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Changelog

Source: NEWS.md

Version 0.8.13 (2024/03/05)

  • Bug fix for models with external data and either nonproportional hazards or covariates on cure probability.

Version 0.8.12 (2024/01/06)

  • irmst, hazard_ratio and hrtime tidied. Fix of bug in irmst introduced in v0.8.9, and all now have a sample argument.

Version 0.8.11 (2023/12/28)

  • Outputs standardised over the covariate values of a reference population can now be produced using the new standardise_to() function.

Version 0.8.10 (2023/12/24)

  • loo no longer ignores covariates on the cure probability in cure models.

  • More internal refactoring of code to produce outputs.

Version 0.8.9 (2023/12/22)

  • Cleaned and simplified internal code for model outputs (rmst, survival etc.).

  • rmst now outputs a tibble, and confidence limits in the default output are renamed to lower and upper for consistency with survival and hazard.

  • Arrays now allowed for coef argument in dsurvspline and related functions.

Version 0.8.8 (2023/12/19)

  • Background hazards in additive hazards models can now be stratified, using the new backhaz_strata argument to survextrap(). This argument names stratifying variables (e.g. age group) that should be in both the background hazards and the individual and/or external data.

  • Bug fix for hsurvmspline_wane and dsurvmspline_wane where offsets were not implemented correctly. This affected hazard predictions for models that included both background hazards and treatment effect waning.

Version 0.8.7 (2023/10/29)

  • A random walk prior can now be specified for the spline coefficients, by smooth_model = "random_walk".

Version 0.8.6 (2023/10/24)

  • Non-proportional hazards models can now be applied to a subset of the covariates, by supplying a formula as the nonprop argument to survextrap.

  • Prior simulation functions such as prior_sample now require an explicit covariate model, specified through formula and newdata, rather than a design matrix X. These functions now fully support nonproportional hazards models and cure probabilities with associated regression models.

Version 0.8.5 (2023/09/30)

  • Code for constructing mspline specification objects tidied, with new mspline_init and mspline_list_init functions.

Version 0.8.4 (2023/09/09)

  • Deprecated Stan array syntax updated. The package now requires rstan version 2.26.

Version 0.8.3 (2023/06/30)

  • Fix for mspline_spec bug introduced in 0.8.2.

Version 0.8.2 (2023/06/14)

  • Individual data can now be excluded, so that the model is fitted to external data alone.

Version 0.8.1 (2023/05/25)

  • Update to work with StanHeaders 2.26.

Version 0.8 (2023/05/06)

The GitHub commit on 6 May 2023 implemented several changes that are listed here. survextrap is now in “beta” status. All major features are now implemented, but there may still be some lack of polish.

New features

  • A new vignette cetuximab, giving an in-depth case study of a realistic use of survextrap. To be included in a forthcoming paper.

  • Improvements to usability and stability of M-splines:

    • iknots and bknots are replaced by a single knots, and the lower boundary knot is always fixed at zero.

    • add_knots can be used to add user-defined knots to the default ones. See the case study.

    • New function mspline_spec to define M-spline knots based on data, in advance of fitting any models.

    • M-splines can now be smoother at the final knot, through an option bsmooth, which is on by default. Thanks to Iain Timmins for the suggestion.

  • Incremental restricted mean survival time (irmst) added.

  • Any summary of the posterior distribution can be produced by supplying a list of summary functions (e.g. mean, quantiles) to output functions (such as rmst and survival).

  • Leave-one-out cross validation for external data.

Bug fixes and improvements

  • Bug fix for hsurvmspline() (hence hazard()) which was using the wrong tail end of psurvmspline().

  • Waning models no longer ignore non-proportional hazards and cure. Waning vignette merged into the methods vignette.

  • Leave-one-out cross validation now supports models with background hazards.

  • More consistent naming of arguments and variables (e.g. hscale for hazard scale, and hsd for hazard smoothing parameter).

  • More information given when printing fitted model objects.

  • Thorough documentation polishing and code tidying.

Version 0.1

Changes

See commit messages on GitHub for a history of developments to survextrap.