similar to: 0-extent matrices?

I tried to use gpuCor function in the gputools package of R to calcuate the pairwise correlations of a matrix of 40,000 columns. Becuase there would be memory issues if I use the whole matrix at a time, I splitted the matrix into submatrix of 10,000 columns and then calculate the pairwise correlation of different submatrices. There are altogether 4 submatrices, so I need to calculate the pearson

Hi, I have a matrix of say 1024x1024 and I want to look at it in chunks. That is I'd like to divide into a series of submatrices of order 2x2. | 1 2 3 4 5 6 7 8 ... | | 1 2 3 4 5 6 7 8 ... | | 1 2 3 4 5 6 7 8 ... | | 1 2 3 4 5 6 7 8 ... | ... So the first submatrix would be | 1 2 | | 1 2 | the second one would be | 3 4 | | 3 4 | and so on. That is I want the matrix to be evenly divided

Does anyone have something like tapply that is extremely fast for matrices when there is a very large number of levels of the grouping variable? I'm referring to, for example, tapply(x, grouping.variable, function.operating.on.submatrix) where x is a matrix and the submatrix is a subset of the rows of x. The grouping variable's length equals the number of rows of x. -- Frank E

Hello everybody I'm very new at using R so probably this is a very stupid question. I have a matrix of "p" columns and I have to calculate for each of them the "two sample t-statistic" and p-value and to save the results into two different vectors. I have divided my matrix into two submatrices: submatrix A containing the first "n1" rows (p columns) and submatrix B

Hi all, I'm working with a large data set (on the order of 300X300) and trying to apply a function which compares the elements of all possible 2x2 submatrices. There are rc(r-1)(c-1) such submatrices, so obviously the naive method of looping through the rows and columns is computationally unfeasible for my data set: for(i in 1:(nrow(data)-1)) { for(j in (i+1):nrow(data)) { for (m

Hello list, I try to optimize some R code and it turns out that the function as.matrix takes a lot of time in my code. There is only one reason why I need as.matrix: My code should work for matrices with ncol=p and p should be allowed to be 1 or larger. Now I have a matrix x with dim(x)=(n,p), and I need to work with the submatrix y <-x[gv,], (gv a vector of n logicals) and to calculate

Dear R-help list, Pls I have this problem. Suppose I have a matrix of size nxn say, generated as follows   z<-matrix(rnorm(n*n,0,1),nrow=n)   I want to write a function such that for i in 1:n, I will remove the rows and columns corresponding to i (so, will be left with n-1*n-1 submatrix in each cases). Now I need the sum of the determinant of each of this submatrices. As an example, if n=3, it

Hi all, I have a R script that creates several input files for an analysis program. It loops through the matrix read into R and picks out submatrices and then creates a separate output file for each submatrix. The loop works great, but I am having trouble getting all the separate output files written. The line I have is: write.table(ch1d,

Both of these used to work and seem useful and harmless: R> matrix(1,ncol=1)%*%c(1,2) Error in matrix(1, ncol = 1) %*% c(1, 2) : non-conformable arguments R> matrix(1,ncol=1)*(1:2) Error: dim<- length of dims do not match the length of object Thomas Lumley -----------------------------------------------------+------ Biostatistics : "Never attribute to malice what : Uni of

Both of these used to work and seem useful and harmless: R> matrix(1,ncol=1)%*%c(1,2) Error in matrix(1, ncol = 1) %*% c(1, 2) : non-conformable arguments R> matrix(1,ncol=1)*(1:2) Error: dim<- length of dims do not match the length of object Thomas Lumley -----------------------------------------------------+------ Biostatistics : "Never attribute to malice what : Uni of

Yes you are right ... an example is mandatory. So ... I have a matrix of 0 with just a single 1 per row and per column I need to extract all maximal 'diagonal' submatrices Let's say I have the following matrix A B C D E a 0 1 0 0 0 b 1 0 0 0 0 c 0 0 1 0 0 d 0 0 0 1 0 e 0 0 0 0 1 well I would like to get, for this example, the two following submatrices A B C D E

On Tue, 1 Apr 1997, Jim Lindsey wrote: > Neither setting environment nor command > line change memory size as given by gc(). However, if I give too small > or too large a value on the command line, it tells me that it is > invalid and is ignoring it!?? I repeat that when I recompiled changing > the default size, gc() changed its values. Am I misunderstanding > something? I

A bug (misfeature) has been found in the S gee library (and thus in the R gee library). The problem, which is shared by nearly all gee implementations, involves the calculation of working correlations when some clusters have only one observation. For compatibility reasons nearly everyone uses the computing formula from the first SAS macro by Karim, rather than the formula from the original GEE

There was a question earlier today, on either r-help or r-devel, about calling R code from FORTRAN (I deleted it accidentally, so I don't know which list it belonged to). Anyway, there is a workaround to call R functions from FORTRAN which is used in the "integrate" library. It was invented for S by Mike Meyer. The FORTRAN code needs to be written to call a fixed C function and

rbind() does something strange to dimnames R : Copyright 1997, Robert Gentleman and Ross Ihaka Version 0.50 Beta (April 1, 1997) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type "license()" for details. > test1 <- data.frame(time= c(4, 3,1,1,2,2,3), + status=c(1,NA,1,0,1,1,0), + x= c(0,

If you subscript a data frame using the names of the columns and there is more than one column with the same name only the first one is found. eg mm<-data.frame(1:10,log(1:10)) names(mm)<-c("(offset)","(offset)") mm[,"(offset)"] # only returns first column mm[,"(offset)"]<-rep(1,10) # only sets first column This *is* compatible with S, but I

The hat() function, returning the diagonal of the hat matrix, currently works only on matrices and doesn't work with weights. Could we make it return lm.influence(x)$hat when inherits(x,"lm")? Thomas Lumley ------------------------------------------------------+------ Biostatistics : "Never attribute to malice what : Uni of Washington : can be adequately explained by :

Dear Rxperts Below is a small vector of values of zeros and non-zeros... was wondering if there is an efficient way to get the block sizes of submatrices of a big matrix similar to the one shown below? diagonal elements can be zero too. Rows with only a diagonal element may be considered as a unit block size. c(1,0,0,0,0,0,0,0,0,0,0, 1,1,0,0,0,0,0,0,0,0,0, 0,0,1,0,0,0,0,0,0,0,0,

Hi there and thanks in advance. I have a large symmetrical matrix stored in a text file. After load in R I would like to extract the same number of columns and rows (symmetrical submatrix) using their labels. I have tried this code in order to extract columns, but R console gives me the "+" sign at the end of the code, pointing out incomplete command, so it is not working:

Hi, (sorry for the wall of text; the issue here appears to be rather complicated) I'm seeing a somewhat strange case where checking whether an S4 object inherits from a parent class defined from another package with 'inherits' fails if that object is materialized through a call to 'load'. That's a mouthful, so I've put together a relatively small reproducible example