[R] glmnet - choosing the number of features

Hi, I am trying to use the glmnet package to do some simple feature selection. However, I would ideally like to be able to specify the number of features to return (the glmnet package, as far as I can tell, only allows specification of a regularization parameter, lambda, that in turn returns a m

[R] ggplot2 errorbarh

Hi, I'm having problems using the 'width' aesthetic attribute for the geom_errorbarh. This is the same problem reported earlier here, but I'll try to write the problem more clearly: http://www.mail-archive.com/r-help@r-project.org/msg62371.html The problem I'm having is that, the 'width' attri

Re: [R] ggplot2 errorbarh

Hi Ben, Indeed this is what i wanted, thanks. height does make more sense, I guess I was just reading the ggplot2 documentation directly, which still refers to width. Brian On Sun, Dec 12, 2010 at 5:12 PM, Ben Bolker wrote: > Brian Tsai gmail.com> writes: > > > > > H

[R] drawing dot plots with size, shape affecting dot characteristics

Hi all, I'm interested in doing a dot plot where *both* the size and color (more specifically, shade of grey) change with the associated value. I've found examples online for ggplot2 where you can scale the size of the dot with a value: http://had.co.nz/ggplot2/graphics/6a053f23cf5bdfe5155ab53d3

[R] glmpath crossvalidation

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 val

[R] logsumexp function in R

Hi, I was wondering if anyone has implemented a numerically stable function to compute log(sum(exp(x))) ? Thanks! Brian [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

[R] cv.glmnet errors

Hi, I am trying to do multinomial regression using the glmnet package, but the following gives me an error (for no reason apparent to me): library(glmnet) cv.glmnet(x=matrix(c(1,2,3,4,5,6,1,2,3,4,5,6), nrow=6),y=as.factor(c(1,2,1,2,3,3)),family='multinomial',alpha=0.5, nfolds=2) The error i get

[R] BFGS versus L-BFGS-B

Hi all, I'm trying to figure out the effective differences between BFGS and L-BFGS-B are, besides the obvious that L-BFGS-B should be using a lot less memory, and the user can provide box constraints. 1) Why would you ever want to use BFGS, if L-BFGS-B does the same thing but use less memory? 2)

Re: [R] BFGS versus L-BFGS-B

formations is "better" > and when. Another > project, which I have made some tentative beginings to carry out. > Collaborations welcome. > > Best, > > JN > > > On 02/25/2011 06:00 AM, r-help-requ...@r-project.org wrote: > > Message: 86 > > Date: Fr

[R] comparing hazard ratios

hi, I'm looking for a package to compare two hazard ratios (and assign statistical significance) obtained from two different predictive models. I know of the hr.comp2 function from the survcomp package, but was wondering if there's any other packages out there. thanks! [[alternative HTM

[R] function to compute pvalue for comparing two ROC curves

hi, I'm looking to compare two area under ROC values for different classifiers on the same data -- is there an r function to do this? Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailm

[R] R sign test for censored data

does anyone know a statistical test implemented in R that can do a sign test for difference of medians, except that can handle censored data? Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch

[R] p values in coxph()

Hi, I'm interested in building a Cox PH model for survival modeling, using 2 covariates (x1 and x2). x1 represents a 'baseline' covariate, whereas x2 represents a 'new' covariate, and my goal is to figure out where x2 adds significant predictive information over x1. Ideally, I could get a p-val

[R] background normalization in rma() in the affy package

Hi, i was looking into the documentation for the rma() function in affy() package, and was trying to figure out how exactly the background normalization is done. I read all three papers cited in the rma() documentation, but the most detailed explanation i could find was in Irizary et al., 2003, w

[R] reading a dense file of binary number

hi all, i have a file of the following format that i want to read into a matrix: 010101001110101 10101001010 01001010010 ... it has no headers or row names. I tried to use read.table(), but it doesn't allow me to specify nothing as the column separator (specifying sep='' means whitespac