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I wrote a function to calculate cosine distances between rows of a matrix. It uses two loops and is slow. Any suggestions to speed this up? Thanks in advance. theta.dist <- function(x){ res <- matrix(NA, nrow(x), nrow(x)) for (i in 1:nrow(x)){ for(j in 1:nrow(x)){ if (i > j) res[i, j] <- res[j, i] else { v1 <- x[i,] v2 <- x[j,]

Full_Name: Yi-Xiong Zhou Version: 1.5.1 OS: win2000pro Submission from: (NULL) (64.169.249.42) Update() can not find objects when it is used in a function, which is in turn being called by another function. Here is a R script to show the problem: ######## begin of the test script ########## fun1 <- function() { x <- matrix(rnorm(500), 20,25) y <- rnorm(20) oo <- lm(y~x)

Using the heatmap function in mva, it seems to be hard to use different colors in the edges leading to different groups of objects, as commonly done in many heatmaps in the microarray graphics. Any suggestions? Thanks. max

Dear Sir/Madam, I am trying to write a R package and I found what has been said in the "Writing R Extensions" is mostly different from what has been done in the existing packages. For example, in MASS package, there is no *.Rd files nor *.rd files. There is an R-ex directory, which has all the .R files, which should be in the R directory according to the manual. Supprisingly, in the R

...-GNOME From: Patrick Gonin <gonin@genethon.fr> Date: Thu, 2 May 2002 09:29:07 +0200 --1) is not a bug, as jpeg etc work. capabilities() has been changed for 1.5.1 --2) system() needs a new version for GNOME. Directory: Models * PR# 1861 * Subject: update() can not find objects From: yzhou@arcturusag.com Date: Thu, 1 Aug 2002 19:01:59 +0200 (MET DST) --The problem is actually deeper than this. -- --Sometime update() wants to evaluate arguments in the environment where the model --was defined, as here. -- --Sometimes it wants to use the current environment, eg this snippet from MASS --ph.fun &...

...-GNOME From: Patrick Gonin <gonin@genethon.fr> Date: Thu, 2 May 2002 09:29:07 +0200 --1) is not a bug, as jpeg etc work. capabilities() has been changed for 1.5.1 --2) system() needs a new version for GNOME. Directory: Models * PR# 1861 * Subject: update() can not find objects From: yzhou@arcturusag.com Date: Thu, 1 Aug 2002 19:01:59 +0200 (MET DST) --The problem is actually deeper than this. -- --Sometime update() wants to evaluate arguments in the environment where the model --was defined, as here. -- --Sometimes it wants to use the current environment, eg this snippet from MASS --ph.fun &...

================================================= This is an automated summary of the status of the R-bugs repository. Note that this may be neither complete nor perfectly correct at any given instance: Not all bugs are reported, and some reported bugs may have been fixed, but the repository not yet updated. Some bug fixes are difficult to verify because they pertain to specific hardware or

...uot;Xianqun (Wilson) Wang" <xwang at aviaradx.com> Subject: [R] survest and survfit.coxph returned different confidence intervals on estimation of survival probability at 5 year To: <r-help at stat.math.ethz.ch> Message-ID: <425B10826271C048A4F65FC6C810F5D638E60A at mail.arcturusag.local> Content-Type: text/plain I wonder if anyone know why survest (a function in Design package) and standard survfit.coxph (survival) returned different confidence intervals on survival probability estimation (say 5 year). I am trying to estimate the 5-year survival probability on a contin...

I have a gene expression matrix n (genes) X p (cases), where n = 8000 and p = 100. I want to fit each gene as univariate in a coxph model, i.e., fitting 8000 models. I do something like this: res <- apply(data, 1, coxph.func) which takes about 4 min, not bad. But I need to do large numbers of permutations of the data (permuting the columns), for example, 2000, which would take 5 days. I would

Hi, There are two packages providing knn classification: class and knnTree. However, it seems both uses Eucleadian distances only. How can I uses a custom distance function with either package? Thanks, Xiao-Jun