

Estimation of the Brier Score (EXPERIMENTAL)

coef.BuyseTestBrier

Extract the Brier Score

.calcIntegralSurv_cpp

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

Substract a vector of values in each row

Check Arguments of a function.

confint.BuyseTestBrier

Extract the Brier Score with its Confidence Interval

iid.BuyseTestAuc

Extract the idd Decomposition for the AUC

calcIntegralSurv2_cpp

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

Column-wise cumulative sum

Substract a vector of values in each column

.colMultiply_cpp

Multiply by a vector of values in each column

plot.S3sensitivity

Graphical Display for Sensitivity Analysis

iid.BuyseTestBrier

Extract the idd Decomposition for the Brier Score

simCompetingRisks

Simulation of Gompertz competing risks data for the BuyseTest

.rowCumProd_cpp

Apply cumprod in each row

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

Row-wise cumulative sum

rbind.performance

Combine Resampling Results For Performance Objects

.calcIntegralCif_cpp

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

summary.performance

Summary Method for Performance Objects

Dividy by a vector of values in each row

.rowMultiply_cpp

Multiply by a vector of values in each row

Simulation of data for the BuyseTest

Assess Performance of a Classifier

Performing simulation studies with BuyseTest

predict.BuyseTTEM

Prediction with Time to Event Model

Adjustment for Multiple Comparisons

BuyseTest.options-methods

Methods for the class "BuyseTest.options"

BuyseTest-package

BuyseTest package: Generalized Pairwise Comparisons

S4BuysePower-class

Class "S4BuysePower" (output of BuyseTest)

Time to Event Model

BuyseTest.options-class

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

Multi-group GPC (EXPERIMENTAL)

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

BuyseTest.options

Global options for BuyseTest package