[R] need some lattice help

2009-01-27 Thread Antje
Hello everybody, I just started with lattice plots and I was wondering why it behaves different than expected. If I generated multiple plots in the past, I just used some code like this: lapply(..., { windows() plot(...) }) I got multiple windows, each containing one plot.

Re: [R] Running R under Sun Grid Engine with OpenMPI tight integration

2009-01-27 Thread Marce
2009/1/27 Rainer M Krug r.m.k...@gmail.com: On Tue, Jan 27, 2009 at 2:30 AM, Peter Waltman peter.walt...@gmail.com wrote: Hi - I saw your posting on the R-help mailing list. Were you ever able to get this working? did you end up switching to use the rsge library? Yes - that is exactly

[R] Help

2009-01-27 Thread Huihua Lu
Hi, All, I want to construct a pareto chart for my data. My data has two columns: modules and defects(each module has several defects). Now I use pareto.chart to create a chart for defects which y axis is cumulative percentage of defect, and x axis is value of defect. That is not what I want.

Re: [R] Running R under Sun Grid Engine with OpenMPI tight integration

2009-01-27 Thread Rainer M Krug
On Tue, Jan 27, 2009 at 11:04 AM, Marce marc...@gmail.com wrote: 2009/1/27 Rainer M Krug r.m.k...@gmail.com: On Tue, Jan 27, 2009 at 2:30 AM, Peter Waltman peter.walt...@gmail.com wrote: Hi - I saw your posting on the R-help mailing list. Were you ever able to get this working? did you

Re: [R] need some lattice help

2009-01-27 Thread Antje
I guess, I got the answer. (http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f) Ciao, Antje Antje schrieb: Hello everybody, I just started with lattice plots and I was wondering why it behaves different than expected. If I generated multiple

[R] Memory issue?

2009-01-27 Thread Daniel Brewer
I have a script that sometimes produces the following error: Error in assign(.target, met...@target, envir = envir) : formal argument envir matched by multiple actual arguments Do you think this is a memory issue? I don't know what else it could be as it doesn't always occur even if the

[R] Odp: working with tables -- was Re: Mode (statistics) in R?

2009-01-27 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 27.01.2009 01:50:39: Ok, so I'm slowly figuring out what a factor is, and was able to follow the related thread about finding a mode by using constructs like my_mode = as.numeric(names(table(x))[which.max(table(x))]) Now, suppose I want to

[R] Need help on running Heckman Correction Estimation using R

2009-01-27 Thread Kishore
Team, I am trying to resolve the self-selection bias of a sample in an experiment and would like to run the Heckman Correction Estimation using R. Can someone help me with the R-Code... I tried searching for the discussion, but not successful. Thanks in advance, Best, Kishore/..

[R] Re : Need help on running Heckman Correction Estimation using R

2009-01-27 Thread justin bem
See the micEcon package. there is and heckit function  Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 De : Kishore gladikish...@gmail.com À : r-help@r-project.org; r-h...@stat.math.ethz.ch Envoyé le : Mardi, 27 Janvier 2009, 11h54mn 00s

Re: [R] Memory issue?

2009-01-27 Thread Paul Hiemstra
Daniel Brewer wrote: I have a script that sometimes produces the following error: Error in assign(.target, met...@target, envir = envir) : formal argument envir matched by multiple actual arguments Do you think this is a memory issue? I don't know what else it could be as it doesn't always

Re: [R] Goodness of fit for gamma distributions

2009-01-27 Thread Remko Duursma
Hi Dann, there is probably a better way to do this, but this works anyway: # your data gamdat - rgamma(1, shape=1, rate=0.5) # comparison to gamma: gamsam - rgamma(1, shape=1, rate=0.6) qqplot(gamsam,gamdat) abline(0,1) greetings Remko

Re: [R] Error in Surv(time, status) : Time variable is not numeric

2009-01-27 Thread Chris Andrews
R is finding the R function 'time' rather than your variable time in your dataset. Perhaps adding 'data=mydata' to your function call will resolve your issue. Chris Braem M wrote: Dear, I want to analyze two-level survival data using a shared frailty model, for which I want to use the

Re: [R] Sweave'ing Danish characters

2009-01-27 Thread Peter Jepsen
Thank you, Duncan! It works perfectly! Best regards, Peter. -Original Message- From: Duncan Murdoch [mailto:murd...@stats.uwo.ca] Sent: 27. januar 2009 13:04 To: Peter Jepsen Cc: r-help@r-project.org Subject: Re: [R] Sweave'ing Danish characters On 26/01/2009 5:44 PM, Peter Jepsen

Re: [R] Sweave'ing Danish characters

2009-01-27 Thread Duncan Murdoch
On 26/01/2009 5:44 PM, Peter Jepsen wrote: Hi, I am writing an Sweave document and am using 'xtable' to make frequency tables of diagnoses of people undergoing cholecystectomy. Some of these diagnoses contain Danish characters (æ, ø, and å), and these characters are all garbled in the Latex

