similar to: Need help on the Lasso cox model with discrete time

I want to do a logistic regression without an intercept term. This option is absent from glm, though present in some of the inner functions glm uses. I gather glm is the standard way to do logistic regression in R. Hoping it would be passed in, I said > r <- glm(brain.cancer~epilepsy+other.cancer, c3, > family=binomial(link="logit"), intercept=FALSE) which produced

Full_Name: José Otero Version: Version 1.5.0 (2002-04-29) OS: Redhat 7.3 Submission from: (NULL) (192.187.16.164) Hi: Installation of package faraway as root, from tarbal: R CMD INSTALL ./faraway.tar.gz ERROR: cannot extract package from './faraway.tar.gz' idem, from zipped package: R CMD INSTALL faraway.zip gzip: faraway.zip has more than one entry--rest ignored ERROR: cannot

Dear R community, I have two questions regarding fitting GLMM using maximum likelihood method. The first one arises from trying repeat an analysis in the Breslow and Clayton 1993 JASA paper. Model 3 of the epileptic dataset has two random effects, one subject specific, and one observation specific. Thus if we count random effects, there are more parameters than observations. When I try to run the

To whom it may concern: My name is Jillian Weinfeld. I am currently and undergraduate student at New York University and working at Mount Sinai School of Medicine doing research with epilepsy patients. At the moment I am creating a manhattan plot with my data set. After reading many forums and such, I have appropriately plotted my data, however, I wanted to see how I can change the colors of the

Using Debian Sarge, samba, CUPS, and an HP G85 mutifunction with HPOJ to use the G85 USB connection, I've been able to get raw printing to work, and Point 'n' Print driver download to work, but not at the same time. The driver download was a chore, because of HP's proprietary install program. Had to install the driver locally to get the needed files and copy them manually to the

But not quite. If I could just get past the sound, I think it might start and run. I'm running Wine in desktop display mode, emulating win98. comdlg32, shell32, shlwapi, and '*' are set to "native, builtin" while the rest of the DLLs that the default installation names are builtin, native. I've tried running it with 'winedbg --gdb civilization3', and it always

Dear R-users, A recent post (Feb 16) to R-help inquired about fitting a glmm with a negative binomial distribution. Professor Ripley responded that this was a difficult problem with the simpler Poisson model already being a difficult case: https://stat.ethz.ch/pipermail/r-help/2005-February/064708.html Since we are developing software for fitting general nonlinear random effects models we

https://forum.linode.com/viewtopic.php?f=19&t=14570&p=72785 I can not figure out what I need to do. Apparently according to linode support, the VM is trying to grab an IPv6 address with some privacy stuff enabled by default causing it to not grab the IPv6 address that is assigned to me. Nothing I have tried seems to work, and it seems that Linode support are far more familiar with

Dear all, I am using glmnet (Coxnet) for building a Cox Model and to make actual prediction, i.e. to estimate the survival function S(t,Xn) for a new subject Xn. If I am not mistaken, glmnet (coxnet) returns beta, beta*X and exp(beta*X), which on its own cannot generate S(t,Xn). We miss baseline survival function So(t). Below is my code which takes beta coefficients from glmnet and creates coxph

Hi, I am trying to play with all the methods in the Array Object. Just wanted to check with you guys if this is the correct explanation of toQueryParams(). If yes, then I''ll add it to the documentation as well. Works for me (but I am not sure if it''s the correct way to use it). /* String.prototype.toQueryParams takes a query string, i.e, string with name value pairs

Dear all, I have used following code but everytime I encounter a problem of not having coefficients for all the variables in the predictor set. # code rm(list=ls()) library(caret) # generating response and design matrix X<-matrix(rnorm(50*100),nrow=50) y<-rnorm(50*1) # Applying caret package con<-trainControl(method="cv",number=10) data<-NULL data<- train(X,y,

I get an error when I try to use glmnet to fit a lasso model on some data. My code: > lasso <- glmnet(predictorPartitionTrainingM, targetPartitionTraining, alpha=1) The error that is returned: Error in elnet(x, is.sparse, ix, jx, y, weights, offset, type.gaussian, : NA/NaN/Inf in foreign function call (arg 5) Some potentially important details: - 50 predictor variables - 300

Hello, I'm trying to select features of cetain numbers(like 100 out of 1000) via LASSO, based on multinomial model, however, it seems the glmnet package provides a very sparse estimation of coefficients(most of coefficients are 0), which selects very few number of variables, like only 10, based on my easy dataset. I try to connect the choice of lambda to the selecting

Dear all: I have a question about how to get the optimal estimate of coefficients using the penalized quantile regression (LASSO penalty in quantile regression defined in Koenker 2005). In R, I found both rq(y ~ x, method="lasso",lambda = 30) and rq.fit.lasso(x, y, tau = 0.5, lambda = 1, beta = .9995, eps = 1e-06) can give the estimates. But, I didn't find a way using either of

Hi Bruno, You advised following no need to find the best s value. CV does it for you: cvres<-cv.lars(X,Y,K=10,type='lasso') sAtBest<-cvres$fraction[which.min(cvres$cv)] fits <- predict.lars(object, type="coefficients", s=sAtBest, mode="fraction") in thread https://stat.ethz.ch/pipermail/r-help/2007-June/133982.html My problem is that, cvres$cv is non empty

Hi all, I want to apply lasso method in AFT model. can anybody help me how to get lasso estimate using AFT model. Hossain [[alternative HTML version deleted]]

I also hope to get the code of using lasso method in the cox model.Could you please send me one? Thank you so much!!!

Dear R user, I am looking for a code on double cross validation in LASSO , one for optimizing the parameter and other one is for MSEP. If any one have it, please foroward to me. I am using different package like LARS, chemometric etc. Thanks in advance Alex [[alternative HTML version deleted]]

Hi, I am interested in a modification to LARS that allows for positive-only constraints in the variables (with details about how to implement this as described in section 3.4 of the Efron et al (2003) LARS paper). Before I dive into the "lars" package code myself, I was wondering if anyone knew of a version where this is available, or if another package that I have not found can do

Dear R community, I'm curious to know how people go about estimating standard errors for parameter estimates after model selection by ridge regression and the lasso. Do you have any practical or theoretical advice? Warmly, Andrew -- Andrew Robinson Department of Mathematics and Statistics Tel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: