similar to: boxplot.formula with missing values (PR#6846)

Dear All, We are about to purchase the second edition of Agresti's "Categorical Data Analysis" (my old copy of the first ed. of that wonderful book is falling apart). I would appreciate suggestions about other comparable books which, if possible, have examples using R/S code (instead of SAS). Thanks, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de

Dear All, I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the

Dear All, I have been using the randomForest package for a couple of difficult prediction problems (which also share p >> n). The performance is good, but since all the variables in the data set are used, interpretation of what is going on is not easy, even after looking at variable importance as produced by the randomForest run. I have tried a simple "variable selection"

Dear All, I have a list, where several components are NULL, and I'd like to obtain that very same list without the NULL components (i.e., I do not want to unlist or otherwise loose the rest of the list structure). I can do that with a loop, but how could I do it without a loop? Thanks, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO)

Dear All, I've read Thomas Lumley's fortune "If the answer is parse() you should usually rethink the question.". But I am not sure it that also applies (and why) to other situations (Lumley's comment http://tolstoy.newcastle.edu.au/R/help/05/02/12204.html was in reply to accessing a list). Suppose I have similarly called functions, except for a postfix. E.g. f.1 <-

Dear All, I was writing a small wrapper to bootstrap a classification algorithm, but if we generate the indices in the "usual way" as: bootindex <- sample(index, N, replace = TRUE) there is a non-zero probability that all the samples belong to only one class, thus leading to problems in the fitting (or that some classes will end up with only one sample, which will be a problem

> x <- matrix(1:10, ncol = 2) > xc <- cor(x[, 2], x[, 0]) > cbind(xc, vector()) Process R floating point exception at Tue Feb 11 19:16:51 2003 > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 6.2 year

Ich habe in R eine Version von SIR gefunden und ausprobiert. Leider kann diese multivariate Responses nicht verarbeiten. Gibt es in R eine ausgefeilte Version von SIR?

To avoid angry replies, let me first say that I know that the use of Type III sums of squares is controversial, and that some statisticians recommend instead that significance be judged using the non-marginal terms in the ANOVA. However, given that type III SS is also demanded by some… is there a function (equivalent to drop1 for lm) to obtain type III sums of squares for mixed models using the

To anyone who can help, I have two stupid questions, and one fairly intelligent question Stupid question (1): is there an R function to calculate a factorial of a number? That is...is there a function g(.) such that g(3) = 6, g(4) = 24, g(6) = 720, etc? Stupid question (2): how do you extract the estimated covariance matrix of the random effects in an lme object? Intelligent question

Dear all, I have a piece of code, call it "FA", that will be called thousands of times in a typical run of function "FB". I can: a) define FA as a function outside of FB (in the global environment), and call it; b) define FA as a function inside the body of FB and call it; c) "expand inline" FA inside FB. FA mainly does data frame subsetting, runs svd's, and

How do I cite a package (not R itself - I know how to do that)? Any thoughts or links? Many thanks in advance? Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/botany/bot/henry.html http://www.muohio.edu/ecology/

Dear All, Under Debian GNU/Linux La.svd (with method = "dgesdd") sometimes gives the error "Error in La.svd(data, nu = 0, nv = min(nrow, ncol), method = "dgesdd") : LAPACK routine DGESDD gave error code -12" It seems not to depend on the data per se, but on the relationship between numbers of rows and columns. For example, if the number of columns is 100,

Dear All, I think I am confused about how I'd be able to use zlib starting with R 2.7.0. I just downloaded the latest development version, built it, etc, but I am not able to find the zlib.h that, I believe, R should place somewhere under "where/you/want/R/to/go" (from --prefix=/where/you/want/R/to/go). There seem to be entry points for zlib in the binary (e.g., grep -r gzopen ./

Hi All, Sorry if this is a repost (a quick browse didn't give me the answer). I wonder if there are packages that can do the feature selection and classification at the same time. For instance, I am using SVM to classify my samples, but it's easy to get overfitted if using all of the features. Thus, it is necessary to select "good" features to build an optimum hyperplane (?).

Hi, You should also check my msc.features.select from caMassClass package. It has feature selection algorithm that I found useful in case of mass-spectra data. It performs individual feature selection and/or removes highly correlated neighbor features. Jarek -----Original Message----- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] Sent: Friday, January

Dear All, I'd like to be able to have R store (in a list component) a compressed data set, and then write it out uncompressed. gzcon and gzfile work in exactly the opposite direction. What would be a good way to handle this? Details: ---------- We have a package that uses C; part of the C output is a large sparse matrix. This is never manipulated directly by R, but always by the C code.

Dear All, How can the height of a leaf be extracted from a dendrogram? Sure, I can print it, but I am not able to, say, store it in an object. I think I understand that the height is a property of the split, not the leaf itself, but the printing functions display a "height" or "h" (which changes with "hang") and that is what I want. Obviously, the info is there

Hi all, I would like to do some QSAR analysis (quantitative structure activity relationship). I need to use some Partial Least Squares (PLS) regression, but I have not seen this option on the R-project. Is it possible to do this kind of regression on R? thank you in advance best regards, olivier [[alternate HTML version deleted]]

Dear All, I found Andy Liaw's suggestion about using a NUMA (instead of SMP) kernel when running R on amd64 with > 1 CPU http://finzi.psych.upenn.edu/R/Rhelp02a/archive/35109.html A couple of questions: 1. Is this still the case with the newer dual-core opterons (e.g., the 275 et al., families) running Linux (kernel 2.6)? 2. How does this affect using Rmpi (and snow, papply, et al.)