Package: RoBSA 1.0.2

František Bartoš

RoBSA: Robust Bayesian Survival Analysis

A framework for estimating ensembles of parametric survival models with different parametric families. The RoBSA framework uses Bayesian model-averaging to combine the competing parametric survival models into a model ensemble, weights the posterior parameter distributions based on posterior model probabilities and uses Bayes factors to test for the presence or absence of the individual predictors or preference for a parametric family (Bartoš, Aust & Haaf, 2022, <doi:10.1186/s12874-022-01676-9>). The user can define a wide range of informative priors for all parameters of interest. The package provides convenient functions for summary, visualizations, fit diagnostics, and prior distribution calibration.

Authors:František Bartoš [aut, cre], Julia M. Haaf [ths], Matthew Denwood [cph], Martyn Plummer [cph]

RoBSA_1.0.2.tar.gz
RoBSA_1.0.2.tar.gz(r-4.5-noble)RoBSA_1.0.2.tar.gz(r-4.4-noble)
RoBSA.pdf |RoBSA.html
RoBSA/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/fbartos/robsa/issues

Pkgdown:https://fbartos.github.io

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

1.70 score 1 scripts 179 downloads 87 exports 42 dependencies

Last updated 2 years agofrom:3400142de1. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-linux-x86_64OKNov 11 2024

Exports:calibrate_meta_analyticcalibrate_quartilescheck_RoBSAcheck_setupcontr.meandifcontr.orthonormaldiagnosticsdiagnostics_autocorrelationdiagnostics_densitydiagnostics_traceexp_aft_densityexp_aft_hazardexp_aft_log_densityexp_aft_log_hazardexp_aft_log_survivalexp_aft_meanexp_aft_pexp_aft_qexp_aft_rexp_aft_sdexp_aft_survivalextract_flexsurvgamma_aft_densitygamma_aft_hazardgamma_aft_log_densitygamma_aft_log_hazardgamma_aft_log_survivalgamma_aft_meangamma_aft_pgamma_aft_qgamma_aft_rgamma_aft_sdgamma_aft_survivalget_default_prior_auxget_default_prior_beta_altget_default_prior_beta_nullget_default_prior_factor_nullget_default_prior_interceptis.RoBSAllogis_aft_densityllogis_aft_hazardllogis_aft_log_densityllogis_aft_log_hazardllogis_aft_log_survivalllogis_aft_meanllogis_aft_pllogis_aft_qllogis_aft_rllogis_aft_sdllogis_aft_survivallnorm_aft_densitylnorm_aft_hazardlnorm_aft_log_densitylnorm_aft_log_hazardlnorm_aft_log_survivallnorm_aft_meanlnorm_aft_plnorm_aft_qlnorm_aft_rlnorm_aft_sdlnorm_aft_survivalplot_densityplot_hazardplot_modelsplot_predictionplot_survivalpriorprior_factorprior_informedprior_informed_medicine_namesprior_noneRoBSARoBSA.get_optionRoBSA.optionsset_autofit_controlset_convergence_checksweibull_aft_densityweibull_aft_hazardweibull_aft_log_densityweibull_aft_log_hazardweibull_aft_log_survivalweibull_aft_meanweibull_aft_pweibull_aft_qweibull_aft_rweibull_aft_sdweibull_aft_survival

Dependencies:BayesToolsbridgesamplingBrobdingnagclicodacolorspaceextraDistrfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigR6rbibutilsRColorBrewerRcppRdpackrjagsrlangrunjagsscalesstringistringrsurvivaltibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
RoBSA: Robust Bayesian survival analysisRoBSA-package RoBSA.package RoBSA_package _PACKAGE
Create meta-analytic predictive prior distributionscalibrate_meta_analytic
Calibrate prior distributions based on quartilescalibrate_quartiles
Check fitted RoBSA object for errors and warningscheck_RoBSA
Prints summary of '"RoBSA"' corresponding to the inputcheck_setup
Mean difference contrast matrixcontr.meandif
Orthornomal contrast matrixcontr.orthonormal
Default prior distributionsdefault_prior get_default_prior_aux get_default_prior_beta_alt get_default_prior_beta_alt, get_default_prior_beta_null get_default_prior_beta_null, get_default_prior_factor_alt get_default_prior_factor_alt, get_default_prior_factor_null get_default_prior_factor_null, get_default_prior_intercept get_default_prior_intercept,
Visualizes MCMC diagnostics for a fitted RoBSA objectdiagnostics diagnostics_autocorrelation diagnostics_density diagnostics_trace
Exponential AFT parametric family.exp-aft exp_aft_density exp_aft_hazard exp_aft_log_density exp_aft_log_hazard exp_aft_log_survival exp_aft_mean exp_aft_p exp_aft_q exp_aft_r exp_aft_sd exp_aft_survival
Extract parameter estimates from 'flexsurv' objectextract_flexsurv
Gamma AFT parametric family.gamma-aft gamma_aft_density gamma_aft_hazard gamma_aft_log_density gamma_aft_log_hazard gamma_aft_log_survival gamma_aft_mean gamma_aft_p gamma_aft_q gamma_aft_r gamma_aft_sd gamma_aft_survival
Reports whether x is a RoBSA objectis.RoBSA
Log-logistic AFT parametric family.llogis-aft llogis_aft_density llogis_aft_hazard llogis_aft_log_density llogis_aft_log_hazard llogis_aft_log_survival llogis_aft_mean llogis_aft_p llogis_aft_q llogis_aft_r llogis_aft_sd llogis_aft_survival
Log-normal AFT parametric family.lnorm-aft lnorm_aft_density lnorm_aft_hazard lnorm_aft_log_density lnorm_aft_log_hazard lnorm_aft_log_survival lnorm_aft_mean lnorm_aft_p lnorm_aft_q lnorm_aft_r lnorm_aft_sd lnorm_aft_survival
Models plot for a RoBSA objectplot_models
Survival plots for a RoBSA objectplot_density plot_hazard plot_prediction plot_survival
Plots a fitted RoBSA objectplot.RoBSA
Predict method for RoBSA objects.predict.RoBSA
Prints a fitted RoBSA objectprint.RoBSA
Prints summary object for RoBSA methodprint.summary.RoBSA
Creates a prior distributionprior
Creates a prior distribution for factorsprior_factor
Creates an informed prior distribution based on researchprior_informed
Names of medical subfields from the Cochrane database of systematic reviewsprior_informed_medicine_names
Creates a prior distributionprior_none
Fit Robust Bayesian Survival AnalysisRoBSA
Control MCMC fitting processRoBSA_control set_autofit_control set_autofit_control, set_convergence_checks
Options for the RoBSA packageRoBSA.get_option RoBSA.options RoBSA_options
Summarize fitted RoBSA objectsummary.RoBSA
Updates a fitted RoBSA objectupdate.RoBSA
Weibull AFT parametric family.weibull-aft weibull_aft_density weibull_aft_hazard weibull_aft_log_density weibull_aft_log_hazard weibull_aft_log_survival weibull_aft_mean weibull_aft_p weibull_aft_q weibull_aft_r weibull_aft_sd weibull_aft_survival