similar to: removing NULL elements from a list

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, 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 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 <-

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 (?).

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

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'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 am using fexact.c on a C++ program I wrote. To minimize dependencies on other files (e.g., to not need to include R.h and ctest.h ---now I only include the R files Boolean.h, Constants.h, and Memory.h), I have re-written all declarations of Sints as ints and, what is potentially more serious, I have re-written the line (lines 329 and 330, in fexact.c on R-1.6.1) /* IMAX is the

hi everybody, anyone knows how we can transform a binary matrix with TRUE and FALSE to 0 and 1 without looping? Thx --------------------------------- [[alternate HTML version deleted]]

(Apologies for double posting; I sent this to r-help and was suggested that I ask here which I should probable have done to begin with). *************** 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

If an array has missing values in different rows, plotting using the formul= a=20 interface can produce errors. Example: fake.data <- matrix(rep(-100:100, 4), ncol =3D 4) par(mfrow =3D c(1,2)) boxplot(fake.data ~ col(fake.data)) abline(h =3D 0, lty =3D 2) boxplot(as.data.frame(fake.data)) abline(h =3D 0, lty =3D 2) ##### Add the missing data fake.data[190:200, 1] <-

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 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 ./

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

Dear All, The "clients.txt" file of the latest Rserve package, by Simon Urbanek, says, regarding its R client, "(...) a simple R client, i.e. it allows you to connect to Rserve from R itself. It is very simple and limited, because Rserve was not primarily meant for R-to-R communication (there are better ways to do that), but it is useful for quick interactive connection to an

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

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?

Dear All, I am having trouble getting an R package to build and install correctly under Windows. In this package, which builds and checks OK under Linux, I use zlib (among other functions, gzprintf). As mentioned by Prof. Ripley a while back, the file "CHANGES" under src/gnuwin32 says explains that to, to use zlib, one has to set $(ZLIB_LIBS) in PKG_LIBS. I have a Makefile.win with

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