Package: biospear 1.0.2

biospear: Biomarker Selection in Penalized Regression Models

Provides some tools for developing and validating prediction models, estimate expected survival of patients and visualize them graphically. Most of the implemented methods are based on penalized regressions such as: the lasso (Tibshirani R (1996)), the elastic net (Zou H et al. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>), the adaptive lasso (Zou H (2006) <doi:10.1198/016214506000000735>), the stability selection (Meinshausen N et al. (2010) <doi:10.1111/j.1467-9868.2010.00740.x>), some extensions of the lasso (Ternes et al. (2016) <doi:10.1002/sim.6927>), some methods for the interaction setting (Ternes N et al. (2016) <doi:10.1002/bimj.201500234>), or others. A function generating simulated survival data set is also provided.

Authors:Nils Ternes [aut], Federico Rotolo [aut], Stefan Michiels [aut, cre]

biospear_1.0.2.tar.gz
biospear_1.0.2.zip(r-4.5)biospear_1.0.2.zip(r-4.4)
biospear_1.0.2.tgz(r-4.4-any)
biospear_1.0.2.tar.gz(r-4.5-noble)biospear_1.0.2.tar.gz(r-4.4-noble)
biospear_1.0.2.tgz(r-4.4-emscripten)
biospear.pdf |biospear.html
biospear/json (API)

# Install 'biospear' in R:
install.packages('biospear', repos = c('https://stefanmichielsgr.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Breast - Early breast cancer data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.48 score 3 scripts 195 downloads 3 mentions 6 exports 227 dependencies

Last updated 6 years agofrom:45bd46eaa0. Checks:OK: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winOKOct 26 2024
R-4.5-linuxOKOct 26 2024
R-4.4-winOKOct 26 2024
R-4.4-macOKOct 26 2024

Exports:BMselexpSurvpredResselRessimdatasimdataV

Dependencies:abindaskpassbackportsbase64encBHBiocParallelbipartitebitopsbootbootstrapbrewbriobroombslibcachemcallrcarcarDatacheckmateclassclicliprclustercobscodacodetoolscolorspacecommonmarkcorpcorcowplotcpp11crayoncredentialscurldata.tableDerivdescdevtoolsdiagramdiffobjdigestdoBydotCall64downlitdplyrellipseellipsisevaluatefansifarverfastmapfieldsfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsgertggplot2ggrepelghgitcredsglmnetglobalsgluegridExtragrplassogsignalgtablehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttr2igraphiniinumipredisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrlabelinglambda.rlarslaterlatticelavalibcoinlifecyclelistenvlme4magrittrmapsMASSMatrixMatrixModelsmatrixStatsmboostmemoisemgcvmicrobenchmarkmimeminiUIminqamixOmicsmodelrmultcompmunsellmvtnormnetworknlmenloptrnnetnnlsnumDerivopensslparallellypartykitpbkrtestpermutepillarpkgbuildpkgconfigpkgdownpkgloadplsplsRcoxplsRglmplyrpolsplinepracmapraiseprettyunitspROCprocessxprodlimprofvisprogressrpromisesPRROCpspurrrquadprogquantregR6raggrappdirsrARPACKrcmdcheckRColorBrewerRcppRcppEigenRCurlrematch2remotesreshape2rglrisksetROCrlangrmarkdownrmetarmsroxygen2rpartrprojrootRSpectrarstudioapirversionssandwichsassscalessessioninfoshapeshinysnasnowsourcetoolsspamSparseMSQUAREMstabsstatnet.commonstringistringrSuppDistssurvAUCsurvcompsurvivalsurvivalROCsyssystemfontstestthattextshapingTH.datatibbletidyrtidyselecttinytexurlcheckerusethisutf8vctrsveganviridisviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzipzoo