search for: glmpath

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 1) One of these models is the best, according to its crossvalidation (PICTURE 2), the red line corresponds to the best crossvali...

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 (...

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 (...

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 problem than the orig...

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.gl...

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 pred...

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 pred...

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...

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 anyone can help me understand how to use the function. > data(lung.data) > attach(lung.data) > fit.a <- co...

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 somehow using cv.coxpath ,...

...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: http://www.nabble.com/glmpath%3A-how-to-choose-best-lambda-tf4505338.html#a12849013 Sent from the R help mailing list archive at Nabble.com.

Hi, When I install new packages from CRAN, I frequently find that some packages were missing from the download queue. For example, on one of my computer with R2.6.2, I can not find package glmpath from the download queue. On my other computer with R2.5.1, I could still find that particular package. What could be the reason for this? Is this computer related or R version related? I downloaded the gz file for package glmpath into my local drive (Windows XP), how can I install it? I tried: in...

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

...odel to explore [REDACTED] and recently decided to build a LASSO-model, having learned of the problems with stepwise variable selection. While I've done a fair amount of reading on the topic, I'm still a bit uncertain when it comes to selecting an appropriate value for lambda when using the glmpath package. > > Any advice you could offer would be much appreciated. In general, what I've done is to use cross validation to find this "best" value for lambda, which I'm defining as the value of lambda that gives me the model with the lowest "objective score" on my...

library(glmpath) data(heart.data) # heart.data is a list, $y a vector, $x a matrix data <- data.frame(x=I(heart.data$x), y = heart.data$y) > data[1:2,] x.1 x.2 x.3 x.4 x.5 x.6 x.7 x.8 x.9 y 1 160 12 5.73 23.11 1 49 25.3 97.2 52 1 2 144 0.01 4.41 28.61 0 55 28....

...month 06 day 26 svn rev 48839 language R version.string R version 2.9.1 (2009-06-26) A related error can be triggered from within R: > install.packages("glmpath", lib="/usr/local/opt/x86_64-pc-solaris2.10/R-2.9.1/lib64/R/library") trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/glmpath_0.94.tar.gz' Content type 'application/x-gzip' length 265253 bytes (259 Kb) opened URL ==================================================...

...vi Varadhan [mailto:rvaradhan at jhmi.edu] Sent: Monday, September 18, 2006 12:38 PM To: Ridgeway, Greg; r-help at stat.math.ethz.ch Subject: Propensity score modeling using machine learning methods. WAS: RE: [R] LARS for generalized linear models Thanks very much, Greg. I will certainly look at glmpath. My goal is to develop (nearly) automatic and flexible procedures for estimating causal effects of risk factors in observational epidemiological studies. A major part of this is the development of a propensity score model (when the exposure is binary). I would like to use tools/approaches that c...

...day = 20 svn rev = 36812 language = R Windows XP Professional (build 2600) Service Pack 2.0 Locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 Search Path: .GlobalEnv, package:glmpath, package:survival, package:splines, package:methods, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, Autoloads, package:base

Hi, Is there an R implementation of least angle regression for binary response modeling? I know that this question has been asked before, and I am also aware of the "lasso2" package, but that only implements an L1 penalty, i.e. the Lasso approach. Madigan and Ridgeway in their discussion of Efron et al (2004) describe a LARS-type algorithm for generalized linear models. Has

Dear R-users, For the purpose of model selection I am looking for a way to exhaustively (and efficiently) search for best subsets of predictor variables for a logistic regression model. I am looking for something like leaps() but that works with glm. Any feedback highly appreciated. -- Harald von Waldow <hvwaldow at chem.ethz.ch> Safety and Environmental Technology Group Institute for