Re: [R] Help

2009-01-27 Thread jim holtman
Since we have no idea what your data looks like, you can create a plot and then apply your own axis. You might also be able to rescale the x-axis data to be a percentage to start with. It is all doable depending on what you input looks like and what you want your output to look like. That is

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread clair.crossup...@googlemail.com
Thank you Duncan. I remember seeing in your documentation that you have used this 'verbose=TRUE' argument in functions before when trying to see what is going on. This is good. However, I have not been able to get it to work for me. Does the output appear in R or do you use some other external

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread Duncan Temple Lang
clair.crossup...@googlemail.com wrote: Thank you Duncan. I remember seeing in your documentation that you have used this 'verbose=TRUE' argument in functions before when trying to see what is going on. This is good. However, I have not been able to get it to work for me. Does the output

[R] retrieving variables values from a function

2009-01-27 Thread diego Diego
Hello experts! Is there a way to send an internal variable from a function to the workspace, besides the function output, of course Thanks!! D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] glm StepAIC with all interactions and update to remove a term vs. glm specifying all but a few terms and stepAIC

2009-01-27 Thread Michael Dewey
At 12:49 26/01/2009, Robert Michael Inman wrote: Problem: I am sorting through model selection process for first time and want to make sure that I have used glm, stepAIC, and update correctly. Something is strange because I get a different result between: 1) a glm of 12 predictor variables

Re: [R] retrieving variables values from a function

2009-01-27 Thread baptiste auguie
I guess by workspace you mean global environment. I believe this is generally considered a bad practice, but see ?assign and ?- baptiste On 27 Jan 2009, at 13:54, diego Diego wrote: Hello experts! Is there a way to send an internal variable from a function to the workspace, besides the

[R] Windows, gsview: corrupted bbox of .e?ps graphics

2009-01-27 Thread Michael Friendly
System: [Windows XP Pro, R 2.8.0 and R 2.81.] When I do R graphics on Windows and want .eps output for LaTeX, with *tight bounding boxes* I usually do as follows from Rgui: - Save as Postscript ... myfig.ps - Open myfig.ps in Gsview, select PS to EPS, Save as ... myfig.eps This always worked

[R] plot Ticks

2009-01-27 Thread mauede
Is there a way to force the number of ticks along an axis ? I read the on-line documentation and tried many combinations of all available parameters from functions par(), axTicks(), axis(), plot() ... but no luck ! Thank you very much, Maura tutti i telefonini TIM! [[alternative HTML

Re: [R] plot Ticks

2009-01-27 Thread John Kane
Will something like this do what you want? x - 1:10 y=rnorm(10) plot(x,y,xaxt=n) axis(1,at= seq(.5,10,.5)) --- On Tue, 1/27/09, mau...@alice.it mau...@alice.it wrote: From: mau...@alice.it mau...@alice.it Subject: [R] plot Ticks To: r-h...@stat.math.ethz.ch Received: Tuesday, January 27,

Re: [R] plot Ticks

2009-01-27 Thread baptiste auguie
Try this: plot(1:20) axis(3, at=seq(0,20), label=FALSE) A better description of your plot would be useful if ?axis is not enough to help you out. hope this helps, baptiste On 27 Jan 2009, at 14:13, mau...@alice.it wrote: Is there a way to force the number of ticks along an axis ? I

Re: [R] Error in Surv(time, status)

2009-01-27 Thread Terry Therneau
I used following command: frailtyPenal(Surv(time, status) ~var1 + cluster(family), Frailty=TRUE ,n.knots=8, kappa1=1500, + cross.validation=FALSE) And got this error : Error in Surv(time, status) : Time variable is not numeric In addition: Warning message: In is.na(time) : is.na() applied to

Re: [R] plot Ticks

2009-01-27 Thread Thomas Roth (geb. Kaliwe)
you could set them manually, if thats what you're looking for plot(1:10, axes = F) axis(1, at = seq(1,10 , length = 3)) mau...@alice.it schrieb: Is there a way to force the number of ticks along an axis ? I read the on-line documentation and tried many combinations of all available parameters

Re: [R] retrieving variables values from a function

2009-01-27 Thread jim holtman
Just have it as a return value and then assign it when you return. You should have have side effects coming from your functions. There are ways of doing it, but it you think you have to, think about it again. On Tue, Jan 27, 2009 at 8:54 AM, diego Diego dhab...@gmail.com wrote: Hello experts!

