search for: bigtabulate

Displaying 10 results from an estimated 10 matches for "bigtabulate".

2017 Jul 03
2
R memory limits on table(x, y) (and bigtabulate)
...64bit machine? It seems like it (given <https://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory-limits.html> and <http://www.win-vector.com/blog/2015/06/r-in-a-64-bit-world/>, but I just want to make sure I understood that right); - I thought I could handle this with the package bigtabulate, but whenever I run xy.tab <- bigtable(data.frame(x, y), ccols=1:2) R crashes as follows: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted Any idea on what I am doing wrong with bigtabulate? Thanks for your consideration
2017 Jul 03
0
R memory limits on table(x, y) (and bigtabulate)
...eems like it > (given <https://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory-limits.html> > and <http://www.win-vector.com/blog/2015/06/r-in-a-64-bit-world/>, but > I just want to make sure I understood that right); > - I thought I could handle this with the package bigtabulate, but whenever I run > > xy.tab <- bigtable(data.frame(x, y), ccols=1:2) > > R crashes as follows: > > terminate called after throwing an instance of 'std::bad_alloc' > what(): std::bad_alloc > Aborted > > Any idea on what I am doing wrong with bigtabulate...
2012 Feb 29
0
Question about tables in bigtabulate
I have a large file backed big. matrix, with millions of rows and 20 columns. The columns contain data that I simply need to tabulate. There are a few dozen unique values. and I just want a frequency count Test code with a small "big" matrix. library(bigmemory) library(bigtabulate) test <- big.matrix(nrow = 100, ncol = 10) test[,1:3]<- sample(150) test[,4:6]<- sample(100) test[,7:10]<- sample(100) ## so we have sample big memory matrix. Its not file backed but will do for testing. ## the result we want is one that you would get if you could run t...
2012 Feb 21
1
tapply for enormous (>2^31 row) matrices
...w above) will show up multiple times in a given file. I want to sum column 4 across each pair of individuals. If I could bring the matrix into R, I could use tapply() to accomplish this by indexing on paste(X[,1],X[,2]), but the matrix doesn't fit into R. I have been trying to use bigmemory and bigtabulate packages in R, but when I try to use the bigsplit function, R never completes the operation (after a day, I killed the process). In particular, I did this: X <- read.big.matrix("file.loc.X",sep=" ",type="double") hap.indices <- bigsplit(X,1:2) #this runs for too...
2010 May 10
0
bigmemory 4.2.3
The long-promised revision to bigmemory has arrived, with package 4.2.3 now on CRAN. The mutexes (locks) have been extracted and will be available through package synchronicity (on R-Forge, soon to appear on CRAN). Initial versions of packages biganalytics and bigtabulate are on CRAN, and new versions which resolve the warnings and have streamlined CRAN-friendly configurations will appear shortly. Package bigalgebra will remain on R-Forge for the time being as the user-interface is developed and the configuration possibilities expand. For more information, please...
2010 May 10
0
bigmemory 4.2.3
The long-promised revision to bigmemory has arrived, with package 4.2.3 now on CRAN. The mutexes (locks) have been extracted and will be available through package synchronicity (on R-Forge, soon to appear on CRAN). Initial versions of packages biganalytics and bigtabulate are on CRAN, and new versions which resolve the warnings and have streamlined CRAN-friendly configurations will appear shortly. Package bigalgebra will remain on R-Forge for the time being as the user-interface is developed and the configuration possibilities expand. For more information, please...
2013 Apr 29
2
bigmemory and R 3.0
Dear helpers, Does anyone have information on the status of bigmemory and R3.0? Will it just take time for the devs to re-code for the new environment? Or is there an alternative for this new version? Thanks Ben Caldwell [[alternative HTML version deleted]]
2012 May 05
2
looking for adice on bigmemory framework with C++ and java interoperability
I work with problems that have rather large data requirements -- typically a bunch of multigig arrays. Given how generous R is with using memory, the only way for me to work with R has been to use bigmatrices from bigmemory package. One thing that is missing a bit is interoperability of bigmatrices with C++ and possibly java. What i mean by that is API that would allow read and write filebacked
2010 Aug 25
1
Documenting S4 Methods
I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })
2010 Jul 18
6
CRAN (and crantastic) updates this week
...the candidate algorithms' order. * biganalytics (1.0.14) Jay and Mike http://crantastic.org/packages/biganalytics This package extends the bigmemory package with various analytics. Functions bigkmeans and binit may also be used with native R objects. For tapply-like functions, the bigtabulate package may also be helpful. For linear algebra support, see bigalgebra. For mutex (locking) support for advanced shared-memory usage, see synchronicity. * bigtabulate (1.0.11) Jay and Mike http://crantastic.org/packages/bigtabulate This package extends the bigmemory package with tab...