Package: spBayesSurv 1.1.8

spBayesSurv: Bayesian Modeling and Analysis of Spatially Correlated Survival Data

Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). See Zhou, Hanson and Zhang (2020) <doi:10.18637/jss.v092.i09>.

Authors:Haiming Zhou [aut, cre, cph], Timothy Hanson [aut]

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spBayesSurv.pdf |spBayesSurv.html✨
spBayesSurv/json (API)

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

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

1.95 score 2 stars 45 scripts 473 downloads 1 mentions 47 exports 12 dependencies

Last updated 9 months agofrom:7510450162. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64NOTENov 20 2024
R-4.5-linux-x86_64NOTENov 20 2024
R-4.4-win-x86_64OKNov 20 2024
R-4.4-mac-x86_64OKNov 20 2024
R-4.4-mac-aarch64OKNov 20 2024
R-4.3-win-x86_64OKNov 20 2024
R-4.3-mac-x86_64OKNov 20 2024
R-4.3-mac-aarch64OKNov 20 2024

Exports:anovaDDPbaselineBF.SpatDensRegbsplinecox.snell.survregbayesfrailtyGAFTfrailtypriorGetCurvesindeptCoxphmakepredictcall.bsplineplot.anovaDDPplot.frailtyGAFTplot.indeptCoxphplot.SpatDensRegplot.spCopulaCoxphplot.spCopulaDDPplot.SuperSurvRegBayesplot.survregbayesplot.survregbayes2predict.bsplineprint.frailtyGAFTprint.indeptCoxphprint.SpatDensRegprint.spCopulaCoxphprint.summary.frailtyGAFTprint.summary.indeptCoxphprint.summary.SpatDensRegprint.summary.spCopulaCoxphprint.summary.SuperSurvRegBayesprint.summary.survregbayesprint.summary.survregbayes2print.SuperSurvRegBayesprint.survregbayesprint.survregbayes2SpatDensRegspCopulaCoxphspCopulaDDPsummary.frailtyGAFTsummary.indeptCoxphsummary.SpatDensRegsummary.spCopulaCoxphsummary.SuperSurvRegBayessummary.survregbayessummary.survregbayes2SuperSurvRegBayessurvregbayessurvregbayes2

Dependencies:codadotCall64fieldslatticemapsMASSMatrixRcppRcppArmadillospamsurvivalviridisLite

Readme and manuals

Help Manual

Help pageTopics
Bayesian Nonparametric Survival ModelanovaDDP
Stratification effects on baseline functionsbaseline
Generate a Cubic B-Spline Basis Matrixbspline makepredictcall.bspline
Cox-Snell Diagnostic Plotcox.snell.survregbayes
Generalized Accelerated Failure Time Frailty ModelfrailtyGAFT print.frailtyGAFT print.summary.frailtyGAFT summary.frailtyGAFT
Frailty prior specificationfrailtyprior
Density, Survival, and Hazard EstimatesGetCurves plot.anovaDDP plot.frailtyGAFT plot.indeptCoxph plot.SpatDensReg plot.spCopulaCoxph plot.spCopulaDDP plot.SuperSurvRegBayes plot.survregbayes
Bayesian Proportional Hazards ModelindeptCoxph print.indeptCoxph print.summary.indeptCoxph summary.indeptCoxph
The Leukemia Survival DataLeukSurv
Evaluate a Cubic Spline Basispredict.bspline
Bayesian Nonparametric Spatially Smoothed Density EstimationBF.SpatDensReg print.SpatDensReg print.summary.SpatDensReg SpatDensReg summary.SpatDensReg
Marginal Bayesian Proportional Hazards Model via Spatial Copulaprint.spCopulaCoxph print.summary.spCopulaCoxph spCopulaCoxph summary.spCopulaCoxph
Marginal Bayesian Nonparametric Survival Model via Spatial CopulaspCopulaDDP
Bayesian Semiparametric Super Survival Modelprint.summary.SuperSurvRegBayes print.SuperSurvRegBayes summary.SuperSurvRegBayes SuperSurvRegBayes
Bayesian Semiparametric Survival Modelsprint.summary.survregbayes print.survregbayes summary.survregbayes survregbayes
Bayesian Semiparametric Survival Modelsplot.survregbayes2 print.summary.survregbayes2 print.survregbayes2 summary.survregbayes2 survregbayes2