Package: sharp
Type: Package
Title: Stability-enHanced Approaches using Resampling Procedures
Version: 1.3.0
Date: 2023-01-17
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <b.bodinier@imperial.ac.uk>
URL: https://github.com/barbarabodinier/sharp
BugReports: https://github.com/barbarabodinier/sharp/issues
Description: 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 by the negative log-likelihood under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2021) <arXiv:2106.02521>). 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. 
License: GPL (>= 3)
Language: en-GB
Encoding: UTF-8
RoxygenNote: 7.2.0
Depends: fake (>= 1.3.0), R (>= 3.5)
Imports: beepr, glassoFast (>= 1.0.0), glmnet, grDevices, huge, igraph,
        impute, MASS, mclust, parallel, randomcoloR, Rdpack, withr (>=
        2.4.0)
Suggests: cluster, corpcor, dbscan, elasticnet, gglasso, mixOmics,
        nnet, plotrix, RCy3, rmarkdown, rCOSA, sgPLS, sparcl, survival
        (>= 3.2.13), testthat (>= 3.0.0), visNetwork
Additional_repositories: https://barbarabodinier.github.io/drat
Config/testthat/edition: 3
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2023-01-17 16:29:18 UTC; barbara
Repository: CRAN
Date/Publication: 2023-01-17 22:50:02 UTC
Built: R 4.2.0; ; 2023-01-17 23:50:43 UTC; unix
