Re: [R] dataframe of dataframes?

2010-09-14 Thread Jeff Newmiller
raje...@cse.iitm.ac.in wrote: Hi, I create several dataframes in a nested loop and would like to maintain them in a matrix form with each dataframe represented by the row and the column. How can I do this? You can't, at least as you describe it. However, you can add a column for row ID

Re: [R] xlab with text and expression

2010-09-14 Thread threshold
One more question, given that plot(rnorm(1),rnorm(1), ylab=expression(a~b = 3), cex.lab=1.2) then sign = seems to be smaller than the rest, seems like cex.lab=1.2 affects only the text in ylab. 1) Is there any way to alter its size to follow the size of the whole expression? It works nice for

Re: [R] apply over parallel lists and their elements

2010-09-14 Thread Liviu Andronic
On Tue, Sep 14, 2010 at 12:44 AM, David Winsemius dwinsem...@comcast.net wrote: The second argument to mean is trim. I am not sure what mean(1, 3) is supposed to do but what it return is 1. Thanks for the info. On this particular point I find the documentation confusing. In ?mapply : '‘mapply’

Re: [R] dataframe of dataframes?

2010-09-14 Thread Henrik Bengtsson
You can create an empty matrix (or even array) of list elements and then assign your data frames to whichever element you want. Example: # Allocate empty matrix... x - matrix(list(), nrow=2, ncol=3); # ...alternatively x - array(list(), dim=c(2,3)); print(x); [,1] [,2] [,3] [1,] NULL

[R] solve integrate(,..) varying limits of integration

2010-09-14 Thread Tonja Krueger
Dear List, Is there a way to solve integrate(func.1,x, Inf) $value =0.05 by varying the lower limit of integration (x in the example above)? So far I got: r- 0.730163 s--2 func.1- function(t) {1/(2*pi*sqrt(1-r^2))*exp(-1/(2*(1-r^2))*(s^2-2*r*s*t+t^2))} I can change the lower limit manually,

[R] Object oriented programming in R.

2010-09-14 Thread Alaios
Hello everyone. I would like to create many objects with R. Does R support objects? The number of objects needed is not predetermined and it is a parameter specified by the user. If the user selects to create many objects like 100, would it be possible to handle each one by some index? I would

Re: [R] solve integrate(,..) varying limits of integration

2010-09-14 Thread Dimitris Rizopoulos
have a look at uniroot(), e.g., ff - function (low, r, s) { f - function (t, r, s) { exp(-(s^2 - 2*r*s*t + t^2) / (2*(1-r^2))) / (2*pi*sqrt(1-r^2)) } integrate(f, low, Inf, r = r, s = s)$value - 0.05 } uniroot(ff, c(-3, -2), r = 0.730163, s = -2)$root I hope it helps.

Re: [R] Object oriented programming in R.

2010-09-14 Thread Tal Galili
Hello Alaios, I see a bunch of good materials here: http://www.google.co.il/search?sourceid=chromeie=UTF-8q=Object+oriented+programming+in+R http://www.google.co.il/search?sourceid=chromeie=UTF-8q=Object+oriented+programming+in+RDid you look into them ? Contact

[R] How to uncompress a gz file in R

2010-09-14 Thread Wonsang You
Dear Fellows, I would like to know how to uncompress a gz file at the R console. I could not find out any help from the R-help archive. Thanks for your great help. Best Regards, Wonsang You - -- Wonsang You Special Lab Non-Invasive Brain Imaging Leibniz Institute for Neurobiology

Re: [R] How to uncompress a gz file in R

2010-09-14 Thread Uwe Ligges
See ?gzfile Uwe Ligges On 14.09.2010 11:02, Wonsang You wrote: Dear Fellows, I would like to know how to uncompress a gz file at the R console. I could not find out any help from the R-help archive. Thanks for your great help. Best Regards, Wonsang You - -- Wonsang You Special Lab

Re: [R] The future of R - Ross Ihaka stirs discussions around the web

2010-09-14 Thread Uwe Ligges
On 14.09.2010 04:02, Spencer Graves wrote: Hello: On 9/13/2010 3:44 PM, Vojtěch Zeisek wrote: Hello Dne Po 13. září 2010 14:51:39 Tal Galili napsal(a): snip But here, I wish point out one issue, which can be fixed relatively easily: R would deserve much more better web running some

Re: [R] xyplot legends

2010-09-14 Thread Peter Ehlers
On 2010-09-13 17:45, array chip wrote: Thanks David. It almost does what I wanted, except it's plotting the point characters 3 time for each line (left, middle and right): o---o---o I can live with that if there is no way to get rid of the point characters at the ends. You can add the

Re: [R] Problem (environment?) with R CMD CHECK

2010-09-14 Thread Uwe Ligges
I do not see any problem, we'd need to look at the package in order to help, I think. Best, Uwe Ligges On 14.09.2010 00:20, Peter Langfelder wrote: Hi all, I have a package that contains a function foo that calls a function .fooInternal via match.fun('.fooInternal'). This step is necessary

Re: [R] Specify a minimum number of valid arguments for the mean function

2010-09-14 Thread Uwe Ligges
On 13.09.2010 17:43, Luana Marotta wrote: Hello all, I want to specify a minimum number of valid arguments for the mean function--I have 5 variables but I want the mean only of cases that have at least 3 valid answers. What is the best way to do that? If your 5 variables are in a

Re: [R] Transparent Labels for Polar Plot

2010-09-14 Thread Jim Lemon
On 09/14/2010 06:25 AM, James MacCarthy wrote: Hello, I am currently using the polar.plot function in the plotrix package to graph data. Unfortunately, it seems that the default for the labels is to have a background color that is covering the line representing my data, making it difficult

Re: [R] Homogeneity of regression slopes

2010-09-14 Thread Clifford Long
Hi Thomas, Thanks for the additional information. Just wondering, and hoping to learn ... would any lack of homogeneity of variance (which is what I believe you mean by different stddev estimates) be found when performing standard regression diagnostics, such as residual plots, Levene's test (or

[R] Problem with cat()

2010-09-14 Thread Christofer Bogaso
Dear all, I have a problem with the cat() function. Let say I have following: fn1 - function(n = 5){ mat - matrix(rnorm(5*5), 5, 5) cat(as.character(mat)) return(n) } However when I run above function I get this: fn1() -0.601930631438248 -1.16950049447942 0.469257329394626 -1.39766868242906

Re: [R] Problem with cat()

2010-09-14 Thread Joshua Wiley
Hello, If it does not *have* to be cat(), this would work: fn1 - function(n = 5){ mat - matrix(rnorm(5*5), 5, 5) print(mat) return(n) } Cheers, Josh On Tue, Sep 14, 2010 at 4:00 AM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Dear all, I have a problem with the cat() function. Let

[R] R install in Fedora

2010-09-14 Thread wesley mathew
Dear All I was trying to install R-2.10.0-2.fc11.X86 in Fedora-13-i386 but it makes error. Could you please tell me which is the exact version of R for Fedora 13. Thanks in advance Kind Regards Wesley [[alternative HTML version deleted]] __

[R] Content analysis

2010-09-14 Thread Sametrie Neurones
Dear all, I planning to carry out a content analysis in R but I don't know which package to use. I tried rqda (http://rqda.r-forge.r-project.org/index.html) but it doesn't help. Any suggestion will be appreciated. Christian [[alternative HTML version deleted]]

Re: [R] dataframe of dataframes?

2010-09-14 Thread raje...@cse.iitm.ac.in
This is great. Thanks - Original Message - From: Henrik Bengtsson h...@stat.berkeley.edu To: Jeff Newmiller jdnew...@dcn.davis.ca.us Cc: raje...@cse.iitm.ac.in, r-help r-help@r-project.org Sent: Tue, 14 Sep 2010 12:27:38 +0530 (IST) Subject: Re: [R] dataframe of dataframes? You can

Re: [R] Object oriented programming in R.

2010-09-14 Thread Alaios
Thank you very much. I checked the tutorials that on that list but still I do not know how to create many objects of the same type. Can you please help me with that? Best Regards Alex From: Tal Galili tal.gal...@gmail.com Cc: Rhelp r-help@r-project.org

[R] question on staRt package

2010-09-14 Thread Paulo Teles
Dear Sirs, I have been using the package staRt but it has disappeared from the latest R versions. I emailed the author but he never replied. Is it possible to let me know if that package has been removed or if it has been replaced by another or what happened? The latest version is 1.1.12.

Re: [R] Object oriented programming in R.

