Bayesian Flexible Parametric Survival Modelling and Extrapolation
Estimates of cumulative hazard from a survextrap model
Cumulative background hazards
Posterior draws from a survextrap model
Hazard ratio against time in a survextrap model
Estimates of hazard from a survextrap model
Hazard ratio between high and low values of the hazard over time
Incremental restricted mean survival time
Mean survival time
Evaluate an M-spline basis matrix at the specified times.
Determine M-spline basis coefficients which give a constant function.
Create a default M-spline model structure
Validate an M-spline object supplied as a list, choosing defaults if n...
Data for plotting an M-spline function, showing how it is built up fro...
Get basis for an illustration of an M-spline with given knots.
Make default M-spline knot specification given a survival dataset.
Create an M-spline survival model, both structure and parameters.
Derive a normal prior for the log hazard ratio parameter based on a gu...
Derive a normal prior for the log hazard scale parameter based on a gu...
Plot hazard ratio against time from a survextrap model
Plot hazard curves from a survextrap model
Plot a M-spline function, showing how it is built up from its basis
Plot survival curves from a survextrap model
Plot method for survextrap model objects
Print the priors used in a fitted survextrap model
Print a fitted survextrap model
Summarises the prior for the constant hazard implied by a particular p...
Determine priors for time-varying hazards and hazard ratios
Summarises the prior for the hazard ratio implied by a particular prio...
Simulate a dataset from the prior predictive distribution of survival ...
Generate and/or plot a sample from the prior distribution of M-spline ...
Sample from the joint prior of parameters in a survextrap model
Prior distributions and options
Restricted mean survival time
Constructor for a standardising population used for survextrap outputs
Posterior summary statistics for parameters of survextrap models
The 'survextrap' package.
Flexible Bayesian parametric survival models
Estimates of survival from a survextrap model
M-spline survival distribution under treatment effect waning
M-spline survival distribution
Survival analysis using a flexible Bayesian model for individual-level right-censored data, optionally combined with aggregate data on counts of survivors in different periods of time. An M-spline is used to describe the hazard function, with a prior on the coefficients that controls over-fitting. Proportional hazards or flexible non-proportional hazards models can be used to relate survival to predictors. Additive hazards (relative survival) models, waning treatment effects, and mixture cure models are also supported. Priors can be customised and calibrated to substantive beliefs. Posterior distributions are estimated using 'Stan', and outputs are arranged in a tidy format. See Jackson (2023) <doi:10.1186/s12874-023-02094-1>.
Useful links