similar to: Vector multiplication wrap-around

Hello all: I have a protein sequence alignment in a data frame (align1, 72 x 236), where each row is a protein and each column a site in the alignment. AA is vector of amino acid symbols plus "-" (gap). I can calculate amino acid frequencies at each site by: >align1.F <- matrix(0,nrow=22,ncol=236,dimnames=list(AA,seq(1:236))) >for(i in 1:236) >

Hello all: I have written a few R scripts and am trying to turn them into a package for submission to CRAN. All of these scripts are R code only, no C or C++ or anything else. I'm working with R 2.0.1 running on a Windows XP machine. So far running ">rcmd install --build --docs=normal mypkge" seems to work (i.e., the library "mypkge" is installed in R\rw2001\library and

Hello: I am attempting to use R to analyze amino acid frequencies in aligned protein sequences and need some help. So far, I have imported my sequence alignment into a data frame (lets call it "alignment") with each site in one column, so that I have a data frame consisting of columns of letters (the 21 amino acid symbols plus "-") with row names being the corresponding

Greetings all: OK, this is bugging the @#@%* out of me. I know the answer is simple and straightforward but for the life of me I cannot find it in the documentation, in the archives, or in my notes (because I know I've encountered this in the past). My problem is: I have a data frame with columns A, B, C, D, and E. A, B, and E are factors and C and D are numeric. I need a new data frame with

Greetings. Apologies if I missed something like this in the archives or internet, but I''m having issues using Ferret with Rails. Specifically, I have a class class "Weight" in my application (it happens to be a model). My app runs perfectly fine until it first executes "require ''ferret''". At that point, my definition of the class "Weight"

Greetings. Apologies if I missed something like this in the archives or internet, but I''m having namespace issues using Ferret with Rails, but this looks to be an issue with any library and Rails. Specifically, I have a model class "Weight" in my application and Ferret also has a class "Weight" in it (Ferret::Search::Weight). My app runs perfectly fine until it first

Doing package development on a Windows 7 machine, and I want to tell R check not to worry about the "suggested" packages. I realize this can be done using the ~/.R/check.Renviron file, but what directory corresponds to "~"? Is that supposed to be the user directory? Or is it some other directory? I have this _R_CHECK_FORCE_SUGGESTS_=false (have also tried FALSE) in

First, apologies for no example data but I don't think it's needed in this case, Q: Can (and if so how ) the line end style be changed for 'cloud' plots? I've tried par(lend=2), trellis.par.set(add.line = list(lend=2)) and much googling but to no avail Thanks in advance Dan P.S. the reason for this is that the round end looks bad at lwd=3 or more Daniel Alcock Malaria

Hi R friends, I've been attempting to create plots with multiple alpha values using Cairo to save them on a windows (32b XP) platform as it doesn't support more than 3 alpha values. This worked well until I wanted a postscript file (unsupported) and as a attempted work around I installed RGtk2. So far so good, however now when I try to use a >CairoPDF("alpha.pdf", 6, 6,

Hi, Tonight I managed to sliently hardlock my linux box with windows. I had mounted (some hours before) a rw smb share from a win95 machine via: smbmount \\\\hemlock\\c somepass -c 'mount /mnt/samba/hemlock/c/' Some hours later I went to shutdown the windows machine (for the night) in the middle of lwn and returned to my linux machine a minute later to finish off reading lwn, and found

Hello all, When I execute "smbclient -L SAZZLE -N", I get back a three part response: Sharename Type Comment --------- ---- ------- software Disk Network Software Server Comment --------- ------- SAZZLE Samba PDC Server 2.0.3 CRACKLE FACULTY

Hi I hope someone can shed some light on this: For some reason when I read.table("bfx.txt") R decides to only give back the first character from each column in each row as one single column. Like this: V1 1 ÿþr 2 \n 3 r 4 1 5 0 6 A 7 G 8 \n 9 r 10 1 11 0 12 T 13 C 14 \n The data should be:

Hi All, I was wondering if there would be any interest in adding an option to the "save" function in R that I think would be useful. I was thinking that it might be useful to have an option that would generate a ".sessionInfo" variable that contains the output of "sessionInfo()", and adds it to the list of objects to be saved. This way, whenever an RData object is

Hi all, a quick question I couldn't find the answer to in the usual places: Is there a way to turn off line-wrapping in the R console? Or set the line width-before-wrapping manually? Currently it looks like the console linewraps after about 70 characters, this occurs even if I increase the window size. (I want to output some simple tables to screen for students in a computer lab

Hi all, I googled this but no luck. I am using R.app 2.10.1 on Mac OSX 10.4. Here's the problem: When I type at the R.app command line and hit the carriage return "Enter" (right pinky, "Return" on some keyboards), it just adds a blank line. To actually get the command to execute, I have to go all the way over to the number-keypad and hit "Enter" there.

Hi all, I am running R.app on Mac OS X 10.4. I am trying to figure out if there is a .plist file of some sort, or a similar parameter file, that will let me turn on and off e.g. line-wrapping in the R.app GUI console. The only hint I could find online is this: https://stat.ethz.ch/pipermail/r-sig-mac/2010-April/007264.html ...but it doesn't seem to specify where to find the file in

Hi all, I'm using the R GUI on a Mac. It is easy to produce a number of plots and put them into a Quartz window, and then use Command-left or Command-right to flip between them. However, Quartz seems to hold a maximum of about 15 plots, and then discards anything plotted before that. This is pretty annoying, does anyone know of way to change this default setting? Cheers, Nick --

Hi, Is there a way to parse a postscript (*.ps) file with R (or perhaps with some other command-line utility)? E.g., I have a map in postscript format with lots of features, but I just want to extract the coastline and it's coordinates. Any help very much appreciated! Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate

Hi all! I'm trying to build a simple class, but I'm getting a weird error. E.g. if I do: ========== gregion = setClass("gregion", contains = "data.frame", representation(name = "character", poly.x = "numeric", poly.y = "numeric" )) gregion$name = "North America" ========== Then I get this message: Warning message: In

Hi all, Working at the R command line, how do I get strings to display e.g. tab or newline characters as they should be displayed, rather than as e.g. \n or \t? e.g.: > x="\t" > x="\t" > x [1] "\t" > print(x) [1] "\t" -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher