similar to: Difficulty with terminal properly displaying help function in an ESS remote session

Hi all, My graduate student is logging onto my macpro and running R through ESS aquamacs (with Mx ssh and then Mx ess-remote). Everything is working fine until we get to graphing. We are trying to give him the ability to look at graphics interactively. The ESS manual is not too helpful: "If you run X11 (See Section 13.3.2 [X11], page 68, X-windows) on both the local and remote machines

Hi all, Probably a rudimentary question. I have a flat file that looks like this (the real one has ~10e6 elements): 10110100101001011101011 and I want to pull that into R as a vector, but with each digit being it's own element. There are no separators between the digits. How can I accomplish this? Thanks in advance! Matt -- Matthew C Keller Asst. Professor of Psychology University of

Hi all, Is there a way to skip non-sequential lines using the "skip" argument in the scan function? E.g., I have a matrix with 100 rows and 1e7 columns. I open a connection and want to read only lines 5, 7, 9, etc [i.e., seq(5,99,2)] It might seem that the syntax to do this would be something like this (if only the "skip" allowed vectors in the same way colClasses does in

Hello all, I hate to add to the daily queries regarding R's handling of large datsets ;), but... I read in an online powerpoint about the ff package something about the "length of an ff object" needing to be smaller than .Machine$integer.max. Does anyone know if this means that the # of elements in an ff object must be < .Machine$integer.max [i.e., that ff provides no help with

Hi all, Perhaps this is more of a unix question, but I'll give it a try here. I am running 9 different R processes at the same time (called from a shell script using R CMD BATCH). When I use the top program to monitor how they are doing, it is impossible to tell which R process is related to which R script. Is there a way to rename a specific instantiation of an R process in top with

Hi all, I have a vector, most of which is missing. The data is always increasing, but may do so in jumps. I would like to interpolate the NAs with 'best guesses', using something like filter(), which doesn't work due to the NAs. Here is an example: > x <- c(2,3,NA,NA,NA,3.2,3.5,NA,NA,6,NA) > x [1] 2.0 3.0 NA NA NA 3.2 3.5 NA NA 6.0 NA I would like a function that

hi all, I'm full of questions today :). Thanks in advance for your help! Here's the problem: x <- c('18x.6','12x.9','302x.3') I want to get a vector that is c('18x','12x','302x') This is easily done using this code: unlist(lapply(strsplit(x,".",fixed=TRUE),function(x) x[1])) So far so good. The problem is that x is a vector

Hello all, I have some genetic datasets (gzipped) that contain 6 columns and upwards of 10s of billions of rows. The largest dataset is about 16 GB on file, gzipped (!). I need to sort them according to columns 1, 2, and 3. The setkey() function in the data.table package does this quickly, but of course we're limited by R not being able to index vectors with > 2^31 elements, and bringing

Hi all, I've had one of my most miserable R weeks in memory. I'm trying to deal with huge datasets (>1GB each) but am running up against those pesky memory limits. The libraries filehash and g.data are not very suitable for what I need. I haven't gotten into the sql thing yet. Most recently I've been trying to install the new package ff (not yet on the CRAN repository). I

Hi all, I used to use fwrite() function in data.table but I cannot get it to work now. The function is not in the data.table package, even though a help page exists for it. My session info is below. Any ideas on how to get fwrite() to work would be much appreciated. Thanks! > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat

Hi all, SETUP: I have pairwise data on 22 chromosomes. Data matrix X for a given chromosome looks like this: 1 13 58 1.12 6 142 56 1.11 18 307 64 3.13 22 320 58 0.72 Where column 1 is person ID 1, column 2 is person ID 2, column 3 can be ignored, and column 4 is how much chromosomal sharing those two individuals have in some small portion of the chromosome. There are 9000 individual people, and

Hi all, I'm on a Linux server with 48Gb RAM. I did the following: x <- big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000)) #Gets around the 2^31 issue - yeah! in Unix, when I hit the "top" command, I see R is taking up about 18Gb RAM, even though the object x is 0 bytes in R. That's fine: that's how bigmemory is supposed to

Hi Matt Your method is the easiest way for me to install the 64-bit R. I followed the directions on your web site and then did the following: R --arch=x86_64 source("http://bioconductor.org/biocLite.R") biocLite(type = "source",lib = "/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64") I got many errors and warnings which I copied to the attached file.

Hi all, My code: x <- scan(gzfile("file"),what='integer') x is imported, but as mode "character" rather than "integer". I know I can do as.integer() when importing, but am still trying to figure out why the above occurs. When I do summary(as.integer(x)), there are no NAs introduced by coercion, so the vector really is all integer. Also, is the above

Hi all, I have two data frames, two columns each, 1000s of rows. Each row represents a segment of the genome where a deletion has occurred. First column is start position of the deletion in genomic distance, second is end position. So, e.g., first 3 rows of data frame A is: 1003 1023 5932 6120 12348 12689 first 3 rows of data frame B is: 852 5305 1010 1015 8500 9500 10000 13000 I want to merge

I am running ess/emacs on Linux and have an R instance running on a remote Unix server. I would like to be able to direct input from my ess buffer to R (hope I am using the right lingo, I am new to emacs). The ess manual contains a section describing how to do just that, but a prerequisite is to install a lisp file ssh.el , which can be found at

Hi all, For computational reasons, I need to estimate an 18x18 polychoric correlation matrix two variables at a time (rather than trying to estimate them all simultaneously using ML). The resulting polychoric correlation matrix I am getting is non-positive definite, which is problematic because I'm using this matrix later on as if it were a legitimately estimated correlation matrix (in order

Hi all, I'm giving a talk in a few days to a group of psychology faculty and grad students re the R statistical language. Most people in my dept. use SAS or SPSS. It occurred to me that it would be nice to have a few concrete examples of things that are fairly straightforward to do in R but that are difficult or impossible to do in SAS or SPSS. However, it has been so long since I have used

+1--this is the single most-annoying issue with R that I know of. My usual solution, after accomplishing nothing as R spins idly for a couple hours, is to kill the process and lose any un-saved work. save.history() is my friend, but is a big delay when you work with big data sets as I do, so I don't run it after every command. I have cc'd r-help here, however, because I experience this

Hi all, I will be teaching a graduate-level course on R at CU Boulder next semester. I have a teaching idea that might also help improve the R wiki page... I wanted to know what you all thought of it and wanted to solicit some advice about doing it. During the latter part of the course, students will choose a topic of interest (e.g., hierarchical linear modeling), and show how to achieve it in