Re: [R] Extract Stata estimates to use in R

2009-05-08 Thread Rob Denniker
Might as well answer myself in case anyone has this problem again... To save a variance-covariance matrix from Stata as a CSV file that can be read into R, it's something like: regress mpg weight foreign matrix V=e(V) svmat V,names(vvector) outsheet vvector* using vv1.csv, replace > -Origi

Re: [R] Beyond double-precision?

2009-05-08 Thread spencerg
Are all your numbers positive? If yes, have you considered using logarithms? I would guess it is quite rare for people to compute likelihoods. Instead I think most people use log(likelihoods). Most of the probability functions in R have an option of returning the logarithms.

[R] Extract Stata estimates to use in R

2009-05-08 Thread Rob Denniker
Before you flame me, the reason I am using Stata is that I didn't get a response to my query below, so I have my cluster robust covariance matrix in Stata [one line of code], but now I need to take all those parameter estimates and put them back in R so I can simulate properly. Anyone done this

[R] Barplot, Bold font in superscript cm^-2

2009-05-08 Thread Arnaldo Russo
Hi, I`m trying to put my superscript type in bold style. Could somebody help me? My text is inside a barplot. #!/bin/Rbarplot(x, ylab=expression(paste("org.", cm^-2))) # so I tried this way, *barplot(x, ylab=expression(bold(paste("org.", cm^-2* # but my superscript maintain its shape in re

Re: [R] by-group processing

2009-05-08 Thread hadley wickham
On Wed, May 6, 2009 at 8:12 PM, jim holtman wrote: > Ths should do it: > >> do.call(rbind, lapply(split(x, x$ID), tail, 1)) >         ID Type N > 45900 45900    I 7 > 46550 46550    I 7 > 49270 49270    E 3 Or with plyr: library(plyr) ddply(x, "id", tail, 1) plyr encapsulates the common split-

[R] new book on (Perl and) R for computational biology

2009-05-08 Thread Gabriel Valiente
There is a new book on (Perl and) R for computational biology, G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press (2009) http://www.crcpress.com/product/isbn/9781420063677 I hope it will be of much use to R developer

[R] Beyond double-precision?

2009-05-08 Thread joaks1
I need to perform some calculations with some extremely small numbers (i.e. likelihood values on the order of 1.0E-16,000). Even when using the double() function, R is rounding these values to zero. Is there any way to get R to deal with such small numbers? For example, I would like to be able

Re: [R] partial mantel tests "Ecodist"

2009-05-08 Thread ddepew
Thanks Sarah, Looking again at #2, I see your point. As for the standardization, I didn't see it mentioned in the JSS paper, but I'll have another look. Assuming a significant r is returned, I guess I would need to look at the raw data to infer the type of relationship (+ or -). -- David De

Re: [R] RGoogleDocs

2009-05-08 Thread Farrel
This is exactly the problem that I was having. I see that you (Duncan) have updated from version 0.2-0 to 0.2-1. Cannot wait to try it. Do you have a compiled version of it for easy use in a Windows environment? If this works it is going to be utterly amazing. Google forms allows one to collect d

Re: [R] I don't see libR.so in my installation directory

2009-05-08 Thread Tena Sakai
Hi, Maybe I know the answer to my own question. When I built R 2.9.0, I didn't say: ./configure --enable-R-shlib I know I have given "--prefix" flag, but that's the only flag I used. I would appreciate it, if someone would give me a definitive answer, however. Regards, Tena Sakai tsa...@gal

[R] I don't see libR.so in my installation directory

2009-05-08 Thread Tena Sakai
Hi, I installed R 2.9.0 a couple of days ago on a linux machine. At the root of installation, I see 4 directories: bin, lib64, share, and src. I don't see libR.so anywhere. (In the following context, . (dot) indicates the root of my insta- llation.) I do see: ./lib64/R/lib/libRblas.so ./lib64/

Re: [R] by-group processing

2009-05-08 Thread Jun Shen
This is a problem much like the one I had a few weeks ago. David's solution is more concise. Try xtfrm() or rank() for factor sorting d=data[order(data$ID,-xtfrm(data$Type)),] should work. By the way I got it from Duncan. Jun On Fri, May 8, 2009 at 4:09 PM, David Freedman <3.14da...@gmail.com> w

[R] Citing R/Packages Question

2009-05-08 Thread Derek Ogle
I used R and the quantreg package in a manuscript that is currently in the proofs stage. I cited both R and quantreg as suggested by citation() and noted the version of R and quantreg that I used in the main text as "All tests were computed with the R v2.9.0 statistical programming language

Re: [R] Merging two data frames with 3 common variables makes duplicated rows

2009-05-08 Thread Thomas Lumley
On Fri, 8 May 2009, Rock Ouimet wrote: I am new to R (ex SAS user) , and I cannot merge two data frames without getting duplicated rows in the results. How to avoid this happening without using the unique() function? 1. First data frame is called "tmv" with 6 variables and 239 rows: tmv[1:10,

Re: [R] Plotting counts vs. intervals for a shingle

2009-05-08 Thread David Winsemius
On May 8, 2009, at 4:55 PM, Deepayan Sarkar wrote: On Fri, May 8, 2009 at 1:30 PM, David Winsemius > wrote: Took a bit of inspecting, looking at hidden functions, but this seems to do it: library(lattice) a <- c(1:10, 5:10) b <- cbind(c(0,2.5,4.5,6.5), c(5.5,7.5,9.5,11)) c <- shingle(a,

[R] Merging two data frames with 3 common variables makes duplicated rows

2009-05-08 Thread Rock Ouimet
I am new to R (ex SAS user) , and I cannot merge two data frames without getting duplicated rows in the results. How to avoid this happening without using the unique() function? 1. First data frame is called "tmv" with 6 variables and 239 rows: > tmv[1:10,] temps nomprenom sex

Re: [R] by-group processing

2009-05-08 Thread David Freedman
sorry about the mistake - the -data$Type doesn't work: the '-' sign isn't valid for factors. I *thought* I had checked this before submitting a response ! HufferD wrote: > > On Thursday, May 07, 2009 7:45 PM, David Freedman wrote: > > > ...how about: > > d=data[order(data$ID,-data$Type),]

Re: [R] Plotting counts vs. intervals for a shingle

2009-05-08 Thread Deepayan Sarkar
On Fri, May 8, 2009 at 1:30 PM, David Winsemius wrote: > > Took a bit of inspecting, looking at hidden functions, but this seems to do > it: > > library(lattice) >  a <- c(1:10, 5:10) >  b <- cbind(c(0,2.5,4.5,6.5), c(5.5,7.5,9.5,11)) >  c <- shingle(a, b) >  summary(c, showValues=FALSE) > > apply

[R] Vim R plugin-2

2009-05-08 Thread Jakson A. Aquino
Dear R users, People who uses vim in Linux/Unix may be interested in checking the plugin for R that I'm developing: http://www.vim.org/scripts/script.php?script_id=2628 The plugin includes omni completion for R objects, code indentation and communication with R running in a terminal emulator (

Re: [R] Plotting counts vs. intervals for a shingle

2009-05-08 Thread David Winsemius
Took a bit of inspecting, looking at hidden functions, but this seems to do it: library(lattice) a <- c(1:10, 5:10) b <- cbind(c(0,2.5,4.5,6.5), c(5.5,7.5,9.5,11)) c <- shingle(a, b) summary(c, showValues=FALSE) apply(as.matrix(levels(c)), 1, function(x) length(c[ c>= x[[1]][1] & c <=

Re: [R] centering axis labels in lattice

2009-05-08 Thread Deepayan Sarkar
On Fri, May 8, 2009 at 8:08 AM, Paul Boutros wrote: > Hello, > > I'm attempting to alter the location of text in my axis labels in lattice > plots and have been unsuccessful so far.  For example, the y-axis labels are > always right-justified, but I would like them to be horizontally centered. > >

[R] caching of the .Rprofile file

2009-05-08 Thread Tom H
Hi, It seems that if I make a change to the .Rprofile file in my working directory, it is not immediately reflected when the session is restarted. (I am using statET and rJava) Is that something I should expect? Thanks, #T __ R-help@r-project.org mai

Re: [R] documenting quirky behavior of as.POSIXct, as.POSIX.lt regarding AM/PM, possibly other cases

2009-05-08 Thread David Winsemius
Also works as expected on the MacOSX 64 bit binary for R 2.8.1 (patched). On May 5, 2009, at 4:06 PM, jim holtman wrote: Seems to work fine for me on R 2.9.0: as.POSIXct("2009/03/26 01:00:00 AM" , format="%Y/%m/%d %I:%M:%S %p" ) [1] "2009-03-26 01:00:00 GMT" as.POSIXct("2009/03/26 01:00:0

Re: [R] Installing RGtk2 on Mac OS

2009-05-08 Thread Prof Brian Ripley
Please use R-sig-mac for Mac OS X questions, as the posting guide asks. But there is a binary of Gtk2 on r.research.att.com that matches the binary RGtk2 package on CRAN, and that worked for me earlier today. Mixing fink (or darwinports) with the binary R distribution is warned against in the

Re: [R] Help to extract results from lme.object

2009-05-08 Thread Auston
Dear Luc, Thank you so much for your help! The VarCorr() did the trick. Many thanks! Best, Auston __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guid

Re: [R] display data ( text) on leveplot / Superpose panel

2009-05-08 Thread Deepayan Sarkar
On Thu, May 7, 2009 at 10:13 PM, kulwinder banipal wrote: > > I am trying to display data ion top of colored rectangle on the same > levelplot. While using superpose the shape and symbol for levelplot changes > to small circle. I am unable to figure what exactly I am doing wrong... It > may be

[R] Rmysql linking to an old-ish mysql build

2009-05-08 Thread Jose Quesada
Hi, I'm trying to get Rmysql to work o windows server 2008 64-bit. I have the latest build of mysql installed (mysql-5.1.34-winx64). When trying to load Rmysql, I got a warning that Rmysql is linking to an old-ish mysql build (5.0.67). I could do some basic stuff (the connection works) but it bre

[R] Installing RGtk2 on Mac OS

2009-05-08 Thread Hana Sevcikova
I'm having trouble to install RGtk2 (from source) on Mac OS 10.4.11 (R 2.9.0). The GTK libraries (2.12.11) were installed into /sw/lib via fink. Even if I set the GTK_LIBS to that path, the installation program doesn't seem to find it (see below). libglade is there too but not found. If I inst

Re: [R] Help to extract results from lme.object

2009-05-08 Thread Luc Villandre
Auston wrote: Hi list, Would someone please give me a hint how to extract the between and within subject StdDev from "lme" fit? Below is the output from the fit, but I couldn't find the number 0.3927714 anywhere in the fitted object. Thanks in advance for your help! Random effects: Formula: ~

Re: [R] RGoogleDocs

2009-05-08 Thread Duncan Temple Lang
Robert Schneider wrote: Hi there, I'm not certain if this is the correct list where to post this question, or if it ought to be on the R developper one... I am trying to use the RGoogleDocs package to import into R the spreadsheets on my Google docs account. I downloaded the latest package (0.

[R] Help to extract results from lme.object

2009-05-08 Thread Auston
Hi list, Would someone please give me a hint how to extract the between and within subject StdDev from "lme" fit? Below is the output from the fit, but I couldn't find the number 0.3927714 anywhere in the fitted object. Thanks in advance for your help! Random effects: Formula: ~1 | group

[R] Probit cluster-robust standard errors

2009-05-08 Thread Rob Denniker
If I wanted to fit a logit model and account for clustering of observations, I would do something like: library(Design) f <- lrm(Y1 ~ X1 + X2, x=TRUE, y=TRUE, data=d) g <- robcov(f, d$st.year) What would I do if I wanted to do the same thing with a probit model? ?robcov says the input model mus

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Wacek Kusnierczyk
Simon Pickett wrote: > I bet at least a few people offered their services! It might be an > undercover sting operation to weed out the unethical amongst us :-) > ... written by some of the r core developers? vQ __ R-help@r-project.org mailing list http

[R] plm: plm.data vs pdata.frame

2009-05-08 Thread Stephen J. Barr
Hello, I am trying to use the plm package for panel econometrics. I am just trying to get started and load my data. It seems from most of the sample documentation that I need to use the pdata.frame function to get my data loaded. However, even after installing the "plm" package, my R installation

Re: [R] ADAPTIVE QUADRATURE WEIGHTS AND NODES

2009-05-08 Thread spencerg
Beyond what Doug said, if you have a specific R function that does adaptive quadrature, you could read the code for that function. You can get that without comments by typing the function name at a commands prompt. To get the source code with comments, you can download the appropriate so

Re: [R] graph resolution windows (dpi) using x11 device

2009-05-08 Thread Einar Arnason
Marta You have to install ghostscript and update your R to the latest version. Here is a test function I used when trying this out a while ago. You could plot different parts of your figure using a similar approach. The bitmap option of my function dropped colors from the lattice panels. However

Re: [R] dotplot: labeling coordinates for each point

2009-05-08 Thread Qifei Zhu
Thank you Deepayan! It works perfectly. Best, Tony -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Deepayan Sarkar Sent: Thursday, May 07, 2009 12:20 PM To: Qifei Zhu Cc: r-help@r-project.org Subject: Re: [R] dotplot: labeling coor