2010-09-14 Thread Liviu Andronic
On Tue, Sep 14, 2010 at 12:55 PM, Alaios ala...@yahoo.com wrote: Thank you very much. I checked the tutorials that on that list but still I do not know how to create many objects of the same type. Can you please help me with that? Is this what you need? for(i in 1:100){

Re: [R] xyplot axis line width

2010-09-14 Thread Deepayan Sarkar
On Tue, Sep 14, 2010 at 4:26 AM, array chip arrayprof...@yahoo.com wrote: Hi, another question: is there any argument that controls the line width of axis box of xyplot()? I tried lwd=2 or lwd.axis=2 in xyplot() or within scales=list() argument, without success. xyplot(1:10 ~ 1:10,

Re: [R] lattice package - wireframe plot : adding more than one surface and addiding a curve overlaid on the plot

2010-09-14 Thread Deepayan Sarkar
On Sat, Sep 11, 2010 at 2:28 AM, Raffaello Vardavas r_varda...@hotmail.com wrote: Dear R help, Suppose I have a dataframe with three columns named  p, v and C. Here C is a function of both p and v.  I can plot the surface C(p,v) using the package lattice using the function wireframe. Now

Re: [R] splines package (problem finding it)

2010-09-14 Thread Uwe Ligges
On 14.09.2010 13:25, stephen sefick wrote: I can not install the splines package. Has it been removed/moved from/on CRAN? kindest regards, It should come with R since it is a base package. Uwe Ligges __ R-help@r-project.org mailing list

Re: [R] Object oriented programming in R.

2010-09-14 Thread Rainer M Krug
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 14/09/10 13:51, Liviu Andronic wrote: On Tue, Sep 14, 2010 at 12:55 PM, Alaios ala...@yahoo.com wrote: Thank you very much. I checked the tutorials that on that list but still I do not know how to create many objects of the same type. Can you

Re: [R] Object oriented programming in R.

2010-09-14 Thread Michael Bedward
Hello, I think you will have to specify your requirements (or at least area of interest) in much greater detail to get any very meaningful input from people here. Meanwhile there are countless examples of object-oriented programming using R on the web complete with code. Michael On 14

Re: [R] average matrices across a list

2010-09-14 Thread Ben Bolker
Gregory Ryslik rsaber at comcast.net writes: mymats - vector('list', 5) set.seed(246) # Generate a list of five 3 x 3 matrices for(i in 1:5) mymats[[i]] - matrix(sample(1:9), nrow = 3) mymats[[5]][1,1]-NA mymats[[4]][2,2]-NA mymats matrixadder-function(u,v){ na.u-is.na(u)

Re: [R] Object oriented programming in R.

2010-09-14 Thread jim holtman
It depends on what you mean by objects. If you are just looking at creating many named variables that are going to hold values (e.g., reading in data from several files that you want to correlate separately), then consider the use of 'lists'. Can you provide a little more detail on exactly the

Re: [R] Object oriented programming in R.

2010-09-14 Thread Alaios
Here are some more information: I would like to create some agents that span over a specific area map.Every agent needs to have its own data structures like one or two matrices and one list. I think that the best way to do this is to create objects and every instance of an object will be used

Re: [R] TimeStamp

2010-09-14 Thread Uwe Ligges
On 06.09.2010 03:51, Roberto Badilla Fuentes wrote: Hi, I have a dataset in .dbf format. It contains Coordinates and Time. The TIMESTAMP is as follows: 03/18/2006 13:30:37 I am not working with the TIMESTAMP column, but when I print out my manipulated dataset using *write.dbf* I get the

Re: [R] question on staRt package

2010-09-14 Thread Uwe Ligges
On 14.09.2010 12:25, Paulo Teles wrote: Dear Sirs, I have been using the package staRt but it has disappeared from the latest R versions. I emailed the author but he never replied. Is it possible to let me know if that package has been removed or if it has been replaced by another or what

Re: [R] R install in Fedora

2010-09-14 Thread Marc Schwartz
On Sep 14, 2010, at 6:14 AM, wesley mathew wrote: Dear All I was trying to install R-2.10.0-2.fc11.X86 in Fedora-13-i386 but it makes error. Could you please tell me which is the exact version of R for Fedora 13. Thanks in advance Kind Regards Wesley The current R version for F13 is

Re: [R] average matrices across a list

2010-09-14 Thread Henrique Dallazuanna
You can try this also: Reduce('+', lapply(mymats, function(x)replace(x, is.na(x), 0))) On Sun, Sep 12, 2010 at 10:36 PM, Gregory Ryslik rsa...@comcast.net wrote: Hi Everyone, Thanks to everyone for their help. With your suggestions and some poking around, the following works for what I

