NEWS
hdnom 6.0.4 (2024-09-05)
Bug fixes
- Fixed C code compatibility issues with
_R_USE_STRICT_R_HEADERS_
(upcoming default in R 4.5.0) (#13):
- Defined
STRICT_R_HEADERS
.
- Replaced
Calloc
and Free
with R_Calloc
and R_Free
.
- Included
float.h
for FLT_EPSILON
.
hdnom 6.0.3 (2024-03-03)
Improvements
- Fix "lost braces" check notes on r-devel.
- Export S3 method per guidelines in roxygen2 7.3.0.
- Use GitHub Actions to build the pkgdown site.
- Fix code linting issues.
hdnom 6.0.2 (2023-04-24)
Improvements
- Use all samples instead of a much smaller set of samples in some code examples
as a temporary fix for reverse dependency check errors which result in the
null model. A proper fix will involve updating the logic to use
ncvsurv()
in a pathwise manner instead of with a single value of lambda.
hdnom 6.0.1 (2022-05-18)
Improvements
- Removed the dependency on
survAUC
. Ported the essential C code for computing
time-dependent AUC and fixed the build issues in r-devel.
hdnom 6.0.0 (2019-06-23)
This version is a major refactor of the package, with several technical adjustments to improve the functional interface, code structure, and execution performance. As a result, a few critical API-breaking changes have been made. Please update your previous code that calls hdnom accordingly. For the detailed changes, please check the updated items below.
Improvements
General
- Renamed exported functions. Most of the exported function have been renamed to be more meaningful and succinct. For example,
hdcox.*()
are renamed as fit_*()
, hdnom.nomogram()
is renamed as as_nomogram()
, hdnom.validate()
is renamed as validate()
, and so on.
- Removed the dependency on
rms
, by reusing a minimal set of code from rms
for nomogram construction and plotting. This results in clearer code structure, better maintainability, and faster package installation/loading speed. Also removed other non-essential package dependencies.
- The first argument for
print
functions are now returned invisbily, to make it easier to use them in a pipe.
Model Fitting
- The components in the model fitting function returns are now unified across model types. For example, the model object can all be accessed by
fit$model
, and the selected "optimal" hyperparameters can be accessed by fit$lambda
. The model type is now stored explicitly as fit$type
.
Nomograms
as_nomogram
(previously hdnom.nomogram()
) now accepts the fitted model objects directly instead of the $model
component. It now will recognize the model type automatically, thus the previous arguments model.type
has been deprecated. so that it is easier to chain the function calls together using magrittr
.
- In
as_nomogram
, the previous ddist
argument is not needed anymore and has been removed. There is also no more need to set a datadist
object as a into the global options variable (which was required in the rms
user flow).
- The new nomogram implementation prints and plots the nomogram for the penalized regression models directly. This supersedes the old implementation, which fits an OLS model to regress the linear predictors on the same set of predictors selected by the penalized Cox regression model, aiming to approximate the penalized model. The numerical or visual difference is minimal, though.
Visualizations
- Add a new ggplot2 theme
theme_hdnom()
and applies it to most of the validation, calibration, and comparison plots for a consistent, cleaner look across plots within the package.
hdnom 5.0 (2018-05-14)
Improvements
- Exported the survival curve prediction functions (
glmnet.survcurve()
, ncvreg.survcurve()
, penalized.survcurve()
) and Breslow baseline hazard estimator functions (glmnet.basesurv()
, ncvreg.basesurv()
, penalized.basesurv()
).
- New URL for the documentation website: https://nanx.me/hdnom/.
hdnom 4.9 (2017-09-29)
Improvements
- Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.
hdnom 4.8 (2017-03-25)
Improvements
- Reduced example running time to less than 10s for
hdnom.calibrate()
.
hdnom 4.7
Improvements
- Better code indentation style.
- Reduced example running time for fused lasso.
- Updated gallery images in
README.md
.
- HTTPS enabled for the website.
hdnom 4.6 (2017-01-08)
Bug Fixes
- Fixed issues in parameter tuning and cross-validation procedures for
fused lasso models (nanxstats/hdnom@afc49c9).
The user-visible change is that two parameters
lambda1
and lambda2
instead of a single "lambda" are now required to fit, validate, and
calibrate fused lasso models.
Improvements
- The argument
lambda
in hdnom.nomogram
is no longer needed and has
been deprecated.
- Allow users to specify
eps
and max.iter
for MCP and SCAD penalty
related models. Setting the default values to be 1e-4
and 10000
,
which is consistent with ncvreg 3.8-0.
hdnom 4.5 (2016-12-25)
Bug Fixes
- Fixed vanishing axis problem in Kaplan-Meier plot
hdnom.kmplot()
under
ggplot2 2.2.0, which is caused by a previous workaround for a bug introduced
in ggplot2 2.1.0.
- Fixed potential convergence issues for examples under ncvreg >= 3.7-0 new
convergence criterion, by increasing
max.iter
for ncvsurv
to a
substantially higher value (5e+4).
- Fixed single lambda support issues in
ncvsurv
under ncvreg >= 3.7-0.
Improvements
- Added Windows continuous integration using AppVeyor.
- New website design for project website: consistent with the web application.
hdnom 4.0 (2016-07-05)
Improvements
- More concrete examples for several functions.
- Introduce argument
ylim
for plot.hdnom.validate()
,
plot.hdnom.external.validate()
, and plot.hdnom.compare.validate()
(#4).
hdnom 3.7
Bug Fixes
- Removed one redundant color from the lancet color palette.
hdnom 3.6 (2016-03-25)
New Features
- Added 4 new color palettes (JCO, Lancet, NPG, AAAS) for all plots.
See the vignette for details.
Bug Fixes
- Fixed vanishing axis problem in Kaplan-Meier plot due to ggplot2 2.1.0 update.
Improvements
- New CSS style for the HTML vignette.
hdnom 3.0 (2016-01-04)
New Features
Package
- New function
hdnom.compare.validate()
for model comparison by validation
- New function
hdnom.compare.calibrate()
for model comparison by calibration
- New function
hdnom.external.validate()
for external validation
- New function
hdnom.external.calibrate()
for external calibration
- New
predict
and print
methods for hdcox.model
objects
- New function
hdnom.kmplot()
: Kaplan-Meier analysis for risk groups using
internal/external calibration results
- New function
hdnom.logrank()
: Log-rank test for risk groups using
internal/external calibration results
Web Application
- The web application is substantially improved to reflect the new features
- Record random seeds in the generated reports to improve reproducibility
- Allow users to download the model objects for further exploration in
R
Improvements
- Improvements on random seed handling for internal validation and calibration
- The vignette is extended to reflect the new features
Bug Fixes
- Fixed an error in internal calibration which mistakenly used
testing data when should use training data in computation
hdnom 2.1 (2015-10-27)
New Features
- New documentation website.
- New Shiny web application.
Improvements
- Added exception handling for null models in all
hdcox.*()
functions.
Make examples compatible with ncvreg 3.5-0, which refined CV
implementation for survival models and improved computation speed.
hdnom 2.0 (2015-09-16)
New Features
hdnom 1.2 (2015-08-28)
Improvements
- Reduced example running time for
hdnom.validate()
, hdnom.calibrate()
,
hdcox.aenet()
, and hdcox.enet()
by reducing resampling times.
hdnom 1.1
Bug Fixes
- Added argument
parallel
to hdcox.aenet()
and hdcox.enet()
to enable
or disable the use of parallel parameter tuning.
hdnom 1.0
New Features
- Initial version
- Nomograms for glmnet models
- Validation for glmnet models
- Calibration for glmnet models