similar to: glmpath: how to choose best lambda

We have uploaded to CRAN a new version of glmpath, a package which fits the L1 regularization path for generalized linear models. The revision includes: - coxpath, a function for fitting the L1-regularization path for the Cox ph model; - bootstrap functions for analyzing sparse solutions; - the ability to mix in L2 regularization along with L1 (elasticnet). We have also completed a report that

We have uploaded to CRAN a new version of glmpath, a package which fits the L1 regularization path for generalized linear models. The revision includes: - coxpath, a function for fitting the L1-regularization path for the Cox ph model; - bootstrap functions for analyzing sparse solutions; - the ability to mix in L2 regularization along with L1 (elasticnet). We have also completed a report that

We have uploaded to CRAN the first version of glmpath, which fits the L1 regularization path for generalized linear models. The lars package fits the entire piecewise-linear L1 regularization path for the lasso. The coefficient paths for L1 regularized glms, however, are not piecewise linear. glmpath uses convex optimization - in particular predictor-corrector methods- to fit the

We have uploaded to CRAN the first version of glmpath, which fits the L1 regularization path for generalized linear models. The lars package fits the entire piecewise-linear L1 regularization path for the lasso. The coefficient paths for L1 regularized glms, however, are not piecewise linear. glmpath uses convex optimization - in particular predictor-corrector methods- to fit the

I'm trying to do LASSO in R with the package glmpath. However, I'm not sure if I am using the accompanying prediction function *predict.glmpath()* correctly. Suppose I fit some regularized binomial regression model like so: library(glmpath);load(heart.data);attach(heart.data); fit <- glmpath(x, y, family=binomial) Then I can use predict.glmpath() to estimate the value of the

Hi all, I'm relatively new to using R, and have been trying to fit an L1 regularization path using coxpath from the glmpath library. I'm interested in using a cross validation framework, where I crossvalidate on a training set to select the lambda that achieves the lowest error, then use that value of lambda on the entire training set, before applying to a test set. This seems to entail

Hi, perhaps you can help me to find out, how to find the best Lambda in a LASSO-model. I have a feature selection problem with 150 proteins potentially predicting Cancer or Noncancer. With a lasso model fit.glm <- glmpath(x=as.matrix(X), y=target, family="binomial") (target is 0, 1 <- Cancer non cancer, X the proteins, numerical in expression), I get following path (PICTURE

The problem first appeared in R 2.6.1 and is still there in R 2.6.2 On Windows running R CMD check command for glmpath package fails. The reason seems to be that when R is running the examples file (glmpath-Ex.R), it skips about 50 lines and as a result gives a syntax error. I'm working with a modified version of the CRAN glmpath 0.94. My version happens to give a more clear example of a

Hi R-users! I am trying to learn how to use the glmpath package. I have a dataframe like this > dim(data) [1] 605 109 and selected the following > response <- data[,1] > features<-as.matrix(data[,3:109]) > mymodel <- glmpath(features,response, family = binomial) Error in if (lambda <= min.lambda) { : missing value where TRUE/FALSE expected Reading the glmpath pdf, I

Hi, I am new to model selection by coefficient shrinkage method such as lasso. And I became particularly interested in variable selection in Cox regression by lasso. I became aware of the coxpath() in R package glmpath does lasso on Cox model. I have tried the sample script on the help page of coxpath(), but I have difficult time understanding the output. Therefore, I would greatly appreciate if

Hi Claire, I'm replying and CC-ing to the R-help list to get more eyes on your question since others will likely have more/better advice, and perhaps someone else in the future will have a similar question, and might find this thread handy. I've removed your specific research aim since that might be private information, but you can include that later if others find it necessary to know

This update adds an intercept option (by popular request) - now one can fit a model without an intercept Glmnet is a package that fits the regularization path for a number of generalized linear models, with with "elastic net" regularization (tunable mixture of L1 and L2 penalties). Glmnet uses pathwise coordinate descent, and is very fast. The current list of models covered are:

This update adds an intercept option (by popular request) - now one can fit a model without an intercept Glmnet is a package that fits the regularization path for a number of generalized linear models, with with "elastic net" regularization (tunable mixture of L1 and L2 penalties). Glmnet uses pathwise coordinate descent, and is very fast. The current list of models covered are:

This is a new version of glmnet, that incorporates some bug fixes and speedups. * a new convergence criterion which which offers 10x or more speedups for saturated fits (mainly effects logistic, Poisson and Cox) * one can now predict directly from a cv.object - see the help files for cv.glmnet and predict.cv.glmnet * other new methods are deviance() for "glmnet" and coef() for

glmnet is a package that fits the regularization path for linear, two- and multi-class logistic regression models with "elastic net" regularization (tunable mixture of L1 and L2 penalties). glmnet uses pathwise coordinate descent, and is very fast. Some of the features of glmnet: * by default it computes the path at 100 uniformly spaced (on the log scale) values of the

glmnet is a package that fits the regularization path for linear, two- and multi-class logistic regression models with "elastic net" regularization (tunable mixture of L1 and L2 penalties). glmnet uses pathwise coordinate descent, and is very fast. Some of the features of glmnet: * by default it computes the path at 100 uniformly spaced (on the log scale) values of the

glmnet_1.2 has been uploaded to CRAN. This is a major upgrade, with the following additional features: * poisson family, with dense or sparse x * Cox proportional hazards family, for dense x * wide range of cross-validation features. All models have several criteria for cross-validation. These include deviance, mean absolute error, misclassification error and "auc" for logistic or

glmnet_1.2 has been uploaded to CRAN. This is a major upgrade, with the following additional features: * poisson family, with dense or sparse x * Cox proportional hazards family, for dense x * wide range of cross-validation features. All models have several criteria for cross-validation. These include deviance, mean absolute error, misclassification error and "auc" for logistic or

Hi, I am analyzing a set of variables in order to create a survival model for a set of patients. I have checked the reference manual for glm path and coxpath in order to achieve it. However I have a doubt about the class of the covariates I can use with the last mentioned package. In the example, the package loads a list called "lung.data". This object has a matrix with the covariate

SoftImpute is a new package for matrix completion - i.e. for imputing missing values in matrices. SoftImpute was written by myself and Rahul Mazumder. softImpute uses uses squared-error loss with nuclear norm regularization - one can think of it as the "lasso" for matrix approximation - to find a low-rank approximation to the observed entries in the matrix. This low-rank approximation