[R] Unable to do a post hoc test after Friedman's

2010-09-14 Thread shivanair
I have R version 2.11.1 I am able to run a Friedman.test, but cant do further post.hoc test. Tried running friedman.test.with.post.hocetc It comes with Error: object 'friedman.test.with.post.hoc' not found This is after loading the packages coin and multcomp Could anyone please send in any

[R] splines package (problem finding it)

2010-09-14 Thread stephen sefick
I can not install the splines package. Has it been removed/moved from/on CRAN? kindest regards, -- Stephen Sefick | Auburn University                                   | | Department of Biological Sciences           | | 331 Funchess Hall                     

[R] how to compute when row length is different

2010-09-14 Thread rasanpreet
hi guys..please help me with this i am working on two data frames one goes like this: DF1 Sample_id RepairHours Denatured Dose ZeroMean FourtyFiveMean NinetyMean 1 SDM071 0 1B 60.5 19.0 45.0 2 SDM071 1 1B 46.0

[R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Katie Surrence
Hi all, I know from googling that this is a common problem; I've just tried what I understand to be the common solutions to know avail -- maybe I'm just confused. I installed Miktex 2.8 -- it seems to be working fine. I'm using this demo document: http://www.stat.berkeley.edu/~houston/demo.Rnw

[R] NA confusion (length question)

2010-09-14 Thread Stratford, Jeffrey
Hi folks, I am running a very simple regression using mylm - lm(mass ~ tarsus, na.action=na.exclude) I would like the use the residuals from this analysis for more regression but I'm running into a snag when I try cbind(mylm$residuals, mydata) # where my data is the original

Re: [R] Object oriented programming in R.

2010-09-14 Thread Dennis Murphy
Hi: You could create a list of lists, where the outer list would be between agents and the inner list within agents. The inner list could have the 'matrices and one list' as separate components for each agent. Of course, you would have to be able to keep all of this straight :) HTH, Dennis On

Re: [R] How to uncompress a gz file in R

2010-09-14 Thread Henrik Bengtsson
To uncompress an *.gz file into another file on disk, see also ?gunzip in the R.utils package. /Henrik 2010/9/14 Uwe Ligges lig...@statistik.tu-dortmund.de: See ?gzfile Uwe Ligges On 14.09.2010 11:02, Wonsang You wrote: Dear Fellows, I would like to know how to uncompress a gz file at

Re: [R] average matrices across a list

2010-09-14 Thread Dennis Murphy
Hi: It's certainly fast (0.97s for 1 reps on my box), but doesn't replacement by zero affect the denominator of the sum, thereby deflating the means (assuming the contents of the matrices are nonnegative or NA)? Dennis On Tue, Sep 14, 2010 at 5:28 AM, Henrique Dallazuanna

Re: [R] NA confusion (length question)

2010-09-14 Thread Joshua Wiley
Hi Jeffrey, As a bit of a side note, data copied in html emails tends to show up poorly (since emails to the list are converted to plain text). Anyways, note the difference between: length(mylm$residuals) length(residuals(mylm)) Accessing the residuals value from mylm is *not* quite the same as

Re: [R] how to compute when row length is different

2010-09-14 Thread Nikhil Kaza
DF3 - merge(DF1, DF2, by=c(Sample_id, RepairHours), all.y=T) DF3$subtract - DF3$Day_0_Read1-DF3$ ZeroMean Nikhil Kaza Asst. Professor, City and Regional Planning University of North Carolina nikhil.l...@gmail.com On Sep 14, 2010, at 8:38 AM, rasanpreet wrote: hi guys..please help me with

Re: [R] average matrices across a list

2010-09-14 Thread Gregory Ryslik
Hi, The denominator i compute seperately counting how many observations there were that were not NA. Thus the I divide each (n,m) cell by the number of counts it was not NA. Thanks, Greg On Sep 14, 2010, at 9:23 AM, Dennis Murphy wrote: Hi: It's certainly fast (0.97s for 1 reps on my

Re: [R] NA confusion (length question)

2010-09-14 Thread Stratford, Jeffrey
Josh, I am raising my cup of coffee to you - that worked perfectly. Cheers and thanks again! -Original Message- From: Joshua Wiley [mailto:jwiley.ps...@gmail.com] Sent: Tuesday, September 14, 2010 9:29 AM To: Stratford, Jeffrey Cc: r-help@r-project.org Subject: Re: [R] NA confusion

Re: [R] Unable to do a post hoc test after Friedman's

2010-09-14 Thread David Winsemius
On Sep 14, 2010, at 7:07 AM, shivanair wrote: I have R version 2.11.1 I am able to run a Friedman.test, but cant do further post.hoc test. Tried running friedman.test.with.post.hocetc It comes with Error: object 'friedman.test.with.post.hoc' not found This is after loading the packages

Re: [R] Object oriented programming in R.