Re: [R] ADAPTIVE QUADRATURE WEIGHTS AND NODES

2009-05-08 Thread Douglas Bates
On Fri, May 8, 2009 at 7:07 AM, Boikanyo Makubate wrote: > Can anyone help me on how to get the nodes and weights of the adaptive > quadrature > using R. You need to be more specific about which quadrature formula. I'm guessing that you probably have Gauss-Hermite quadrature in mind because it

Re: [R] 'Dynamic' 3D plot

2009-05-08 Thread Greg Snow
Some options: The rgl package The Rggobi package (along with the ggobi program) The rotate.cloud function in the TeachingDemos package (or tkexamp in the same package for a way to GUIize your favorite plot) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s

Re: [R] Plotting questions

2009-05-08 Thread Greg Snow
For question 2, dev.new (in more recent versions) will start a new instance of the default device (which are the ones listed below), but in a cross-platform way (so you don't need to remember all 3, and code will work on the other platforms). A link to dev.new should probably be included in the

Re: [R] graph resolution windows (dpi) using x11 device

2009-05-08 Thread Uwe Ligges
Marta M. Rufino wrote: Dear colleagues, Thank you for the reply. Einer: I tried to so, but I had an error: "Error in system(paste(gsexe, "-help"), intern = TRUE, invisible = TRUE) : gswin32c.exe not found" I think would need "|ghostscript|" (in the help file: "You will need |ghostscript|:

[R] cn is not a nb object

2009-05-08 Thread Penner, Johannes
Dear all, I am trying to calculate barriers with the monmonier algorithm (adegenet). mon1 <- monmonier(mycoordinates, mydistancamatrix, network$cn, ...) The network beforehand looked alright. However, I always get the error: "cn is not a nb object". I am not really sure what this means, probably

Re: [R] How to save independent R sessions in BATCH mode???

2009-05-08 Thread Uwe Ligges
mcnda...@mncn.csic.es wrote: Hi guys, I already have put this question some time ago however replies were not straight to the problem. Even so thanks a lot for the answers! I reformulate the problem. I have a script file with the following commands: for (i in 1:300) - open session --> loa

Re: [R] plotting with gap in x-axis range

2009-05-08 Thread Uwe Ligges
If plotrix does not help, you need to be mroe specific and give an example as the posting guide asks you to do anyway. Uwe Ligges BARRES-DE-ALMEIDA U. wrote: Hi, I need to make a plot of data from multiple epochs, and so I'd need to introduce a couple of breaks in the x-axis not to have to

Re: [R] partial mantel tests "Ecodist"

2009-05-08 Thread Sarah Goslee
Hi David, On Fri, May 8, 2009 at 10:27 AM, wrote: > My questions are as follows; > > 1) can "raw" data be used to construct the dissimilarity matricies? or > should they be standardized? different variables have different measurment > scales, my inclination is to standardize, but I don't know i

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Barry Rowlingson
On Fri, May 8, 2009 at 4:06 PM, Mitchell Maltenfort wrote: > And the crazy thing is that if he went to Amazon and ordered 2 R books > with one-day shipping, he could do it himself and probably spend half > as much. And the crazier thing is that if homework cheats "lurked moar" then they could p

[R] plotting with gap in x-axis range

2009-05-08 Thread BARRES-DE-ALMEIDA U.
Hi, I need to make a plot of data from multiple epochs, and so I'd need to introduce a couple of breaks in the x-axis not to have too many empty space in my plot. I discovered a function in the package "plotrix" which makes breaks in axis, but it is not what I was actually looking for, becaus

[R] partial mantel tests "Ecodist"

2009-05-08 Thread ddepew
Hi all, I'm searching for a little clarification on partial mantel tests (ecodist package) I've a distance matrix (x,y), and several others containing environmental/chemical variables. Based on the help file, and the package instructions I've managed to implement the tests as; var1 ~ en

Re: [R] Linear least squares fit with errors in both x and y values.

2009-05-08 Thread James Allsopp
Found an answer here, don't know if anyone's implemented it for R though. www.iop.org/EJ/article/0022-3735/22/4/002/jev22i4p215.pdf James Gerard M. Keogh wrote: > James, > > look up "errors in variables" models or "instrumental variable" models in > econometrics. > > The statistics alternative

[R] centering axis labels in lattice

2009-05-08 Thread Paul Boutros
Hello, I'm attempting to alter the location of text in my axis labels in lattice plots and have been unsuccessful so far. For example, the y-axis labels are always right-justified, but I would like them to be horizontally centered. Here's an example: library(lattice); # create fake data

