Package: penalized 0.9-52
Jelle Goeman
penalized: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Authors:
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penalized.pdf |penalized.html✨
penalized/json (API)
| # Install 'penalized' in R: |
| install.packages('penalized', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org')) |
- nki70 - The 70 gene signature of the Netherlands Cancer Institute for prediction of metastasis-free survival, measured on 144 independent lymph node positive patients.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:054894f8cf. Checks:OK: 1 NOTE: 8. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 02 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 02 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 02 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 02 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 02 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 02 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 02 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 02 2024 |
Exports:as.data.frameas.listas.matrixbasehazbasesurvcoefcoefficientscontr.diffcontr.nonecvlfittedfitted.valueslinear.predictorsloglikoptL1optL2penalizedpenaltyplotplotpathpredictprofL1profL2residualsshowsurvivaltimeweights
Dependencies:latticeMatrixRcppRcppArmadillosurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Breslow estimator object | as.data.frame,breslow-method as.list,breslow-method as.matrix,breslow-method breslow breslow-class plot,breslow-method show,breslow-method survival survival,breslow-method time,breslow-method [,breslow,ANY,ANY,ANY-method [,breslow-method [[,breslow-method |
| Cross-validated penalized regression | cvl optL1 optL2 profL1 profL2 |
| The 70 gene signature of the Netherlands Cancer Institute for prediction of metastasis-free survival, measured on 144 independent lymph node positive patients. | nki70 |
| Penalized regression | penalized |
| Contrast functions for penalized regression | contr.diff contr.none |
| Penalized regression object | as.data.frame,penfit-method basehaz,penfit-method basesurv basesurv,penfit-method coef,penfit-method coefficients,penfit-method fitted,penfit-method fitted.values,penfit-method linear.predictors linear.predictors,penfit-method loglik loglik,penfit-method penalty penalty,penfit-method penfit penfit-class residuals,penfit-method show,penfit-method weights,penfit-method |
| Plotting the LASSO path | plotpath |
| Prediction based on penfit objects | predict predict,penfit-method |