2010-09-14 Thread Alaios
I would like to thank you very much all that you helped me so far. So I tried to check how the following works fred - list(happy = 1:10, name = squash) rep(fred, 5) This returns the following : fred[1] $happy [1] 1 2 3 4 5 6 7 8 9 10 fred[2] $name [1] squash What I am trying to

Re: [R] NA confusion (length question)

2010-09-14 Thread Joshua Wiley
You're quite welcome. If you've a hankering to learn more you can see the documentation for ?residuals.lm (note the .lm addition, which designates the particular method that gets dispatched since your object class was lm). For even more fun: ?naresid (which residuals() calls) and to see how it

[R] biclust - jaccardind

2010-09-14 Thread James Nead
Hi, I looked at the help documentation, but couldn't find the algorithm for calculating the modified jaccard index for separate sets of biclusters. Is there a link to some documentation on this? many thanks! [[alternative HTML version deleted]]

Re: [R] Object oriented programming in R.

2010-09-14 Thread David Winsemius
On Sep 14, 2010, at 9:29 AM, Alaios wrote: I would like to thank you very much all that you helped me so far. So I tried to check how the following works fred - list(happy = 1:10, name = squash) rep(fred, 5) This returns the following : fred[1] $happy [1] 1 2 3 4 5 6 7 8 9 10

Re: [R] Object oriented programming in R.

2010-09-14 Thread jim holtman
I think this is what you want. Notice the use of 'list' in the rep to create a list of list: fred - list(happy = 1:10, name = squash) x - rep(list(fred), 5) str(x) List of 5 $ :List of 2 ..$ happy: int [1:10] 1 2 3 4 5 6 7 8 9 10 ..$ name : chr squash $ :List of 2 ..$ happy: int

Re: [R] Problem with cat() == A related question

2010-09-14 Thread Peng, C
Code: fn1 - function(n = 5){ + mat - matrix(rnorm(5*5), 5, 5) + cat(print(mat)) + } fn1() [,1][,2] [,3][,4] [,5] [1,] -0.7101952 0.78992424 -0.8310871 2.49560703 -0.9543827 [2,] -0.1425682 -2.69186367 -0.5937949 0.03188572 -0.5512154 [3,]

Re: [R] how to compute when row length is different

2010-09-14 Thread Dennis Murphy
Hi: Just to be different, here's a data.table solution: library(data.table) # It's always a good idea to have your merge key variables match in each data frame/table names(DF1)[1] - 'SampleId' dt1 - data.table(DF1, key = 'SampleId, RepairHours') dt2 - data.table(DF2, key = 'SampleId,

[R] Multiple CPU HowTo in Linux?

2010-09-14 Thread Edwin Groot
Hello all, I upgraded my R workstation, and to my dismay, only one core appears to be used during intensive computation of a bioconductor function. What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When I fully load it, top reports about 25% user, 75% idle and 0.98 short-term load.

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Dennis Murphy
Hi: Start here: http://docs.miktex.org/manual/localadditions.html#id573835 I have a LocalTeXfiles directory under my home directory on Windows 7, with nested folders for tex - latex - Sweave. All of my Sweave files (*.fd, *.cfg, *.sty) are in the Sweave directory. The manual linked above shows

[R] Error: cannot allocate vector of size X.0 Mb

2010-09-14 Thread John1983
Hi, I am working with a file (900MB in size) that has around 10 million records (in particular FASTQ records). I am able to read in the file as an object of BStringSet. When I start to manipulate the data, after almost 4 hours, I get the error message as Error: cannot allocate vector of size X.0

Re: [R] Multiple CPU HowTo in Linux?

