Function reference • survextrap

Fitting models

survextrap(): Flexible Bayesian parametric survival models

Utilities to determine prior distributions for M-spline models

p_normal() p_t() p_beta() p_gamma(): Prior distributions and options

prior_sample(): Sample from the joint prior of parameters in a survextrap model

p_meansurv(): Derive a normal prior for the log hazard scale parameter based on a guess at survival times

p_hr(): Derive a normal prior for the log hazard ratio parameter based on a guess at the hazard ratio

prior_haz_const(): Summarises the prior for the constant hazard implied by a particular prior on the hazard scale parameter and spline specification.

prior_haz_sd() prior_hr_sd(): Determine priors for time-varying hazards and hazard ratios

prior_hr(): Summarises the prior for the hazard ratio implied by a particular prior on the log hazard ratio

prior_sample_hazard() plot_prior_hazard(): Generate and/or plot a sample from the prior distribution of M-spline hazard curves

prior_pred(): Simulate a dataset from the prior predictive distribution of survival times in an M-spline survival model.

print_priors(): Print the priors used in a fitted survextrap model

Getting results from fitted models

print(<survextrap>): Print a fitted survextrap model

summary(<survextrap>): Posterior summary statistics for parameters of survextrap models

survival(): Estimates of survival from a survextrap model

hazard(): Estimates of hazard from a survextrap model

cumhaz(): Estimates of cumulative hazard from a survextrap model

hazard_ratio(): Hazard ratio against time in a survextrap model

standardise_to() standardize_to(): Constructor for a standardising population used for survextrap outputs

plot_survival(): Plot survival curves from a survextrap model

plot_hazard(): Plot hazard curves from a survextrap model

plot_hazard_ratio(): Plot hazard ratio against time from a survextrap model

plot(<survextrap>): Plot method for survextrap model objects

mean(<survextrap>): Mean survival time

rmst(): Restricted mean survival time

irmst(): Incremental restricted mean survival time

get_cum_backhaz(): Cumulative background hazards

get_draws(): Posterior draws from a survextrap model

hrtime(): Hazard ratio between high and low values of the hazard over time

Datasets

colons: Colon cancer survival data

cetux cetux_seer cetux_bh: Datasets for evaluation of cetuximab in head and neck cancer

curedata: Simulated data for testing mixture cure models

M-spline utilities

psurvmspline() Hsurvmspline() hsurvmspline() dsurvmspline() qsurvmspline() rsurvmspline() rmst_survmspline() mean_survmspline(): M-spline survival distribution

Hsurvmspline_wane() psurvmspline_wane() hsurvmspline_wane() dsurvmspline_wane() qsurvmspline_wane() rsurvmspline_wane() rmst_survmspline_wane() mean_survmspline_wane(): M-spline survival distribution under treatment effect waning

mspline_spec(): Make default M-spline knot specification given a survival dataset.

mspline_basis(): Evaluate an M-spline basis matrix at the specified times.

mspline_constant_coefs(): Determine M-spline basis coefficients which give a constant function.

mspline_plotdata(): Data for plotting an M-spline function, showing how it is built up from its basis

mspline_plotsetup(): Get basis for an illustration of an M-spline with given knots.

plot_mspline(): Plot a M-spline function, showing how it is built up from its basis

mspline_init(): Create a default M-spline model structure

mspline_list_init(): Validate an M-spline object supplied as a list, choosing defaults if needed.

msplinemodel_init(): Create an M-spline survival model, both structure and parameters.

Package overview

survextrap-package: The 'survextrap' package.