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https://github.com/bozenne/buysetest

Generalized Pairwise Comparisons
https://github.com/bozenne/buysetest

generalized-pairwise-comparisons non-parametric r statistics

Last synced: 7 days ago
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Generalized Pairwise Comparisons

Host: GitHub
URL: https://github.com/bozenne/buysetest
Owner: bozenne
License: gpl-3.0
Created: 2016-07-23T08:54:32.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2024-10-13T19:09:42.000Z (3 months ago)
Last Synced: 2024-12-17T20:07:40.477Z (10 days ago)
Topics: generalized-pairwise-comparisons, non-parametric, r, statistics
Language: R
Homepage:
Size: 24.9 MB
Stars: 4
Watchers: 5
Forks: 6
Open Issues: 0
Metadata Files:
- Readme: README.org
- Changelog: NEWS
- License: LICENSE

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README

        #+BEGIN_HTML











#+END_HTML

* 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.

* Tutorial

A half day tutorial is planned at the DAG Stat 2025 conference

(https://dagstat2025.de/, Berlin, 24-28th of March):

- title: a practical guide to the design and analysis of patient-centric trials (Verbeek et al)

- instructors: Johan Verbeeck and Brice Ozenne

* Installation

You can download the latest stable version on =CRAN= using:

#+BEGIN_SRC R :exports both :eval never

install.packages("BuyseTest")

#+END_SRC

or download the development version from =GitHub=:

#+BEGIN_SRC R :exports both :eval never

library(remotes)

install_github("bozenne/BuyseTest")

#+END_SRC

* Citation

To cite this package in a publications please use:

#+BEGIN_SRC R :exports both :results output :session *R* :cache no

citation("BuyseTest")

#+END_SRC

#+RESULTS:

#+begin_example

To cite the 'BuyseTest' package in publications use the citation from

2021.

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 (2021). BuyseTest: Implementation of

  the Generalized Pairwise Comparisons. R package version 2.3.1.

  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(,

bibtex=TRUE)', 'toBibtex(.)', or set

'options(citation.bibtex.max=999)'.

#+end_example

#+BEGIN_SRC R :exports both :results output :session *R* :cache no

toBibtex(citation("BuyseTest"))

#+END_SRC

#+RESULTS:

#+begin_example

@Manual{,

  title = {BuyseTest: Implementation of the Generalized Pairwise Comparisons},

  author = {Brice Ozenne and Julien Peron},

  year = {2021},

  note = {R package version 2.3.1},

}

@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},

}

#+end_example

* Functionalities

See the vignette "Overview of the package BuyseTest" in [[./vignettes/overview.pdf]]