2010-09-14 Thread Johnson, Cedrick W.
?multicore perhaps On 09/14/2010 10:01 AM, Edwin Groot wrote: Hello all, I upgraded my R workstation, and to my dismay, only one core appears to be used during intensive computation of a bioconductor function. What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When I fully load it,

Re: [R] Error: cannot allocate vector of size X.0 Mb

2010-09-14 Thread Marc Schwartz
On Sep 14, 2010, at 9:09 AM, John1983 wrote: Hi, I am working with a file (900MB in size) that has around 10 million records (in particular FASTQ records). I am able to read in the file as an object of BStringSet. When I start to manipulate the data, after almost 4 hours, I get the error

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Greg Johnson
Katie Surrence tiburona at gmail.com writes: ... I've copied the Sweave.sty file into at this point multiple places on the Miktex path, including folders where I can see that it is looking for, and successfully finding, sty files (e.g. Miktex 2.8/tex/latex/base). I also went to the Miktex

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Duncan Murdoch
On 14/09/2010 8:56 AM, Katie Surrence wrote: Hi all, I know from googling that this is a common problem; I've just tried what I understand to be the common solutions to know avail -- maybe I'm just confused. I installed Miktex 2.8 -- it seems to be working fine. I'm using this demo

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Duncan Murdoch
On 14/09/2010 10:27 AM, Greg Johnson wrote: Katie Surrencetiburonaat gmail.com writes: ... I've copied the Sweave.sty file into at this point multiple places on the Miktex path, including folders where I can see that it is looking for, and successfully finding, sty files (e.g. Miktex

Re: [R] Multiple CPU HowTo in Linux?

2010-09-14 Thread Edwin Groot
Hello Cedrick, Ah, yes, that looks like it would apply to my situation. I was previously reading on snow, which is tailored for clusters, rather than a single desktop computer. Anyone with experience adapting multicore to an R-script? I have to admit I know little about parallel processing,

Re: [R] how to compute when row length is different

2010-09-14 Thread Jeff Newmiller
You need to line up the rows before you do the arithmetic. Check out ?merge rasanpreet rasanpreet.k...@gmail.com wrote: hi guys..please help me with this i am working on two data frames one goes like this: DF1 Sample_id RepairHours Denatured Dose ZeroMean FourtyFiveMean NinetyMean 1 SDM071

Re: [R] Error: cannot allocate vector of size X.0 Mb

2010-09-14 Thread John1983
Yes I see. So I typed as you mentioned and I get an 8 (therefore this is a 64-bit R). Is there anything else I need to check to remove this error? -- View this message in context: http://r.789695.n4.nabble.com/Error-cannot-allocate-vector-of-size-X-0-Mb-tp2539031p2539078.html Sent from the R

[R] ASA Stat. Computing Stat. Graphics Student Paper Competition 2011

2010-09-14 Thread Fei Chen
Statistical Computing and Statistical Graphics Sections American Statistical Association Student Paper Competition 2011 The Statistical Computing and Statistical Graphics Sections of the ASA are co-sponsoring a student paper competition on the topics of Statistical Computing and Statistical

Re: [R] Can I save my console contents automatically?

2010-09-14 Thread Nobuaki Michihata
Dear All, I found a following solution from http://r.789695.n4.nabble.com/;. However this command can save only the result. Is there any good solution to save both commands themselves and the results. Thank you for your help. sink(Filename_here.log, type=c(output,message), split=TRUE) # Put

Re: [R] Error: cannot allocate vector of size X.0 Mb

2010-09-14 Thread Uwe Ligges
On 14.09.2010 16:47, John1983 wrote: Yes I see. So I typed as you mentioned and I get an 8 (therefore this is a 64-bit R). Is there anything else I need to check to remove this error? Yes: If the amount of RAM in your machine is sufficient Best, Uwe

Re: [R] Error: cannot allocate vector of size X.0 Mb

2010-09-14 Thread Marc Schwartz
On Sep 14, 2010, at 9:47 AM, John1983 wrote: Yes I see. So I typed as you mentioned and I get an 8 (therefore this is a 64-bit R). Is there anything else I need to check to remove this error? 1. Add more RAM. 2. Depending upon what you are doing relative to data management/analysis,

Re: [R] Problem with cat() == A related question

2010-09-14 Thread jim holtman
Try the following: fn1 - function(n = 5){ mat - matrix(rnorm(5*5), 5, 5) cat(print(mat)) invisible(NULL)} On Tue, Sep 14, 2010 at 9:59 AM, Peng, C cpeng@gmail.com wrote: Code: fn1 - function(n = 5){ +  mat - matrix(rnorm(5*5), 5, 5) +  cat(print(mat)) + } fn1()           [,1]  

Re: [R] Multiple CPU HowTo in Linux?

