Package: psbcSpeedUp 2.0.7

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_2.0.7.tar.gz
psbcSpeedUp_2.0.7.zip(r-4.5)psbcSpeedUp_2.0.7.zip(r-4.4)
psbcSpeedUp_2.0.7.tgz(r-4.4-x86_64)psbcSpeedUp_2.0.7.tgz(r-4.4-arm64)
psbcSpeedUp_2.0.7.tar.gz(r-4.5-noble)psbcSpeedUp_2.0.7.tar.gz(r-4.4-noble)
psbcSpeedUp_2.0.7.tgz(r-4.4-emscripten)
psbcSpeedUp.pdf |psbcSpeedUp.html✨
psbcSpeedUp/json (API)
NEWS

# 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 omics-data survival-analysis

4.78 score 3 stars 172 downloads 2 exports 119 dependencies

Last updated 5 months agofrom:ae3ab77acb. Checks:OK: 1 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 29 2024
R-4.5-win-x86_64	NOTE	Oct 29 2024
R-4.5-linux-x86_64	NOTE	Oct 29 2024
R-4.4-win-x86_64	NOTE	Oct 29 2024
R-4.4-mac-x86_64	NOTE	Oct 29 2024
R-4.4-mac-aarch64	NOTE	Oct 29 2024

Exports:plotBrier psbcSpeedUp

Dependencies:backports base64enc bslib cachem checkmate cli cluster cmprsk codetools colorspace cpp11 crayon data.table diagram digest doParallel dplyr evaluate fansi farver fastmap fontawesome forcats foreach foreign Formula fs future future.apply generics GGally ggplot2 ggstats 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 mgcv mime multcomp munsell mvtnorm nlme nnet numDeriv parallelly patchwork pillar pkgconfig plotrix plyr polspline prettyunits prodlim progress progressr Publish purrr quantreg R6 ranger rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen riskRegression rlang rmarkdown rms rpart rstudioapi sandwich sass scales shape SparseM SQUAREM stringi stringr survival TH.data tibble tidyr tidyselect timereg tinytex utf8 vctrs viridis viridisLite withr xfun xml2 yaml zoo

Penalized Semiparametric Bayesian Cox Models

Rendered fromBayesCox.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-03-21
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-package psbcSpeedUp