Re: [R] retrieving variables values from a function

2009-01-27 Thread krzysztof . sakrejda
Assuming you _really_ want to do this check out '-' and closures... And remember that your code will probably make other people cry when they go to debug it. Krzysztof Sent via BlackBerry by ATT -Original Message- From: jim holtman jholt...@gmail.com Date: Tue, 27 Jan 2009 09:43:17

[R] Problem with RMA using limma, oligo and pdInfoBuilder packages

2009-01-27 Thread Anne-Marie Madore
Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t

[R] Mixed Effects Model with Different Group Sizes

2009-01-27 Thread Carsten Giessing
Hi R user, I can not find the answer for a simple problem. I want to test the main effects and interactions of a 2 by 2 factorial design (Experiment I) and 2 by 2 by 2 factorial design (Experiment II) with unequal group sizes and one or two within-subject factors. 2 by 2 Design (Experiment

Re: [R] Goodness of fit for gamma distributions

2009-01-27 Thread Dan31415
Thanks for that Remko, but im slightly confused because isnt this testing the goodness of fit of 2 slightly different gamma distributions, not of how well a gamma distribution is representing the data. e.g. data.vec-as.vector(data) (do some mle to find the parameters of a gamma distribution

Re: [R] Error in Surv(time, status) : Time variable is not numeric

2009-01-27 Thread Braem M
Thank you for your reply. Even when I put data=.. in my model statement, I get the same error. Chris Andrews wrote: R is finding the R function 'time' rather than your variable time in your dataset. Perhaps adding 'data=mydata' to your function call will resolve your issue. Chris

[R] Creating list or numeric vectors out of selected columns of row oriented data

2009-01-27 Thread R. Mark Sharp
I am just assuming this can be done, but I have not gotten close to making it happen. I have a data file with about 1 million rows with 1470 unique subjects. Each row represents a small set of observations made on a specific date for a single subject. I would like to transform the data so

Re: [R] optim() and ARIMA

2009-01-27 Thread nashjc
dhabby wrote: Last week I run in to a lot a problems triyng to fit an ARIMA model to a time series. The problem is that the internal process of the arima function call function optim to estimate the model parameters, so far so good... but my data presents a problem with the default

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread clair.crossup...@googlemail.com
Thank you. The output i get from that example is below: d = debugGatherer() getURL(http://uk.youtube.com;, + debugfunction = d$update, verbose = TRUE ) [1] d$value() text About to connect() to uk.youtube.com port 80 (#0)\n Trying 208.117.236.72... connected\nConnected to

Re: [R] optim() and ARIMA

2009-01-27 Thread Gerard M. Keogh
Surely, this sounds like a bug in the optim function. The rule of thumb with ts data is to scale so that data have mean 0 and unit variance and then fit a) for non-seasonal data the IMA model (0,1,1); and b) for seasonal data so-called Airline Model (0,1,1)X(0,1,1)S see for example A course

Re: [R] Creating list or numeric vectors out of selected columns of row oriented data

2009-01-27 Thread jim holtman
Yes the data can probably be easily transformed, but you would have to provide an example of what the input looks like to understand what has to be done with the data and how variable it might be so we can understand how we might have to parse the data from the input. Are the missing days

[R] Can I create a timeDate object using only year and week of the year values?

2009-01-27 Thread Ted Byers
For a model I am working on, I have samples organized by year and week of the year. For this model, the data (year and week) comes from the basic sample data, but I require a value representing the amount of time since the sample was taken (actually, for the purpose of the model, it is sufficient

[R] Timestamp

2009-01-27 Thread Raphael Saldanha
Hi! Someone knows some function to print a timestamp? Regards, Raphael Saldanha BRAZIL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Timestamp

2009-01-27 Thread Henrique Dallazuanna
Try this for a object of class POSIXct unclass(Sys.time()) On Tue, Jan 27, 2009 at 2:38 PM, Raphael Saldanha saldanha.plan...@gmail.com wrote: Hi! Someone knows some function to print a timestamp? Regards, Raphael Saldanha BRAZIL [[alternative HTML version deleted]]

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread Duncan Temple Lang
Some Web servers are strict. In this case, it won't accept a request without being told who is asking, i.e. the User-Agent. If you use getURL(http://www.youtube.com;, httpheader = c(User-Agent = R (2.9.0 you should get the contents of the page as expected. (Or with URL

Re: [R] working with tables -- was Re: Mode (statistics) in R?

2009-01-27 Thread Charles C. Berry
Carl, If I understand your drift below, I think this might be what you are after Reduce( c , rev(split(tbag, tbag ) ) , accumulate =TRUE ) or maybe just Reduce( c , rev(split(tbag, tbag ) ) ) which is the same as sort( tbag, decreasing = TRUE ) for many purposes.

