The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
survextrap is an R package for parametric survival
modelling with either or both of:
| Survival time | Death | Predictors… |
|---|---|---|
| 2 years | Yes | |
| 5 years | No | |
| etc… |
| Follow-up period | Number | Predictors… | ||
|---|---|---|---|---|
| Start time \(t\) | End time \(u\) | Alive at \(t\) | Still alive at \(u\) | |
| \(t_{1}\) | \(u_{1}\) | \(n_{1}\) | \(r_{1}\) | |
| \(t_{2}\) | \(u_{2}\) | \(n_{2}\) | \(r_{2}\) | |
| etc… | ||||
Any number of rows can be supplied for the “external” data, and the time intervals do not have to be distinct or exhaustive.
Many forms of external data that might be useful for survival extrapolation (such as population data, registry data or elicited judgements) can be manipulated into this common “count” form.
Extrapolations from short-term individual level data should be done using explicit data or judgements about how risk will change over time.
Extrapolations should not rely on standard parametric forms (e.g. Weibull, log-normal, gamma…) that are only used out of convention and do not have interpretations as plausible mechanisms for how risk will change over time.
Instead of selecting (or averaging) traditional parametric models, an arbitrarily flexible parametric model should be used, that adapts to give the optimal fit to the short-term and long-term data in combination.
Bayesian multiparameter evidence synthesis is used to jointly model all sources of data and judgements.
An M-spline is used to represent how the hazard changes through time (as in rstanarm). The Bayesian fitting method automatically chooses the optimal level of smoothness and flexibility. Spline “knots” should span the period covered by the data, and any future period where there is a chance that the hazard may vary. Then if there is no data in the future period, the uncertainty will be acknowledged and the predicted hazards will have wide credible intervals.
A proportional hazards model or a flexible non-proportional hazards model can be used to describe the relation of survival to predictors.
Mixture cure, relative survival and treatment effect waning models are supported.
It has an R interface, designed to be friendly to those familiar with standard R modelling functions.
Stan is used under the surface to do MCMC (Hamiltonian Monte Carlo) sampling from the posterior distribution, in a similar fashion to rstanarm and survHE.
Estimates and posterior summaries and samples for outputs, such as survival, hazard and (restricted) mean survival, can easily be extracted.
The model is fully described in a paper: Jackson, BMC Medical
Research Methodology (2023). See also
vignette("methods").
vignette("priors") goes into detail on how prior
distributions and judgements can be specified in survextrap
- an important but often-neglected part of Bayesian analysis.
Two papers by Timmins et al. describe simulation studies that show good performance of the methods for (a) short-term estimation from individual-level data and (b) extrapolation including external data.
vignette("examples") gives a rapid tour of each feature,
using simple textbook examples and simulated data.
The cetuximab
case study is a more in-depth demonstration of how
survextrap could be used in a typical health technology
evaluation, based on clinical trial, disease registry, general
population and elicited data. This vignette accompanies Section 4 of the
preprint paper.
The package can be installed in the usual way from CRAN, as:
install.packages("survextrap")The latest development version on Github can be installed as
remotes::install_github("chjackson/survextrap")or more easily as (but a day behind the code on Github)
install.packages("survextrap", repos=c('https://chjackson.r-universe.dev',
'https://cloud.r-project.org'))If you use it, I would be very happy to know!
Feedback, suggestions or problem reports are welcome. Or just let me know what you are using it for, and how well it worked for your application.
github issues, or email are fine.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.