Re: [R] 'Dynamic' 3D plot

2009-05-08 Thread Juergen Rose
Hi Tony, Am Freitag, den 08.05.2009, 14:06 +0100 schrieb Tony Breyal: > Hi mate, > > i think you mistakenly emailed this message only to me rather than the > whole list. > > Tony. Thank you for forwarding my mail to the list. I post to seldom to r-help. And I am used from other mailing list

Re: [R] Plotting questions

2009-05-08 Thread S Ellison
>>> lehe 08/05/2009 09:58:40 >>> >1. How to plot several lines in a figure? See ?lines >2. How to open another figure window? see ?windows *** This email and any attachments are confidential. Any use...{{dropped:8}} _

[R] RGoogleDocs

2009-05-08 Thread Robert Schneider
Hi there, I'm not certain if this is the correct list where to post this question, or if it ought to be on the R developper one... I am trying to use the RGoogleDocs package to import into R the spreadsheets on my Google docs account. I downloaded the latest package (0.2.0) and installed it. I

Re: [R] sscanf

2009-05-08 Thread jim holtman
You can always use regular expressions: > x <- "Condition: 311" > as.integer(sub(".*?(\\d +).*", "\\1 ", x, perl=TRUE)) [1] 311 > On Fri, May 8, 2009 at 10:16 AM, Matthias Gondan wrote: > Dear list, > > Apparently, there is no function like sscanf in R. > > I have a string, "Condition: 311", an

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Mitchell Maltenfort
On Fri, May 8, 2009 at 12:19 AM, ayaku1...@gmail.com wrote: > There are six assignments in total. It won't take you long if you were > familiar with R. For those who are interested, please send me an email > with your profile (your experience with R, how long and how often have > you been using it

Re: [R] by-group processing

2009-05-08 Thread David Huffer
On Thursday, May 07, 2009 7:45 PM, David Freedman wrote: > ...how about: > d=data[order(data$ID,-data$Type),] > d[!duplicated(d$ID),] Does the "-data$Type" argument to the order function work? -- David   - David Huffer, Ph.D.

Re: [R] postscript()-resolution

2009-05-08 Thread Gavin Simpson
On Fri, 2009-05-08 at 15:47 +0200, Henning Wildhagen wrote: > Dear users, > > another question concerning graphics for publications. My favourite journal > wants .eps-graphics, > and from older postings i adapted the following code: > > postscript(file="Figure1.eps", title="Figure 1", width=11.5

Re: [R] display data ( text) on leveplot / Superpose panel

2009-05-08 Thread David Winsemius
I would have expected that Sarkar's response to a similar question about dotplot offered yesterday ought to have a good chance of answering this question. Search on dotplot: "labeling coordinates for each point" -- David Winsemius On May 8, 2009, at 1:13 AM, kulwinder banipal wrote: I am

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Steve_Friedman
Wacek raises a very valid perspective. I have previously not responded to these requests, and I've seen a bunch. I have thought they were a waste of my time to respond to. In the future I think I'll simpy disregard these requests, because I simply can not "crystal ball" the true needs of the or

Re: [R] postscript()-resolution

2009-05-08 Thread Eik Vettorazzi
Hi Henning, maybe you just lost the extension (.eps) of the file when "converting" it with ghostview. But R postscript(..,onefile=FALSE) produces actually an eps compatible file. An (encapsulated) postscript file is a vector based file format, so there isn't such a thing as a "resulution", sin

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Simon Pickett
I bet at least a few people offered their services! It might be an undercover sting operation to weed out the unethical amongst us :-) - Original Message - From: "Wacek Kusnierczyk" To: "Tung86" Cc: "R help" Sent: Friday, May 08, 2009 3:18 PM Subject: Re: [R] I'm offering $300 for

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Wacek Kusnierczyk
Tung86 wrote: > well..why shame? He doesn't say it's a homework really. > indeed; while it might of course have been a serious offer, i can't get rid of the feeling that what we see could also be a deliberate -- and quite successful -- provocation, and that the author might be now having lots

Re: [R] Plotting questions (ROCR)

2009-05-08 Thread Tobias Sing
To have several performance curves on a single plot, use the "add=TRUE" option, e.g. as follows: plot(perf1) plot(perf2, add=TRUE, col='red') Please read the help to ?plot.performance. It also tells you how you can adjust all graphical parameters for the individual curves. This slide deck contain

[R] sscanf

2009-05-08 Thread Matthias Gondan
Dear list, Apparently, there is no function like sscanf in R. I have a string, "Condition: 311", and I would like to read out the number and store it to a numeric variable. Is there an easy way to do this? Best wishes, Matthias -- __ R-help@r-project

