Package index

Details

spsurv-package spsurv

The 'spsurv' package.

Fitter functions

Functions for fitting a BP based survival regression model.

bpph()

Bernstein PH Model

bppo()

Bernstein PO Model

bpaft()

Bernstein AFT Model

spbp()

spbp: The BP Based Survival Analysis Function

spbp(<default>)

spbp: The BP Based Semiparametric Survival Analysis Function

Extraction and inference

Coefficients, confidence and credible intervals, residuals, survival curves.

coef(<spbp>)

Estimated regression coefficients

confint(<spbp>)

Confidence intervals for the regression coefficients

credint()

Generic S3 method credint

credint(<spbp>)

Credible intervals for the regression coefficients

vcov(<spbp>)

Covariance of the regression coefficients

residuals(<spbp>)

BP based models residuals.

survfit(<spbp>) as.data.frame(<survfitbp>)

BP-based model survival curves

predict(<spbp>)

Predicted survival as a tidy data frame

augment(<spbp>)

Augment data with spbp model information

tidy(<spbp>)

Tidy summary for fitted spbp models

glance(<spbp>)

Glance at a fitted spbp model

model.matrix(<spbp>)

Model.matrix method for fitted spbp models

as_draws_df.spbp()

Convert spbp Bayesian fit to posterior draws

spread_surv_draws.spbp()

Posterior survival curves in long tidy format

tidymodels

parsnip model specifications and engines.

proportional_odds()

Proportional odds regression model specification

bp_survival_reg()

Bernstein survival regression specification

Model comparison and extraction

Bernstein baseline helper, parameter estimates, and information criteria.

bernstein()

Bernstein polynomial baseline specification

estimates()

Parameter estimates for fitted spbp models

se()

Standard errors for fitted spbp model parameters

logLik(<spbp>)

Log-likelihood for fitted spbp models

AIC(<spbp>)

Akaike information criterion for fitted spbp models

extractAIC(<spbp>)

Extract AIC from a fitted spbp model

anova(<spbp>)

Analysis of deviance table for nested spbp models

rank_models()

Rank fitted spbp models by AIC

Bernstein polynomial basis

Functions for the BP basis.

bp.basis()

Bernstein basis polynomials calculations

pw.basis()

Power basis polynomials calculations

Plot and print

S3 methods for spbp objects.

plot(<spbp>)

BP based models plot.

ggresiduals()

ggplot2 residual diagnostic plots for spbp models

print(<spbp>)

Bernstein Polynomial Based Regression Object Print

summary(<spbp>)

Bernstein Polynomial Based Regression Object Summary

print(<summary.bpaft.bayes>)

Bernstein Polynomial Based Regression Object Summary BPAFT Bayes

print(<summary.bpaft.mle>)

Bernstein Polynomial Based Regression Object Summary BPAFT MLE

print(<summary.bpph.bayes>)

Bernstein Polynomial Based Regression Object Summary BPPH Bayes

print(<summary.bpph.mle>)

Bernstein Polynomial Based Regression Object Summary BPPH MLE

print(<summary.bppo.bayes>)

Bernstein Polynomial Based Regression Object Summary BPPO Bayes

print(<summary.bppo.mle>)

Bernstein Polynomial Based Regression Object BPPO MLE

print(<summary.spbp.bayes>)

Bernstein Polynomial Based Regression Object Summary Bayes

print(<summary.spbp.mle>)

Bernstein Polynomial Based Regression Object Summary MLE