Package: BayesSurvive 0.0.2
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_0.0.2.tar.gz
BayesSurvive_0.0.2.tar.gz(r-4.5-noble)BayesSurvive_0.0.2.tar.gz(r-4.4-noble)
BayesSurvive_0.0.2.tgz(r-4.4-emscripten)
BayesSurvive.pdf |BayesSurvive.html✨
BayesSurvive/json (API)
NEWS
# Install 'BayesSurvive' in R: |
install.packages('BayesSurvive', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ocbe-uio/bayessurvive/issues
- simData - Simulated survival data
Last updated 6 months agofrom:4c24b33005. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 02 2024 |
R-4.5-linux-x86_64 | OK | Dec 02 2024 |
Exports:BayesSurvivefunc_MCMCfunc_MCMC_graphplotBrierUpdateGammaUpdateRPlee11VS
Dependencies:backportsbase64encbslibcachemcheckmatecliclustercmprskcodetoolscolorspacecpp11crayondata.tablediagramdigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsfuturefuture.applygenericsGGallyggplot2ggstatsglobalsgluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetsisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalifecyclelistenvmagrittrMASSMatrixMatrixModelsmemoisemetsmgcvmimemultcompmunsellmvtnormnlmennetnumDerivparallellypatchworkpillarpkgconfigplotrixplyrpolsplineprettyunitsprodlimprogressprogressrPublishpurrrquantregR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenriskRegressionrlangrmarkdownrmsrpartrstudioapisandwichsassscalesshapeSparseMSQUAREMstringistringrsurvivalTH.datatibbletidyrtidyselecttimeregtinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo
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 |