similar to: matrix problem

I have a list (length 750), each element containing a vector of unique strings (unique gene ids), with length up to ~40 (median 15). I want to compile a matrix of all possible triplets and their frequency within gene elements. Using combn and a lot of looping, I am accomplishing this but it is VERY slow. I've tried to figure out a way to vectorize this, using "match" and

FYI. http://leonardo-m.livejournal.com/73732.html If anyone is motivated, please file bugs for the losing cases. Also, it might make sense to incorporate the tests into our nightly tester test suite. Thanks, Evan

Dear useRs, I want to write a function that generates all the possible combinations of diff(). Example: If my vector has length 5, I need the diff() until lag=4 -> c(diff(my.vec), diff(my.vec, lag=2), diff(my.vec, lag=3), diff(my.vec, lag=4)) If it has length 4, I need until lag=3 -> c(diff(my.vec), diff(my.vec, lag=2), diff(my.vec, lag=3)) So, it must be until lag=(length(my.vec)-1).

Dear R-Helpers: I am a entry level user of R. Have the following question. Many thanks in advance. # value.vec stores values value.vec <- c('a','b','c') # which.vec stores the locations/indexs of values in value.vec. which.vec <- c(3, 2, 2, 1) # How can I obtain the following vector based on the value.vec and which.vec mentioned above # vector.I.want <-

Dear helpRs Does anyone have an elegant way of doing the following: For a given numeric vector, e.g. vec <- c(3,2,6,4,7) Create a series of vectors where all but 1 of the values are replaced by 0's, e.g. vec.a <- c(3,0,0,0,0) vec.b <- c(0,2,0,0,0) vec.c <- c(0,0,6,0,0) vec.d <- c(0,0,0,4,0) vec.e <- c(0,0,0,0,7) I have looked at `replace', but can't think of a

Recently our automated testing system has caught a curious assertion while testing Xen 4.1.5 on a HaswellDT system. (XEN) Assertion ''(sp == 0) || (peoi[sp-1].vector < vector)'' failed at irq.c:1030 (XEN) ----[ Xen-4.1.5 x86_64 debug=n Not tainted ]---- (XEN) CPU: 0 (XEN) RIP: e008:[<ffff82c48016b2b4>] do_IRQ+0x514/0x750 (XEN) RFLAGS: 0000000000010093 CONTEXT:

I found myself wanting to average a vector [vec] within each level of a factor [Fac], returning a vector of the same length as vec. After a while I realised that lm1 <- lm(vec ~ Fac) fitted(lm1) did what I want. But there must be another way to do this, and it would be good to be able to apply other functions than mean() in this way. Cheers, Murray -- Dr Murray Jorgensen

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Hi all I have the following regular expression problem: I want to find complete elements of a vector that end in a repeated character but where the repetition doesn't make up the whole word. That is, for the vector vec: vec<-c("aaaa", "baaa", "bbaa", "bbba", "baamm", "aa") I would like to get "baaa" "bbaa"

For a long time I've wanted a way to conveniently extract multiple elements from a list, which [[ doesn't allow. Can anyone suggest an efficient function to do this? Wouldn't it be a sensible addition to R? For example, alist <- list() alist[[1]] <- list() alist[[1]]$name <- "first" alist[[1]]$vec <- 1:4 alist[[2]] <- list() alist[[2]]$name <-

The attached patch adds some sanity checks to the "type" argument of quantile(). Output from the following commands show the change of behavior with the current patch: vec <- 1:10 quantile(vec, type = c(1, 2)) quantile(vec, type = 10) quantile(vec, type = "aaa") quantile(vec, type = NA_real_) quantile(vec, type = 4.3) quantile(vec, type = -1) Current behavior

On Tuesday 16 December 2008 01:03:36 Evan Cheng wrote: > FYI. http://leonardo-m.livejournal.com/73732.html > > If anyone is motivated, please file bugs for the losing cases. Also, > it might make sense to incorporate the tests into our nightly tester > test suite. FWIW, I just ported my ray tracer benchmark to C and found that llvm-gcc gives much worse performance than gcc on x86

Dear list, I have a character vector such vec.names<- c("a", "b") It happens that I have also two R objects called "a" and "b" that I would like to merge. Is it possible to do something like cbind(vec.names[1], vec.names[2]) ending up with the same result as cbind(a,b) Bellow is a reproducible example of what I need to to: dat<-

Hi there, I wrote a function that wraps MASS::boxcox as: bc <- function(vec) { lam <- boxcox(lm(vec ~ 1)) lam <- lam$x[which.max(lam$y)] (vec^lam - 1)/lam } When I invoke it as: > x <- runif(20) > bc(x) Error in eval(predvars, data, env) : object 'vec' not found I have googled, and rewrote the above function as: bc <- function(vec) { dat <<-

Hi there, I wrote a function that wraps MASS::boxcox as: bc <- function(vec) { lam <- boxcox(lm(vec ~ 1)) lam <- lam$x[which.max(lam$y)] (vec^lam - 1)/lam } When I invoke it as: > x <- runif(20) > bc(x) Error in eval(predvars, data, env) : object 'vec' not found I have googled, and rewrote the above function as: bc <- function(vec) { dat <<-

Hello, I'm not sure how to state my question in a technically accurate manner, so I'll use a short example to clarify my problem: Say I have a vector, vec<-c(1,2,3,2) I would like to be able to "reference" the vector by using the string containing the name of the vector - that is, I would like to know of some function which is able to convert the string "vec"

I don't understand how this function can subset by i when i is missing.... ## My function: myfun = function(vec, i){ ret = vec[i] ret } ## My data: i = 10 vec = 1:100 ## Expected input and behavior: myfun(vec, i) ## Missing an argument, but error is not caught! ## How is subsetting even possible here??? myfun(vec) Is there a way to check for missing function arguments, *and*

Hi, I apologize for the previous posting, where the message was not formatted properly. Here is a better version: I have written the following function to check whether a vector has elements satisfying monotonicity. is.monotone <- function(vec, increase=T){ ans <- TRUE vec.nomis <- vec[!is.na(vec)] if (increase & any(diff(vec.nomis,1) < 0, na.rm=T)) ans <- FALSE

Hi all, I have got 2 function (see bellow) which are simplifications of what I need to do. These functions are precisely the same, except for the last line. My question is, why doesn't function testA work in the same way as function testB. Both functions produce two objects, "a" and "b" that must merged with rbind. The difference is that in testA, I specify the name

Hi I wrote a function implementing an algoritm for simulation of spatial sampling plans (using geoR). I'm using a range of parameters to perform several simulation and sometimes this parameters create function errors wich cause the algoritm to stop. How can I avoid this ? Below there's a small example that I made to study the problem but I was not able to solve it. I've tried