2010-09-14 Thread Christian Raschke
Edwin, I'm not sure what you mean by adapting; other than installing multicore, there is nothing else to set up. How and whether you could then parallelise your code strongly depends on the specific problem you are facing. What have done in the past was to look at the source of the

Re: [R] R2WinBugs problem

2010-09-14 Thread Uwe Ligges
If the exactly same code runs on one machine and not on another where R version, script, model file, inits, data etc. are all identical, then I suspect you have different versions of R2WinBUGS installed. Please check is really all files and all version numbers are the same. If you still have

[R] Model averaging with (and without) interaction terms

2010-09-14 Thread Leslie Young
I’ve used logistic regression to create models to assess the effect of 3 variables on the presence or absence of a species, including the interaction terms between variables and model averaging using MuMI: model.avg The top models (delta4) include several models with interaction terms and some

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Katie Surrence
Thank you very much, Dennis. That worked. I had tried pointing the list of Roots to the R directory where the Sweave file was originally located, and had gotten an error, but I had not tried making my own directory. On Tue, Sep 14, 2010 at 9:08 AM, Dennis Murphy djmu...@gmail.com wrote: Hi:

[R] ASA John M. Chambers Statistical Software Award - 2011

2010-09-14 Thread Fei Chen
John M. Chambers Statistical Software Award - 2011 Statistical Computing Section American Statistical Association The Statistical Computing Section of the American Statistical Association announces the competition for the John M. Chambers Statistical Software Award. In 1998 the Association for

Re: [R] proportion

2010-09-14 Thread Greg Snow
Learn to use functions like help.search, RSiteSearch, or the sos package, these tools will help you answer your own questions like this. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From:

Re: [R] TimeStamp

2010-09-14 Thread Roberto Badilla Fuentes
Thanks. Both methods definitely help. -Roberto 2010/9/14 Uwe Ligges lig...@statistik.tu-dortmund.de On 06.09.2010 03:51, Roberto Badilla Fuentes wrote: Hi, I have a dataset in .dbf format. It contains Coordinates and Time. The TIMESTAMP is as follows: 03/18/2006 13:30:37 I am not

[R] predict(backSpline(x)): losing my marbles?

2010-09-14 Thread Ben Bolker
I'm sure I'm doing something completely boneheaded here, but I've used this idiom (constructing an interpolation spline and using prediction from a backSpline to find an approximation profile confidence interval) many times before and haven't hit this particular problem: r2 -

Re: [R] xyplot axis line width

2010-09-14 Thread array chip
Thank you Deepayan. This is exactly what I needed. John - Original Message From: Deepayan Sarkar deepayan.sar...@gmail.com To: array chip arrayprof...@yahoo.com Cc: r-help@r-project.org Sent: Tue, September 14, 2010 4:52:29 AM Subject: Re: [R] xyplot axis line width On Tue, Sep 14,

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Duncan Murdoch
On 14/09/2010 11:51 AM, Katie Surrence wrote: Thanks Duncan -- I'm running R 2.11 and ??texify gets me no recognition. There is a command by that name in the tools package (not loaded by default, so that's why help didn't work), but I was talking about entering it at the command prompt, as

[R] Problems with pdf device using plot glht function on multcomp library.

2010-09-14 Thread Kenneth Roy Cabrera Torres
Hi R users: I have de following data frame (called Sx) Descripcion Nitratos Cont85g72.40 Cont85g 100.50 Cont85g 138.30 Cont80g 178.33 Cont80g79.01 Cont80g74.16 Cont75g

[R] nlme numeric data format

2010-09-14 Thread ziggyvic
Dear R help folks I am trying to run nlme for the first time (currently without guidance of any textbooks), apologies if this is a bit simplistic. My model is 15 env predictors of diversity, grouped by 3 locations:

Re: [R] Can I save my console contents automatically?

2010-09-14 Thread David Winsemius
On Sep 14, 2010, at 10:33 AM, Nobuaki Michihata wrote: Dear All, I found a following solution from http://r.789695.n4.nabble.com/;. However this command can save only the result. Is there any good solution to save both commands themselves and the results. Thank you for your help.

Re: [R] Problems with pdf device using plot glht function on multcomp library.

2010-09-14 Thread Kenneth Roy Cabrera Torres
Thank you Jorge Iván: Im working on a Linux platform, and with a recent pathed version of R. Does it work on windows? R version 2.11.1 Patched (2010-09-10 r52887) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=es_CO.UTF-8 LC_NUMERIC=C LC_TIME=es_CO.UTF-8

[R] Good example ANCOVA in R

2010-09-14 Thread choisj70
I could find a couple of useful examples of ANCOVA. However, any of them did not contain a good example of how to get the adjusted means in ANCOV using R. Is there anyone who knows or has a good example of it? Thanks in advance. -- View this message in context:

[R] Using McNemar's test to detect shifts in response from pre- to post-treatment

