easysurv 2.0.1
- 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 with
system.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 using tidyverse
principles. From the tidymodels
framework, we take
advantage of the parsnip
and censored
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 a parsnip
extension that provides engines for various models to handle censored
data in survival analysis.
- New functions!
inspect_surv_data()
allows quick inspection of survival
data.
get_km()
replaces quick_KM()
as the
function to fit Kaplan-Meier curves.
test_ph()
replaces quick_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
to
ggsurvfit
. ggsurvplot
generates warning
messages when median survival lines are added and generates misaligned
risk tables as of ggplot2
version 3.5.0, while
ggsurvfit
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 of fit_models()
acts as a call to predict_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 in
predict_fits()
. The original prediction method (via survHE)
can be used instead by setting the new argument
plot_predictions = "survHE"
for plot_fits()
and any functions that use plot_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 setting include_ci = FALSE
. The
include_ci
argument is available for all functions that use
predict_fits()
or objects generated by
predict_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 the
quick_to_XL()
function.
easysurv 1.0.0