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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.