Package: psbcSpeedUp 2.1.1

Zhi Zhao

psbcSpeedUp: Penalized Semiparametric Bayesian Cox Models

Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).

Authors:Zhi Zhao [aut, cre], Manuela Zucknick [aut], Maral Saadati [aut], Axel Benner [aut]

psbcSpeedUp_2.1.1.tar.gz
psbcSpeedUp_2.1.1.zip(r-4.7)psbcSpeedUp_2.1.1.zip(r-4.6)psbcSpeedUp_2.1.1.zip(r-4.5)
psbcSpeedUp_2.1.1.tgz(r-4.6-x86_64)psbcSpeedUp_2.1.1.tgz(r-4.6-arm64)psbcSpeedUp_2.1.1.tgz(r-4.5-x86_64)psbcSpeedUp_2.1.1.tgz(r-4.5-arm64)
psbcSpeedUp_2.1.1.tar.gz(r-4.7-arm64)psbcSpeedUp_2.1.1.tar.gz(r-4.7-x86_64)psbcSpeedUp_2.1.1.tar.gz(r-4.6-arm64)psbcSpeedUp_2.1.1.tar.gz(r-4.6-x86_64)
psbcSpeedUp_2.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
psbcSpeedUp/json (API)

# Install 'psbcSpeedUp' in R:

install.packages('psbcSpeedUp', repos = c('https://ocbe-uio.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ocbe-uio/psbcspeedup/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

exampleData - Simulated data set

On CRAN:

bayesian-cox-models bayesian-lasso omics-data survival-analysis openblas cpp openmp

4.48 score 3 stars 232 downloads 2 exports 115 dependencies

Last updated from:502743f25d. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	473
linux-devel-x86_64	OK	225
source / vignettes	OK	284
linux-release-arm64	OK	177
linux-release-x86_64	OK	199
macos-release-arm64	OK	121
macos-release-x86_64	OK	279
macos-oldrel-arm64	OK	111
macos-oldrel-x86_64	OK	332
windows-devel	OK	168
windows-release	OK	174
windows-oldrel	OK	163
wasm-release	OK	155

Exports:plotBrier psbcSpeedUp

Dependencies:backports base64enc bslib cachem checkmate cli cluster cmprsk codetools colorspace cpp11 crayon data.table diagram digest doParallel dplyr evaluate farver fastmap fontawesome forcats foreach foreign Formula fs future future.apply generics GGally ggplot2 ggstats glmnet globals glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv magrittr MASS Matrix MatrixModels memoise mets mime multcomp mvtnorm nlme nnet numDeriv parallelly patchwork pillar pkgconfig plotrix polspline prettyunits prodlim progress progressr Publish purrr quantreg R6 ranger rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen riskRegression rlang rmarkdown rms rpart rstudioapi S7 sandwich sass scales shape SparseM SQUAREM stringi stringr survival TH.data tibble tidyr tidyselect timereg tinytex utf8 vctrs viridisLite withr xfun yaml zoo

Penalized Semiparametric Bayesian Cox Models

Rendered fromBayesCox.Rmdusingknitr::rmarkdown

Last update: 2025-09-30
Started: 2023-12-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
coef method for class 'psbcSpeedUp'	coef.psbcSpeedUp
Simulated data set	exampleData
create a plot of estimated coefficients	plot.psbcSpeedUp
Time-dependent Brier scores	plotBrier
Predict survival risk	predict.psbcSpeedUp
Function to Fit the Bayesian Cox Lasso Model	psbcSpeedUp