similar to: glmpath crossvalidation

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

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, 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, 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

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

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

Hi all, I am using glampath package for L1 regularized logistic regression. I have read the article " L1 regularization path algorithm for GLM" by park and Hastie (2006). One thing I can't understand that how to find best lambda for my prediction. I want to use that lambda for the prediction not the entire set. thanks. -- View this message in context:

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

Dear colleagues, I hope someone can help me with my problem. I have fitted a cox model with the following syntax: # cox01def <-cph(Surv(TEVENT,EVENT) ~ ifelse(AGE>50, (AGE-50)^2,0) + BMI + # HDL+DIABETES +HISTCAR2 + log(CREAT)+ as.factor(ALBUMIN)+STENOSIS+IMT,data # = XC, x=T, y=T, surv=T) *1 Furthermore I have estimated my beta's also with a Lasso method - Coxpath ( from

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

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

Hello, Thank you for probably not so new question, but i am new to R. Does any of packages have something like glm+regularization? So far i see probably something close to that as a ridge regression in MASS but I think i need something like GLM, in particular binomial regularized versions of polynomial regression. Also I am not sure how some of the K-fold crossvalidation helpers out there

Hello: I would like to obtain probability of an event for one single patient as a function of time (from survfit.coxph) object, as I want to find what is the probability of an event say at 1 month and what is the probability of an event at 80 months and compare. So I tried the following but it fails miserably. I looked at some old posts but could not figure out the solution. Here's what I did

Hello R helpers: *My first message didn't pass trough filter so here it's again* I would like to obtain probability of an event for one single patient as a function of time (from survfit.coxph) object, as I want to find what is the probability of an event say at 1 month and what is the probability of an event at 80 months and compare. So I tried the following but it fails miserably. I

Full_Name: Noel O'Boyle Version: 2.1.0 OS: Debian GNU/Linux Sarge Submission from: (NULL) (131.111.8.96) (1) Description of error The 10-fold CV option for the svm function in e1071 appears to give incorrect results for the rmse. The example code in (3) uses the example regression data in the svm documentation. The rmse for internal prediction is 0.24. It is expected the 10-fold CV rmse

1. This is _not_ a bug in R itself. Please don't use R's bug reporting system for contributed packages. 2. This is _not_ a bug in svm() in `e1071'. I believe you forgot to take sqrt. 3. You really should use the `tot.MSE' component rather than the mean of the `MSE' component, but this is only a very small difference. So, instead of spread[i] <- mean(mysvm$MSE), you

?s 20:12 de 23/10/2023, varin sacha via R-help escreveu: > Dear R-experts, > > I really thank you all a lot for your responses. So, here is the error (and warning) messages at the end of my R code. > > Many thanks for your help. > > > Error in UseMethod("predict") : > ? no applicable method for 'predict' applied to an object of class

Dear R-experts, I really thank you all a lot for your responses. So, here is the error (and warning) messages at the end of my R code. Many thanks for your help. Error in UseMethod("predict") : ? no applicable method for 'predict' applied to an object of class "c('matrix', 'array', 'double', 'numeric')" > mean(unlist(lst)) [1] NA