How to use method lasso in Cox model using glmnet?
I have the survival data includes 252 patients, 25 independent variables and 35 events. I want to use lasso method in cox model to these data. I use glmnet for it. but, I encountered an error which I cannot explain or solve.
How to apply Lasso logistic regression with caret?
-Id, data = train.df, method = “glmnet”, trControl = trainControl, metric = “F”, # Optimize by F-measure alpha=1, family=”binomial”) The parameter “alpha” is not recognized, and “the model fit fails in every fold”. What am I doing wrong? Help would be much appreciated. Thanks. Try to use tuneGrid. For example as follows:
How is the regularization path computed for Lasso?
The regularization path is computed for the lasso or elastic net penalty at a grid of values (on the log scale) for the regularization parameter lambda. The algorithm is extremely fast, and can exploit sparsity in the input matrix x. It fits linear, logistic and multinomial, poisson, and Cox regression models.
What kind of regression models can glmnet fit?
The algorithm is extremely fast, and can exploit sparsity in the input matrix x. It fits linear, logistic and multinomial, poisson, and Cox regression models. It can also fit multi-response linear regression, generalized linear models for custom families, and relaxed lasso regression models.
How is cv.glmnet used in Cox regression?
The function cv.glmnet can be used to compute K -fold cross-validation (CV) for the Cox model. The usage is similar to that for other families except for two main differences. First, type.measure only supports “deviance” (also default) which gives the partial-likelihood, and “C”, which gives the Harrell C index.
When to use glmnet for Cox proportional hazards?
This vignette describes how one can use the glmnet package to fit regularized Cox models. The Cox proportional hazards model is commonly used for the study of the relationship beteween predictor variables and survival time.
How is the percent of null deviance explained in glmnet?
It shows from left to right the number of nonzero coefficients ( Df ), the percent (of null) deviance explained ( %dev) and the value of λ ( Lambda ). Although glmnet fits the model for 100 values of lambda by default, it stops early if %dev does not change sufficently from one lambda to the next (typically near the end of the path.)
How to use model selection through shrinkage ( LASSO )?
Closed 3 months ago. I would like to use model selection through shrinkage (Lasso) using glmnet. So far I did the following: