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In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
| Version: | 1.4.6 |
| Depends: | fake (≥ 1.4.0), R (≥ 3.5) |
| Imports: | abind, beepr, future, future.apply, glassoFast (≥ 1.0.0), glmnet, grDevices, igraph, mclust, nloptr, plotrix, Rdpack, withr (≥ 2.4.0) |
| Suggests: | cluster, corpcor, dbscan, elasticnet, gglasso, mixOmics, nnet, OpenMx, RCy3, randomcoloR, rCOSA, rmarkdown, rpart, sgPLS, sparcl, survival (≥ 3.2.13), testthat (≥ 3.0.0), visNetwork |
| Published: | 2024-02-03 |
| DOI: | 10.32614/CRAN.package.sharp |
| Author: | Barbara Bodinier [aut, cre] |
| Maintainer: | Barbara Bodinier <barbara.bodinier at gmail.com> |
| BugReports: | https://github.com/barbarabodinier/sharp/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/barbarabodinier/sharp |
| NeedsCompilation: | no |
| Additional_repositories: | https://barbarabodinier.github.io/drat |
| Language: | en-GB |
| Materials: | README NEWS |
| CRAN checks: | sharp results |
| Reference manual: | sharp.pdf |
| Vignettes: |
Sharp-JSS-2024 |
| Package source: | sharp_1.4.6.tar.gz |
| Windows binaries: | r-devel: sharp_1.4.6.zip, r-release: sharp_1.4.6.zip, r-oldrel: sharp_1.4.6.zip |
| macOS binaries: | r-release (arm64): sharp_1.4.6.tgz, r-oldrel (arm64): sharp_1.4.6.tgz, r-release (x86_64): sharp_1.4.6.tgz, r-oldrel (x86_64): sharp_1.4.6.tgz |
| Old sources: | sharp archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.