[R] PRESS and P2 statistics in R

Hello all, Is there any function in R by which I can calculate PRESS and P2 statistics for linear regression in R? Thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Caret package and lasso

Dear Max, Thanks for the reply. I will wait for your further comment on this. Regards Linda Garcia On Wed, Apr 7, 2010 at 8:03 PM, Max Kuhn mxk...@gmail.com wrote: Linda, Thanks for the example. I did this to make it more reproducible: set.seed(1)

[R] Biclustering package

Hello, I am looking for R package which can perform biclustering a part from biclust package. thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] Biclustering package

expression data. Phys Rev E Stat Nonlin Soft Matter Phys 2003 Mar; 67(3 Pt 1) 031902 Best, Gabor On Thu, Feb 11, 2010 at 10:51 AM, Alex Roy alexroy2...@gmail.com wrote: Hello, I am looking for R package which can perform biclustering a part from biclust package. thanks Alex

[R] glmnet in caret packge

, trControl = con) Thanks Alex Roy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide

[R] How can I store the results

Dear R users, I am running a R code which gives me 10 columns and 160 rows. I need to run the code for 100 times and each time I need to store the results in a single file. I do not know how can I store them in a single file without over writting the results? Thanks Alex

[R] penalization regression

Dear all, I am using penalization regression method for my data. I am wandering the following names are synonymous or not? Complexity parameter Penalty parameter Shrinkage factor Shrinkage parameter hyper parameter Thanks Alex [[alternative HTML version deleted]]

[R] Elastic net in R (enet package)

Dear R users, I am using enet package in R for applying elastic net method. In elastic net, two penalities are applied one is lambda1 for LASSO and lambda2 for ridge ( zou, 2005) penalty. But while running the analysis, I realised tht, I optimised only one lambda. ( even

[R] Permutation test and R2 problem

Hi, I have optimized the shrinkage parameter (GCV)for ridge and got my r2 value is 70% . to check the sensitivity of the result, I did permutation test. I permuted the response vector and run for 1000 times and draw a distribution. But now, I get r2 values highest 98% and some of them more

[R] Rank of matrix

Dear all, Rank of a matrix depends on which factors? Only on rows or coumns? or both ? If there is a collinearlity in the variables ( columns ) does it effects the rank? X-matrix((rnorm(1)),50) dim(X) [1] 50 200 qr(X)$rank [1] 50 X[,2]-X[,30] qr(X)$rank [1] 50

[R] Collinearity in Linear Multiple Regression

Dear all, How can I test for collinearity in the predictor data set for multiple linear regression. Thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

[R] Linear Regression Problem

Dear All, I have a matrix say, X ( 100 X 40,000) and a vector say, y (100 X 1) . I want to perform linear regression. I have scaled X matrix by using scale () to get mean zero and s.d 1 . But still I get very high values of regression coefficients. If I scale X matrix, then

Re: [R] Linear Regression Problem

and a relatively small number of subjects may be faced via some regularization approach (ridge or lasso regression..) hope this helps you, vito Alex Roy ha scritto: Dear All, I have a matrix say, X ( 100 X 40,000) and a vector say, y (100 X 1) . I want to perform linear

Re: [R] Linear Regression Problem

] On Behalf Of Alex Roy Sent: Tuesday, July 14, 2009 11:29 AM To: Vito Muggeo (UniPa) Cc: r-help@r-project.org Subject: Re: [R] Linear Regression Problem Dear Vito, Thanks for your comments. But I want to do Simple linear regression not Multiple Linear regression. Multiple Linear

Re: [R] Random Forest Variable Importance Interpretation

Hi, Are you looking for variable selection? If this is the case than you can use LASSO, Elastic net, Sparse PLS regression methods which encourages variable selection. PCA does not select variables as you get all your variables in the PCs. You can sparse PCA. Regards Alex On Wed, Jun 24,

[R] How to save multiple images??

Dear all, How can I save multiple images in my working directory?? I used save.image() but could not succeeded. Thanks in advance Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

[R] How to write loop

Dear all, I want to do the following process as a loop ( to run automatically with dimension of X, here 50). How can I do that? Your cooments will be highly appreciable. Alex *# Code:* library(lars) library(chemometrics) X-matrix(rnorm(2500),ncol=50) dim(X) # [1] 50 50

Re: [R] How to write loop

: It is not exactly clear what you want to iterate on. What is going to be changing each time through the loop? On Sat, Jun 13, 2009 at 10:09 AM, Alex Roy alexroy2...@gmail.comwrote: Dear all, I want to do the following process as a loop ( to run automatically with dimension

[R] Heatmap

Hello Group, How can I draw heatmap with variable names in the plot? Thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

[R] Caret package: coeffcients for regression

Dear All, I am using Caretpackage for SVM regression and elastic net regression . I can get the final fiited vs observed values. How can I get the coefficients? Any ideas? Thanks Alex [[alternative HTML version deleted]] __

[R] loop problem for extract coefficients

Dear R users, I have problem with extracting coefficients from a object. Here, X (predictor)and Y (response) are two matrix , I am regressing X ( dimensions 10 x 20) on each of columns of Y[,1] (10 x 1) and want to store the coefficient values. I have performed a Elastic Net

[R] Sparse PCA problem

Dear R user, I want to do sparse principal component analysis (spca). I am using elastic net package for this and spca() and the code is following from the example. My question is How can I decide the *K =? *and *para=c(7,4,4,1,1,1)) . So, here k=6 i.e the no of Principal

[R] Double Cross validation for LASSO

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

Re: [R] Singularity in a regression?

If collinearity exists, one of the solutions is regulazation version of regression. There are different types of regularization method. like Ridge, LASSO, elastic net etc. For example, in MASS package you can get ridge regression. Alex On Thu, Feb 26, 2009 at 1:58 PM, Bob Gotwals

[R] Leave one out Cross validation (LOO)

Dear R user, I am working with LOO. Can any one who is working with leave one out cross validation (LOO) could send me the code? Thanks in advance Alex [[alternative HTML version deleted]] __ R-help@r-project.org

[R] e1071 package for SVM

Dear all, I got a code for e1071 package in R for SVM regression. I have used *m$coefs* for extracting the coefficients but I am getting only 72 . How can I extract coefficients of the predictors set? Does it mean that I will get only 72 as *Number of Support Vectors: 72. *

[R] SVM regression code

Dear R user, I am looking for SVM regression in R. It willl be helpful for me if some one send me SVM regression code. Thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Subset Regression Package

algorithm) and heuristic (simulated annealing, genetic search, etc.) methods. Regards, A. Pedro Duarte Silva Alex Roy alexroy2008 at gmail.com writes: Dear all , Is there any subset regression (subset selection regression) package in R other than leaps? Lars and Lasso

[R] Subset Regression Package

Dear all , Is there any subset regression (subset selection regression) package in R other than leaps? Thanks and regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

[R] PRESS / RMSEP

Dear all , I want to do PRESS (prediction error sums of squares) or the residual mean square error of prediction (RMSEP) which will give me value that is valid for 'future predictions of independent data'. I am using different methods for example, Multiple Linear Regression,