Package: BayesSurvive 0.0.5
Zhi Zhao
BayesSurvive: Bayesian Survival Models for High-Dimensional Data
An implementation of Bayesian survival models with graph-structured selection priors for sparse identification of omics features predictive of survival (Madjar et al., 2021 <doi:10.1186/s12859-021-04483-z>) and its extension to use a fixed graph via a Markov Random Field (MRF) prior for capturing known structure of omics features, e.g. disease-specific pathways from the Kyoto Encyclopedia of Genes and Genomes database.
Authors:
BayesSurvive_0.0.5.tar.gz
BayesSurvive_0.0.5.tgz(r-4.4-x86_64)BayesSurvive_0.0.5.tgz(r-4.4-arm64)BayesSurvive_0.0.4.tgz(r-4.3-x86_64)BayesSurvive_0.0.4.tgz(r-4.3-arm64)
BayesSurvive_0.0.5.tar.gz(r-4.5-noble)BayesSurvive_0.0.5.tar.gz(r-4.4-noble)
BayesSurvive.pdf |BayesSurvive.html✨
BayesSurvive/json (API)
NEWS
| # Install 'BayesSurvive' in R: |
| install.packages('BayesSurvive', repos = c('https://ocbe-uio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ocbe-uio/bayessurvive/issues
- simData - Simulated survival data
bayesian-cox-modelsbayesian-variable-selectiongraph-learninghigh-dimensional-statisticsomics-data-integrationsurvival-analysis
Last updated 2 months agofrom:2f6a148cb7. Checks:OK: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 03 2024 |
| R-4.5-linux-x86_64 | OK | Nov 03 2024 |
| R-4.4-mac-x86_64 | OK | Nov 03 2024 |
| R-4.4-mac-aarch64 | OK | Nov 03 2024 |
| R-4.3-mac-x86_64 | OK | Aug 19 2024 |
| R-4.3-mac-aarch64 | OK | Aug 19 2024 |
Exports:BayesSurvivefunc_MCMCfunc_MCMC_graphplotBrierUpdateGammaUpdateRPlee11VS
Dependencies:backportsbase64encbriobslibcachemcallrcheckmatecliclustercmprskcodetoolscolorspacecpp11crayondata.tabledescdiagramdiffobjdigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsfuturefuture.applygenericsGGallyggplot2ggstatsglobalsgluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetsisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalifecyclelistenvmagrittrMASSMatrixMatrixModelsmemoisemetsmgcvmimemultcompmunsellmvtnormnlmennetnumDerivparallellypatchworkpillarpkgbuildpkgconfigpkgloadplotrixplyrpolsplinepraiseprettyunitsprocessxprodlimprogressprogressrpsPublishpurrrquantregR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenrematch2riskRegressionrlangrmarkdownrmsrpartrprojrootrstudioapisandwichsassscalesshapeSparseMSQUAREMstringistringrsurvivaltestthatTH.datatibbletidyrtidyselecttimeregtinytexutf8vctrsviridisviridisLitewaldowithrxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fit Bayesian Cox Models | BayesSurvive |
| Create a dataframe of estimated coefficients | coef.BayesSurvive |
| Function to run MCMC sampling | func_MCMC |
| Function to learn MRF graph | func_MCMC_graph |
| Create a plot of estimated coefficients | plot.BayesSurvive |
| Time-dependent Brier scores | plotBrier |
| Predict survival risk | predict.BayesSurvive |
| Simulated survival data | simData |
| Subfunctions to update parameters | UpdateGamma |
| Update coefficients of Bayesian Cox Models | UpdateRPlee11 |
| Function to perform variable selection | VS |
