Bayesian Flexible Parametric Survival Modelling and Extrapolation

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Documentation for package ‘survextrap’ version 1.0

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survextrap-package The 'survextrap' package.
cetux Datasets for evaluation of cetuximab in head and neck cancer
cetux_bh Datasets for evaluation of cetuximab in head and neck cancer
cetux_seer Datasets for evaluation of cetuximab in head and neck cancer
colons Colon cancer survival data
cumhaz Estimates of cumulative hazard from a survextrap model
curedata Simulated data for testing mixture cure models
dsurvmspline M-spline survival distribution
dsurvmspline_wane M-spline survival distribution under treatment effect waning
get_draws Posterior draws from a survextrap model
hazard Estimates of hazard from a 'survextrap' model
hazard_ratio Hazard ratio against time in a survextrap model
hrtime Hazard ratio between high and low values of the hazard over time
Hsurvmspline M-spline survival distribution
hsurvmspline M-spline survival distribution
Hsurvmspline_wane M-spline survival distribution under treatment effect waning
hsurvmspline_wane M-spline survival distribution under treatment effect waning
irmst Incremental restricted mean survival time
mean.survextrap Mean survival time
mean_survmspline M-spline survival distribution
mean_survmspline_wane M-spline survival distribution under treatment effect waning
msplinemodel_init Create an M-spline survival model, both structure and parameters.
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_init Create a default M-spline model structure
mspline_list_init Validate an M-spline object supplied as a list, choosing defaults if needed.
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.
mspline_spec Make default M-spline knot specification given a survival dataset.
plot.survextrap Plot method for survextrap model objects
plot_hazard Plot hazard curves from a survextrap model
plot_hazard_ratio Plot hazard ratio against time from a survextrap model
plot_mspline Plot a M-spline function, showing how it is built up from its basis
plot_prior_hazard Generate and/or plot a sample from the prior distribution of M-spline hazard curves
plot_survival Plot survival curves from a survextrap model
print.survextrap Print a fitted survextrap model
print_priors Print the priors used in a fitted survextrap model
priors Prior distributions and options
prior_haz Determine priors for time-varying hazards and hazard ratios
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 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_hr_sd Determine priors for time-varying hazards and hazard ratios
prior_pred Simulate a dataset from the prior predictive distribution of survival times in an M-spline survival model.
prior_sample Sample from the joint prior of parameters in a survextrap model
prior_sample_hazard Generate and/or plot a sample from the prior distribution of M-spline hazard curves
psurvmspline M-spline survival distribution
psurvmspline_wane M-spline survival distribution under treatment effect waning
p_beta Prior distributions and options
p_gamma Prior distributions and options
p_hr Derive a normal prior for the log hazard ratio parameter based on a guess at the hazard ratio
p_meansurv Derive a normal prior for the log hazard scale parameter based on a guess at survival times
p_normal Prior distributions and options
p_t Prior distributions and options
qsurvmspline M-spline survival distribution
qsurvmspline_wane M-spline survival distribution under treatment effect waning
rmst Restricted mean survival time
rmst_survmspline M-spline survival distribution
rmst_survmspline_wane M-spline survival distribution under treatment effect waning
rsurvmspline M-spline survival distribution
rsurvmspline_wane M-spline survival distribution under treatment effect waning
standardise_to Constructor for a standardising population used for survextrap outputs
standardize_to Constructor for a standardising population used for survextrap outputs
summary.survextrap Posterior summary statistics for parameters of survextrap models
survextrap Flexible Bayesian parametric survival models
survival Estimates of survival from a 'survextrap' model
Survmspline M-spline survival distribution
Survmspline_wane M-spline survival distribution under treatment effect waning