[R] expression(paste with the superscript in bold font

2009-05-08 Thread Arnaldo Russo
Hi, I`m trying to put my superscript type in bold style. Could somebody help me? My text is inside a barplot. #!/bin/Rbarplot(x, ylab=expression(paste("org.", cm^-2))) # so I tried this way, *barplot(x, ylab=expression(bold(paste("org.", cm^-2* # but my superscript maintain its shape in re

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Tung86
well..why shame? He doesn't say it's a homework really. On May 8, 4:48 am, steve_fried...@nps.gov wrote: > Shame on you! > > Steve Friedman Ph. D. > Spatial Statistical Analyst > Everglades and Dry Tortugas National Park > 950 N Krome Ave (3rd Floor) > Homestead, Florida 33034 > > steve_fried...@n

[R] ADAPTIVE QUADRATURE WEIGHTS AND NODES

2009-05-08 Thread Boikanyo Makubate
Can anyone help me on how to get the nodes and weights of the adaptive quadrature using R. Best wishes Boikanyo. - The University of Glasgow, charity number SC004401 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-he

[R] postscript()-resolution

2009-05-08 Thread Henning Wildhagen
Dear users, another question concerning graphics for publications. My favourite journal wants .eps-graphics, and from older postings i adapted the following code: postscript(file="Figure1.eps", title="Figure 1", width=11.5, height=8, paper="a4",onefile=FALSE) However,  when checking the proper

Re: [R] making an Affybatch object for expresso

2009-05-08 Thread Martin Morgan
George Chen writes: > Hi All, > > I have microarray data that does not come in a CEL file. Currently it is in > the form of columns = individual samples and rows = individual probes. There > are about 79 columns and it is in a tab delimited text file. Is there a way > to convert this file i

Re: [R] problem with normalize.quantiles

2009-05-08 Thread Martin Morgan
again, the bioconductor list is appropriate. You'll want to be sure to update your packages using the instructions at http://bioconductor.org/docs/install/ and be sure to provide the output of sessionInfo() to make any actual problems easier to track down. Martin George Chen writes: > H

Re: [R] RSPerl and Statistics::R

2009-05-08 Thread Daniel Klein
Taking a quick gander at RServe — interesting. I think that some of the magic RSPerl is doing in munging R data types into Perl constructs is the tricky part of the exercise. While I like the close binding to R itself that RSPerl uses, going through an intermediary like RServe might prove easier

Re: [R] Plotting questions (ROCR)

2009-05-08 Thread lehe
Thanks! I am now also trying to plot several ROCs in the same figure using ROCR package. The following code: "pred1 <- prediction(yest1,ytest) perf1 <- performance( pred1, "tpr", "fpr" ) plot( perf1 ) pred2 <- prediction(yest2,ytest) perf2 <- performance( pred2, "tpr", "fpr" ) lines( perf2 )" wi

[R] Gantt chart but slightly different

2009-05-08 Thread Beata Czyz
Hello, I am new to this list and rather new to graphics with R. I would like to make a chart like Gantt chart, something like that: require (plotrix) Ymd.format<-"%Y/%m/%d" gantt.info<-list(labels=c("Male 1","Male 1","Male 1", "Male 2", "Male 2"), starts=as.POSIXct(strptime(c("2004/01/01","2004/0

Re: [R] howto find x value where x=max(x)

2009-05-08 Thread Jorge Ivan Velez
Dear Jonas, Try this: with(fp, Frequenz[ which.max(AmpNorm) ] ) HTH, Jorge On Fri, May 8, 2009 at 8:49 AM, Jonas Stein wrote: > Hi, > > fp is a data frame like this > > ,[ fp ] > |Frequenz AmpNorm > | 1 3322 0.0379490639 > | 2 3061 0.0476033058 > | 3 2833 0.059295

Re: [R] Using lme() for split plot

2009-05-08 Thread Joshua Stults
Thanks for the tip. That lead me to find this paper: http://www.ualberta.ca/~baayen/publications/baayenDavidsonBates.pdf which looks like it will answer my problem. Depending on how we actually decide to execute the test it might turn out to be nested like those other examples, but it's nice to

Re: [R] graph resolution windows (dpi) using x11 device

2009-05-08 Thread Philipp Pagel
On Fri, May 08, 2009 at 01:45:22PM +0100, Marta M. Rufino wrote: > "Error in system(paste(gsexe, "-help"), intern = TRUE, invisible = TRUE) > : gswin32c.exe not found" > I think would need "|ghostscript|" (in the help file: > > "You will need |ghostscript|: the full path to the executable can be

