similar to: unix.time

I am getting some unexpected results from some functions of igraph and it is possible that I am misinterpreting the vertex numbers. Eg., the max betweenness measure seems to be from a vertex that is not connected to a single other vertex. Below if my code snippet: require(igraph) my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected")) most.between.vert <-

I have a very long list that I'd like to subset based on a logical value within each element. Example below. I'd like to get just those list elements for further study whose $sig.cor slot is TRUE. In this example, I'd only want element [[2]]. Should be simple, I know. How can I do this? Thanks, Mark > gene.pair.tf.lst [[1]] [[1]]$gene.pair [1] "Lgals1:Pxmp2"

I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive graph displays but R crashes. See my sessionInfo() and a short example below. Ggobi and rggobi installed without complaints. Mark > sessionInfo() R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu locale:

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

I'm doing some work on a potential patch to the Bioconductor package Rgraphviz and have some questions on code that is contained in engine.c. In particular, I am developing some custom shapes using polygon and need to make sure that, with rendering, the line connecting the centers of two polygons stops at the border of each polygon. The polygons can be transparent, so the option of just

Dear People, Consider the following fragment of R code choose <- function(n,r) { if( is.integer(n) && is.integer(r) && n > 0 && r >= 0 ) { .C("choose",as.double(n),as.double(r),comb = double(1))$comb } else stop("n must be a positive integer and r a non-negative integer.") } This is a practice function (n choose r), which I

Hi, Is there a way to check whether a file is empty in R. I did the customary searches, but did not find anything. Please cc me on any reply. Thanks, Faheem.

Dear People, In a qqplot I am doing, I get lines/points that are very thick. I've tried setting the lwd variable to 0.1, but it doesn't seem to have any effect. Also, I have set the value of lty to dashed, but I still get dots. The command looks like qqplot(cdf.inv(seq(0,1,length=size),theta,pos,len),empmargdistvec(len,theta,pos,size), xlim=c(-theta,theta), ylim=c(-theta,theta),

Hi, Consider the following > x = c(1,2) > y = c(3,4) > d = data.frame(cbind(x,y)) > d$x [1] 1 2 > d$"x" [1] 1 2 > > foo = function(val) + { + return(d$val) + } > > bar = function() + { + return(d$"x") + } > > foo("x") NULL > bar() [1] 1 2 I'm a little surprised that R accepts both the form d$x and d$"x", but

Dear People, I am trying to include a barplot (see code below), in a latex document. However, the plot appears in totally the wrong position. I know this is not an R question as such, but the eps file is produced by R and I thought that perhaps other people had had similar problems and could give me pointers. Am I doing anything obviously wrong? Sincerely, Faheem Mitha. PS.

I'm having trouble with a Bioconductor package, an variable expected in an environment does not seem to be there. As part of my investigation of the problem (most likely on my end) I'd like to list the variables contained in an environment. If you have an environment loaded, lets call it "pkgEnv', how does one find what it does contain? Mark

Dear R people, The header practically says it all. I was wanting to include r code in a Latex file. Since R code using{ and }, which are interpreted by Latex as control characters, I would expect it to get upset. I believe that \{ would probably print as {, but I hoping I don't have to go through the code and add lots of \. I would rather use some global commannd, along the lines of

I am doing some work the Rgraphviz, a Bioconductor package, but since my question is of a more general nature, thought I would send to this list in hopes that a graph theory expert could answer my question. I wish to do some statistics on node-node relationships. In particular, I want to see if two connected nodes share a common property. I believe that the more "connected" the two

Dear People, I have been trying to perform concatenation operations on lists without success. Consider the following example. > x <- runif(2) > y <- runif(2) > z <- runif(2) > xy <- list(x,y) > xyz <- list(x,y,z) I want to have a function foo such that foo(xy,z) is the same as xyz. This appears not to be as easy as I thought, though there must be a way. For example

Dear People, After considerable effort, I managed to install gcc-3.0 on my Debian system. However, Debian keeps gcc-2.95 around as the default compiler, and gcc, g++ point to the 2.95 version. The 3.0 versions need to be explicitly invoked as gcc-3.0, g++-3.0 etc. How can I get R CMD SHLIB to invoke gcc-3.0 instead of gcc and g++-3.0 instead of g++? I would like this to be done by default but

I have the following question, which is elementary but I am unable to answer. In a for(i=10) loop, I am trying to represent the 10 1-dimensional vectors l1, l2,... l10 by some expression that will run through these values. ie. soppose I want to add l1 + ... + l10 I could go x <- 0 for(i in 1:10){ x <- x+ l(i)} This should return x to be the sum of the 10 li's for i from 1 to 10

I'm having trouble achieving the results I want using a regular expression. I want to eliminate all characters that fall within square brackets as well as the brackets themselves, returning an "". I'm not sure if it's R's use of double slash escapes or something else that is tripping me up. If I only use one slash I get 1: '\[' is an unrecognized escape in a

Dear R people, I have the following simple bit of code to make a plot. I want to suppress tick marks on the axes of the plot. I've been trying everything I can think of to do so, but have been unsuccessful. Can you help me? If you reply, please cc me, I'm not currently subscribed to the list. Thanks in advance. Sincerely, Faheem Mitha. num <- 1:i inc

Dear People, I need to make a label which both contains math notation as well as substitutes a value for an object. In the following label, len and theta are one dim variables, and I am substituting their values appropriately. This label looks fine except that I want the greek symbol for theta to appear instead of the word `theta'. How can I do so most easily? I don't understand the

Dear rsync people, I have just started using rsync for backups. I have had a couple of issues. Note I'm trying to use rsync as user using ssh between two machines both running Debian GNU/Linux potato (2.2r3). The local machine is currently running 2.4.6-1 and the remote 2.3.2-1.2. 1) When I run rsync with the vv option, stuff scrolls of my screen faster than I can read it. I was wondering if