2010-09-14 Thread Paul Miller
Hello Everyone,   I've been asked to check if there is a significant difference in the following:     Pre    Post Group A 15/19 14/19 Group B 14/19 10/19   My sense is that I need to perform McNemar's test on these data because responses are correlated within

Re: [R] Sweave and Miktex (Sweave.sty not found)

2010-09-14 Thread Katie Surrence
Thanks Duncan -- I'm running R 2.11 and ??texify gets me no recognition. At the moment I'm trying to get something that works -- I'm not nearly to the point of fancy. I solved my Sweave.sty problem although I'm still not managing to generate the graph in the demo file. But maybe I should make

[R] Sweave and graphs

2010-09-14 Thread Katie Surrence
Hi all, Having solved my Sweave.sty question, I'd like to figure out why my pdf doesn't display the graph in my demo code. Here's the demo code I'm using: http://www.stat.berkeley.edu/~houston/demo.Rnwhttp://www.stat.berkeley.edu/%7Ehouston/demo.Rnw When I run Sweave within R (version 2.11) on

Re: [R] Good example ANCOVA in R

2010-09-14 Thread David Winsemius
On Sep 14, 2010, at 11:58 AM, choisj70 wrote: I could find a couple of useful examples of ANCOVA. However, any of them did not contain a good example of how to get the adjusted means in ANCOV using R. Is there anyone who knows or has a good example of it? I'm assuming that whatever

Re: [R] Sweave and graphs

2010-09-14 Thread Duncan Murdoch
On 14/09/2010 12:01 PM, Katie Surrence wrote: Hi all, Having solved my Sweave.sty question, I'd like to figure out why my pdf doesn't display the graph in my demo code. Here's the demo code I'm using:

Re: [R] Multivariate Regression Trees: how to identify sample units?

2010-09-14 Thread Gavin Simpson
On Tue, 2010-09-07 at 19:23 -0300, afso...@unisinos.br wrote: Dear friends, I am sudying the mvpart package, that implements Multivariate Regression Trees, aiming at applying it to a biogeographical dataset of tree speces in southern South America. My doubt is how to access plot

Re: [R] Sweave and graphs

2010-09-14 Thread Katie Surrence
I set my working directory to the location of the file (which I called Demo.Rnw) and I type Sweave(Demo.Rnw) at the R command line. Does that answer your question properly? On Tue, Sep 14, 2010 at 12:08 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 14/09/2010 12:01 PM, Katie Surrence

Re: [R] Homogeneity of regression slopes

2010-09-14 Thread Thomas Stewart
If you are interested in exploring the homogeneity of variance assumption, I would suggest you model the variance explicitly. Doing so allows you to compare the homogeneous variance model to the heterogeneous variance model within a nested model framework. In that framework, you'll have

Re: [R] Sweave and graphs

2010-09-14 Thread Duncan Murdoch
On 14/09/2010 1:18 PM, Katie Surrence wrote: I set my working directory to the location of the file (which I called Demo.Rnw) and I type Sweave(Demo.Rnw) at the R command line. Does that answer your question properly? Yes, that looks fine. So the problem is likely with pdflatex, or maybe

[R] If then else with command for

2010-09-14 Thread Mestat
Hey listers, I am trying to do something simple... Check the program below... I would like to create a variable named COLOR according to the conditions that I stablished... But the problem is that it seems that my variable COLOR is checking just on sample, may be last in the loop... Certainly, I

Re: [R] Problem (environment?) with R CMD CHECK

2010-09-14 Thread Peter Langfelder
2010/9/14 Uwe Ligges lig...@statistik.tu-dortmund.de: I do not see any problem, we'd need to look at the package in order to help, I think. I re-checked again and somehow the package now passes all checks, so I must have mistyped something somewhere. Sorry for that. Peter

Re: [R] Can I save my console contents automatically?

2010-09-14 Thread Greg Snow
Look at the txtStart function in the TeachingDemos package. It (and related functions) can be used as a glorified sink that will save both a copy of the command issued (possibly reformatted) and the results (assuming the command runs without error). Hope this helps, -- Gregory (Greg) L.

[R] stratified Wilcoxon's rank sum test with the locally best weights

2010-09-14 Thread El-Tahtawy, Ahmed
Hello, I have been informed that there is no R package for the stratified Wilcoxon's rank sum test (Van Elteren's test) with the locally best weights. I need to use the alternative test to a clinical endpoint where the distribution approximate normal distribution, and compare to the regular

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