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BuyseTest

BuyseTest is a package for the R software (https://www.r-project.org/) implementing generalized pairwise comparisons (GPC). GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints. The net benefit, win ratio, and Mann-Whitney parameter can then be estimated and corresponding confidence intervals and p-values can be estimated using resampling methods or the asymptotic U-statistic theory. The software enables the use of thresholds of minimal importance difference, stratification, and corrections to deal with right-censored endpoints.

The Generalized Pairwise Comparisons form all possible pairs of observations, one observation being taken from the intervention group and the other is taken from the control group, and compare the value of their endpoints.

If the difference in endpoint value between the two observations of the pair is greater than the threshold of clinical relevance, the pair is classified as favorable (i.e. win). If the difference is lower than minus the threshold of clinical relevance the pair is classified as unfavorable (i.e. loss). Otherwise the pair is classified as neutral. In presence of censoring, it might not be possible to compare the difference to the threshold. In such cases the pair is classified as uninformative.

Simultaneously analysis of several endpoints is performed by prioritizing the endpoints, assigning the highest priority to the endpoint considered the most clinically relevant. The endpoint with highest priority is analyzed first, and neutral and uninformative pair are analyzed regarding endpoint of lower priority.

Installation

You can download the latest stable version on CRAN using:

install.packages("BuyseTest")

or download the development version from GitHub:

library(devtools)
install_github("bozenne/BuyseTest")

Citation

To cite this package in a publications please use:

citation("BuyseTest")
To cite the 'BuyseTest' package in publications use the citation from
2020.

To cite the statistical method used by BuyseTes 'BuyseTest' package,
use the citation from: (2010) when using BuyseTest binary/continous
endpoint or time to event endpoints with scoring.rule="Gehan", (2016)
when using BuyseTest with time to event endpoint with
scoring.rule="Peron".

  Brice Ozenne and Julien Peron (2020). BuyseTest: Implementation of
  the Generalized Pairwise Comparisons. R package version 1.9.1.

  Buyse, M. (2010), Generalized pairwise comparisons of prioritized
  outcomes in the two-sample problem. Statistics in medicine, 29:
  3245-3257. doi:10.1002/sim.3923

  Peron, M. et al. (2018), An extension of generalized pairwise
  comparisons for prioritized outcomes in the presence of censoring.
  Statistical methods in medical research, 27: 1230-1239.
  https://doi.org/10.1177/0962280216658320

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.
toBibtex(citation("BuyseTest"))
@Manual{,
  title = {BuyseTest: Implementation of the Generalized Pairwise Comparisons},
  author = {Brice Ozenne and Julien Peron},
  year = {2020},
  note = {R package version 1.9.1},
}

@Article{,
  title = {Generalized pairwise comparisons of prioritized outcomes in the two-sample problem},
  author = {Marc Buyse},
  year = {2010},
  volume = {29},
  number = {30},
  pages = {3245--3257},
  journal = {Statistics in medicine},
  doi = {10.1002/sim.3923},
}

@Article{,
  title = {An extension of generalized pairwise comparisons for prioritized outcomes in the presence of censoring},
  author = {{P{'e}ron} and {Julien} and {Buyse} and {Marc} and {Ozenne} and {Brice} and {Roche} and {Laurent} and {Roy} and {Pascal}},
  year = {2018},
  volume = {27},
  number = {4},
  pages = {1230--1239},
  journal = {Statistical methods in medical research},
  doi = {10.1177/0962280216658320},
}

Functionalities

See the vignette “Overview of the package BuyseTest” in ./vignettes/overview.pdf