Re: [R] howto find x value where x=max(x)

2009-05-08 Thread Richard . Cotton
> fp is a data frame like this > > ,[ fp ] > |Frequenz AmpNorm > | 1 3322 0.0379490639 > | 2 3061 0.0476033058 > | 3 2833 0.0592954124 > | 4 2242 0.1275510204 > ` > > i want to find the "Frequenz" where "AmpNorm" is max. Use which.max. fp <- data.frame(Freqe

Re: [R] howto find x value where x=max(x)

2009-05-08 Thread Lasse Bombien
Hi, you could use which.max(). > fp$Frequenz[which.max(fp$AmpNorm)] I found the reference in the max() help. Lasse Am Freitag, den 08.05.2009, 14:49 +0200 schrieb Jonas Stein: > Hi, > > fp is a data frame like this > > ,[ fp ] > |Frequenz AmpNorm > | 1 3322 0.0379490639 > | 2

Re: [R] howto find x value where x=max(x)

2009-05-08 Thread baptiste auguie
try this: with(fp, Frequenz[which.max(AmpNorm)]) baptiste On 8 May 2009, at 14:49, Jonas Stein wrote: Hi, fp is a data frame like this ,[ fp ] |Frequenz AmpNorm | 1 3322 0.0379490639 | 2 3061 0.0476033058 | 3 2833 0.0592954124 | 4 2242 0.1275510204 ` i

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread D Chaws
The venom from everyone is to be expected here ayaku. While scientific listservs are a bad place to ask for people to do your homework, they are great for getting advice and soliciting tutors. R is a great program and a lot of fun to learn. Why not put your money to better use and hire a local t

Re: [R] Get (feature, threshold) from Output of rpart() for Stump Tree

2009-05-08 Thread Tim
Thank you so much! It seems that fit$splits[1,] does not contain the feature ID:  "> fit$splits[1,]   count    ncat improve   index adj 124.000  -1.000   0.3437644  13.500   0.000 " However help(rpart.object) says: " splits: a matrix describing the splits.

Re: [R] if ((x >.2 || x<(-.2)) && (col(x)!=row(x))) {x=x[, -col(x)]}

2009-05-08 Thread David Winsemius
You are trying to test the equality of a matrix to a scalar, which will produce a logical vector. You are also using && in an apparent attempt to conjoin a complex object which will probably not give you the results you expect in that context either since it would only return a single TRUE

[R] howto find x value where x=max(x)

2009-05-08 Thread Jonas Stein
Hi, fp is a data frame like this ,[ fp ] |Frequenz AmpNorm | 1 3322 0.0379490639 | 2 3061 0.0476033058 | 3 2833 0.0592954124 | 4 2242 0.1275510204 ` i want to find the "Frequenz" where "AmpNorm" is max. I use this line as workaround: PeakFreqHz = subset(fp,

Re: [R] graph resolution windows (dpi) using x11 device

2009-05-08 Thread Marta M. Rufino
Dear colleagues, Thank you for the reply. Einer: I tried to so, but I had an error: "Error in system(paste(gsexe, "-help"), intern = TRUE, invisible = TRUE) : gswin32c.exe not found" I think would need "|ghostscript|" (in the help file: "You will need |ghostscript|: the full path to the executa

[R] how to calculace the Observational error of an variable (nls fit)

2009-05-08 Thread Jonas Stein
Hi, ich have a List of measured valuepairs (w, AmpNorm) and a formula f(w, a, b) = AmpNorm i used nls to find the two coefficiants a and b: ctfit.nls <- nls(AmpNorm ~ 1/(1 + (w * a - b /w)^2) ...) R> ctfit.nls returns Nonlinear regression model model: AmpNorm ~ 1/(1 + (w * a - b /w)^2)

Re: [R] I'm offering $300 for someone who know R-programming to dothe assignments for me.

2009-05-08 Thread Simon Pickett
at least he/she is resourceful! (but also very naughty) - Original Message - From: To: Cc: ; Sent: Friday, May 08, 2009 12:48 PM Subject: Re: [R] I'm offering $300 for someone who know R-programming to dothe assignments for me. Shame on you! Steve Friedman Ph. D. Spatial Stat

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Richard . Cotton
> There are six assignments in total. It won't take you long if you were > familiar with R. For those who are interested, please send me an email > with your profile (your experience with R, how long and how often have > you been using it.) I will be paying through paypal. Thanks! Now see, you mad

