search for: matrixmodels

Thierry, I have this: if (require(MatrixModels) && require(Matrix)) { X <- model.Matrix(Terms, m, contrasts, sparse = TRUE) in my function rqss() I've tried variants of requireNamespace too without success. If I understand properly model.Matrix is from MatrixModels but it calls sparse.model.matrix which is part of Matrix...

Dear list, I have been working with the MatrixModels package quite a bit this week, and it is proving to be extremely valuable for my current work (I am working with several factors with many levels, leading to a sparse model matrix). However, as my knowledge of statistical theory leaves much to be desired, there are certain aspects of model evaluati...

...le with R CMD check of my quantreg package. All is well until I get to: checking running R code from vignettes ... ?rq.Rnw? ... failed ERROR Errors in running code in vignettes: when running code in ?rq.Rnw? when I see a snippet from the vignette code and then: Loading required namespace: MatrixModels When sourcing ?rq.R?: Error: could not find function "sparse.model.matrix" Execution halted This is baffling to me since sparse.model.matrix is in the namespace of Matrix and it should be loaded at this stage since it is required by MatrixModels which has just been pronounced "lo...

....ku.edu/crmda/tools/lib64/R/3.2/site-library/RcppEigen/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RcppEigen) * installing *source* package 'MatrixModels' ... ** package 'MatrixModels' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading Creating a generic function for 'resid' from package 'stats' in package 'MatrixModels' Creating a generic function for 'fitted.values' fro...

....ku.edu/crmda/tools/lib64/R/3.2/site-library/RcppEigen/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RcppEigen) * installing *source* package 'MatrixModels' ... ** package 'MatrixModels' successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading Creating a generic function for 'resid' from package 'stats' in package 'MatrixModels' Creating a generic function for 'fitted.values' fro...

> On Mar 26, 2015, at 8:50 AM, Martyn Plummer <plummerM at iarc.fr> wrote: > > On Wed, 2015-03-25 at 15:12 -0500, Roger Koenker wrote: >> Thierry, >> >> I have this: >> >> if (require(MatrixModels) && require(Matrix)) { >> X <- model.Matrix(Terms, m, contrasts, sparse = TRUE) > > You have this in the current release, which does not show this problem > in the CRAN tests. This, and the fact that you can build the vignette > manually, suggests that there is a pro...

...e rank of a sparse Matrix, for example from package Matrix (class dgCMatrix)? Here is an example of QR decomposition of a sparse matrix (from the sparseQR class help). library(Matrix) data(KNex) mm <- KNex$mm str(mmQR <- qr(mm)) Similarly, using the functions/classes from the relatively new MatrixModels package: library(MatrixModels) str(trial <- data.frame(counts=c(18,17,15,20,10,20,25,13,12), outcome=gl(3,1,9,labels=LETTERS[1:3]), treatment=gl(3,3,labels=letters[1:3]))) glmS <- glm4(counts ~ 0+outcome + treatment, poisson, trial,...

...tion/x-gzip' length 1453067 bytes (1.4 Mb)opened URL==================================================downloaded 1.4 Mb The downloaded packages are in /var/folders/yx/l4kkhz8j24179y5vq0hp9md00000gp/T//Rtmpqsa0o1/downloaded_packagesalso installing the dependencies ‘mlmRev’, ‘MEMSS’, ‘sfsmisc’, ‘MatrixModels’ trying URL 'http://cran.csiro.au/bin/macosx/leopard/contrib/2.14/mlmRev_1.0-1.tgz'Content type 'application/x-gzip' length 1832388 bytes (1.7 Mb)opened URL==================================================downloaded 1.7 Mb trying URL 'http://cran.csiro.au/bin/macosx/leopard/con...

Thanks. Couldn't you implement model.matrix(..., sparse = TRUE) with a small amount of R code similar to MatrixModels::model.Matrix ? On Mon, Feb 29, 2016 at 10:01 AM, Martin Maechler <maechler at stat.math.ethz.ch> wrote: >>>>>> Karl Millar via R-devel <r-devel at r-project.org> >>>>>> on Fri, 26 Feb 2016 15:58:20 -0800 writes: > > > Generating a m...

...F-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Matrix_0.999375-50 lattice_0.19-30 loaded via a namespace (and not attached): [1] grid_2.13.1 tools_2.13.1 Dear R-help, I am using the Matrix (0.999375-50) and MatrixModels (0.2-1) packages to estimate regressions with 14,791 fixed effects. I use the function sparse.model.matrix() to partial out the fixed effects and then use lm() and an adjustment to the standard errors to study the four regressors that I am interested in. I want to calculate standardized residuals...

Dear all, I am fairly new to R. I would like to perform a step-wise logit regression aiming to select a model on the basis of AIC. I am using some large datasets (up to a million rows and 97 variables). It is taking the 'step' function just too long to complete a single routine. Now, I have tried subsetting the data and perform the same thing. But, 'step' is time consuming still.

...LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252 [4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MatrixModels_0.3-1 Matrix_1.0-6 lattice_0.20-6 loaded via a namespace (and not attached): [1] grid_2.15.0 tools_2.15.0 # # Example # library('MatrixModels') # create a data.frame with two factors dat <- data.frame( "f1" = as.factor(c(1,1,2,2,3,3)), "f2" = as.factor(c(1,2...

Hello list. For some reason, the makers of glmnet do not accept a dataframe as input. They expect the input to be a matrix, where the dummies are already precoded. Now I have created a sample dataset with . 11 factor columns with two levels . 4 factor columns with three levels . 135 continuous columns (from a standard normal) . 100 observations (rows) Say this dataframe is in dfrPredictors. What

Generating a model matrix with very large numbers of columns overflows the stack and/or runs very slowly, due to the implementation of TrimRepeats(). This patch modifies it to use Rf_duplicated() to find the duplicates. This makes the running time linear in the number of columns and eliminates the recursive function calls. Thanks -------------- next part -------------- A non-text attachment was

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

Thanks for all your great answers. The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. I guess for now, my best solution is to divide my app into modules and load/unload packages as the user switch from one module to another. This brought me another question: it seems that unload package with the

CRAN (and crantastic) updates this week New packages ------------ * allan (1.0) Alan Lee http://crantastic.org/packages/allan Automates Large Linear Analysis Model Fitting * andrews (1.0) Jaroslav Myslivec http://crantastic.org/packages/andrews Andrews curves for visualization of multidimensional data * anesrake (0.3) Josh Pasek http://crantastic.org/packages/anesrake This