easysurv 2.0.2
CRAN release: 2025-10-08
- Fix: plot_schoenfeld() now respects point_* aesthetics (col, size, shape, alpha). (#24)
- Increment package dependency on
ggsurvfit
to v1.2.0 to address updates made inggplot2
v4.0.0.
easysurv 2.0.1
CRAN release: 2024-06-21
- Removed wrapping of examples in
if(FALSE){}
. In write_to_xl.Rd, we now use\dontrun{}
to prevent an Excel file from being created, saved and launched. - Updated the Description field in DESCRIPTION, correcting the erroneous reference to ‘flexsurvspline’ as a package; it is a function. The same error was addressed in the README file and in
fit_models()
documentation. - Removed dependency on the
fs
package.fs::path_package()
was replaced withsystem.file()
. - Wrapped external functions in square brackets in
roxygen2
documentation to support auto-linking to external documentation.
easysurv 2.0.0
Major changes
- Transitioned to a
tidymodels
framework for survival analysis. Several updates were required to reflect this change including to function names, arguments, supporting documentation, and templates.- The
tidymodels
framework is a collection of R packages for modeling and machine learning usingtidyverse
principles. From thetidymodels
framework, we take advantage of theparsnip
andcensored
packages to specify models and predict survival outputs. - The
parsnip
package provides an interface to many different modeling packages, allowing for a consistent syntax for fitting models and making predictions. - The
censored
package is aparsnip
extension that provides engines for various models to handle censored data in survival analysis.
- The
- New functions!
-
inspect_surv_data()
allows quick inspection of survival data. -
get_km()
replacesquick_KM()
as the function to fit Kaplan-Meier curves. -
test_ph()
replacesquick_PH()
as the function to test the proportional hazards assumption. -
fit_models()
allows for additional covariates to be specified in model fitting. -
predict_and_plot()
separates the generation of predictions and associated plots from the main model fitting function.
-
Other improvements and bug fixes
- No longer requires any additional font installation.
- Introduced print methods with the
cli
package for key functions to simplify and summarise outputs. - Changed primary plotting package from
ggsurvplot
toggsurvfit
.ggsurvplot
generates warning messages when median survival lines are added and generates misaligned risk tables as ofggplot2
version 3.5.0, whileggsurvfit
is being actively maintained. - To facilitate interpretation of Schoenfeld residual plots, scaled Schoenfeld residuals are now used, and facets are no longer produced per strata.
-
plot()
run on the output offit_models()
acts as a call topredict_and_plot()
, generating predictions and plots for the specified model.
easysurv 1.1.0
-
plot_fits()
now uses flexsurv to generate survival predictions in plots, which matches the prediction method inpredict_fits()
. The original prediction method (via survHE) can be used instead by setting the new argumentplot_predictions = "survHE"
forplot_fits()
and any functions that useplot_fits()
(e.g.,quick_fit_select()
,quick_fit()
). -
predict_fits()
now outputs a list object that includes 95% confidence intervals for the predicted survival probabilities. CIs can be excluded by settinginclude_ci = FALSE
. Theinclude_ci
argument is available for all functions that usepredict_fits()
or objects generated bypredict_fits()
(e.g.,quick_fit_select()
,quick_fit()
). - A dependency on the
cli
package has been added to support aesthetic and informative warning messages, such as in thequick_to_XL()
function.