Re: [R] Error while using rfImpute

2009-05-08 Thread Liaw, Andy
Try re-starting R, load the randomForest package, and then run example(rfImpute) and see if that works. Can you post your sessionInfo() output? Andy From: cosmos science > > Dear Administrator, > > I am using linux (suse 10.2). While attempting rfImpute, I am > getting the > following error

Re: [R] Get (feature, threshold) from Output of rpart() for Stump Tree

2009-05-08 Thread Terry Therneau
--- begin included message -- Hi, I have a question regarding how to get some partial information from the output of rpart, which could be used as the first argument to predict. For example, in my code, I try to learn a stump tree (decision tree of depth 2):    "fit    <- rpart(y~bx, weights

Re: [R] glm fit

2009-05-08 Thread Richardson, Patrick
Interesting. Now the fifth homework question you have posted here. As was stated before (by several members) this is not a homework forum. Patrick -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of mathallan Sent: Friday, May 08, 2

Re: [R] extending strsplit to handle missing text that doesn't have the target on which to split

2009-05-08 Thread jim holtman
Find the values that are missing a comma and add it: > dat <- c("Tue, 15 Nov 2005 09:44:50 EST", + "15 Nov 2005 09:10:00 +0100", + "Tue, 15 Nov 2005 09:44:50 EST", + "Tue, 15 Nov 2005 16:29:57 +", + "Wed, 16 Nov 2005 07:00:45 EST", + "Wed, 16 Nov 2005 05

Re: [R] I'm offering $300 for someone who know R-programming to do the assignments for me.

2009-05-08 Thread Steve_Friedman
Shame on you! Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147

Re: [R] graph resolution windows (dpi) using x11 device

2009-05-08 Thread Uwe Ligges
Marta M. Rufino wrote: Dear list members, After looking in the www, I found this subject has been in discussion previously on the mailing list, although I could not solve it. I also found two wikis, but similarly, could not reach a conclusion. I need to re-produce my figures with 1200 dpi,

Re: [R] creation of a matrix

2009-05-08 Thread jim holtman
Is this what you want: > x <- data.frame(n=sample(10, n, TRUE), text=sample(LETTERS, n, TRUE)) > table(x$text, x$n) 1 2 3 4 5 6 7 8 9 10 A 6 5 2 0 8 1 5 3 6 4 B 2 2 5 2 2 7 5 4 4 5 C 7 4 6 4 3 6 3 6 5 4 D 9 5 1 6 3 1 3 2 6 3 E 2 6

Re: [R] CHM error

2009-05-08 Thread Uwe Ligges
tognox wrote: Hi, I would need some help in solving a problem with my R. Whenever I try to type " ?paste " or in general any command for the html help in R, I receive this error message. The strange thing is that I have never had this kind of problem in the past with R, and now I really don't u

[R] Error while using rfImpute

2009-05-08 Thread cosmos science
Dear Administrator, I am using linux (suse 10.2). While attempting rfImpute, I am getting the following error message: > Members <- rfImpute(Status ~ ., data = Members) Error in .C("classRF", x = x, xdim = as.integer(c(p, n)), y = as.integer(y), : C symbol name "classRF" not in DLL for packag

Re: [R] 'Dynamic' 3D plot

2009-05-08 Thread Tony Breyal
Hi Martial, The rgl package is quite nice for this sort of thing: # this is the example in ?plot3d library(rgl) open3d() x <- sort(rnorm(1000)) y <- rnorm(1000) z <- rnorm(1000) + atan2(x,y) plot3d(x, y, z, col=rainbow(1000)) HTH, Tony Breyal On 8 May, 09:25, Martial Sankar wrote: > Hi, > >

[R] Episode splitting with qualitative covariates

2009-05-08 Thread M. Damman
Dear R-users, To test the effect of training (a time-varying qualitative covariate) on the transition to management rate by means of event history models, I would like to split my data by the training date. Excerpt of my data: StatusN Duration DummyOtherEp TimingOtherTraining 1 0

[R] increasing memory for R bg job

2009-05-08 Thread carol white
if (typeof YAHOO == "undefined") { var YAHOO = {}; } YAHOO.Shortcuts = YAHOO.Shortcuts || {}; YAHOO.Shortcuts.hasSensitiveText = false; YAHOO.Shortcuts.sensitivityType = []; YAHOO.Shortcuts.doUlt = false; YAHOO.Shortcuts.location = "

[R] graph resolution windows (dpi) using x11 device

2009-05-08 Thread Marta M. Rufino
Dear list members, After looking in the www, I found this subject has been in discussion previously on the mailing list, although I could not solve it. I also found two wikis, but similarly, could not reach a conclusion. I need to re-produce my figures with 1200 dpi, in tiff format, for a jo

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