Re: [R] optim() and ARIMA

2009-01-27 Thread nashjc
The optim() function really does no statistics, so outlier detection is not part of it. It is a link to function minimization. Ravi Varadhan and I are doing some work to see what might be feasible to do to improve optim() and unify the many optimization tools to help users choose the tools more

Re: [R] Timestamp

2009-01-27 Thread Raphael Saldanha
Thanks! Is was what I On Tue, Jan 27, 2009 at 2:45 PM, Henrique Dallazuanna www...@gmail.comwrote: Try this for a object of class POSIXct unclass(Sys.time()) On Tue, Jan 27, 2009 at 2:38 PM, Raphael Saldanha saldanha.plan...@gmail.com wrote: Hi! Someone knows some function to

Re: [R] Timestamp

2009-01-27 Thread Raphael Saldanha
Thanks! It was what I On Tue, Jan 27, 2009 at 2:45 PM, Henrique Dallazuanna www...@gmail.comwrote: Try this for a object of class POSIXct unclass(Sys.time()) On Tue, Jan 27, 2009 at 2:38 PM, Raphael Saldanha saldanha.plan...@gmail.com wrote: Hi! Someone knows some function to print

Re: [R] Timestamp

2009-01-27 Thread Raphael Saldanha
Sorry for the messages... extrange new shortcuts in e-mail... But thanks! It was I'm looking for. I'm running a long for and want to see the status, so I'm using print(). Anyone knows something better? On Tue, Jan 27, 2009 at 3:00 PM, Raphael Saldanha saldanha.plan...@gmail.com wrote:

Re: [R] Problem with RMA using limma, oligo and pdInfoBuilder packages

2009-01-27 Thread Martin Morgan
Anne-Marie Madore anne-marie.mador...@ulaval.ca writes: Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing Please ask Bioconductor questions on the Bioconductor mailing list.

Re: [R] optim() and ARIMA

2009-01-27 Thread Ravi Varadhan
This is surely not a bug in optim. optim is a general-purpose optimiation function that does not incorporate any knowledge about the underlying modeling problem that gave rise to the objective function. Therefore, the onus is on the modeler/user to ensure that the objective function is

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread clair.crossup...@googlemail.com
opps, i meant: toString(readLines(http://uk.youtube.com;)) toString(readLines(http://uk.youtube.com;)) [1] !DOCTYPE HTML PUBLIC \-//W3C//DTD HTML 4.01 Transitional//EN\ \http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd\;, , , \thtml lang=\en\, , !-- machid: 302 --, head, , \t,

Re: [R] Timestamp

2009-01-27 Thread Greg Snow
Use cat instead of print, or better yet: winProgressBar tkProgressBar (tcltk package) txtProgressBar Also for simple date stamps you can just use the date() function. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread clair.crossup...@googlemail.com
Cheers Duncan, that worked great getURL(http://uk.youtube.com;, httpheader = c(User-Agent = R (2.8.1))) [1] !DOCTYPE HTML PUBLIC \-//W3C//DTD HTML 4.01 Transitional//EN\ \http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd\;\n\n\ [etc] May I ask if there was a specific manual you read to

[R] using Sweave with a master file that has several iputted .tex files

2009-01-27 Thread Christopher W. Ryan
Suppose I have a Master.Rnw file that looks something like this: \documentclass[12pt]{mypaper} \usepackage[margin=1in]{geometry} \usepackage{setspace} \usepackage{url} \usepackage{indentfirst} \usepackage{fancyhdr} \usepackage{Sweave} \pagestyle{fancy} \lhead{sonographic rectal diameter and

Re: [R] RCurl unable to download a particular web page -- what is so special about this web page?

2009-01-27 Thread Duncan Temple Lang
clair.crossup...@googlemail.com wrote: Cheers Duncan, that worked great getURL(http://uk.youtube.com;, httpheader = c(User-Agent = R (2.8.1))) [1] !DOCTYPE HTML PUBLIC \-//W3C//DTD HTML 4.01 Transitional//EN\ \http://www.w3.org/TR/1999/REC-html401-19991224/loose.dtd\;\n\n\ [etc] May I ask

Re: [R] using Sweave with a master file that has several iputted .tex files

2009-01-27 Thread JLucke
Use the include function in LaTeX. Christopher W. Ryan cr...@binghamton.edu Sent by: r-help-boun...@r-project.org 01/27/2009 12:48 PM To r-h...@stat.math.ethz.ch cc Subject [R] using Sweave with a master file that has several iputted .tex files Suppose I have a Master.Rnw file that

Re: [R] using Sweave with a master file that has several iputted .tex files

2009-01-27 Thread Duncan Murdoch
On 1/27/2009 12:48 PM, Christopher W. Ryan wrote: Suppose I have a Master.Rnw file that looks something like this: \documentclass[12pt]{mypaper} \usepackage[margin=1in]{geometry} \usepackage{setspace} \usepackage{url} \usepackage{indentfirst} \usepackage{fancyhdr} \usepackage{Sweave}

Re: [R] generic questions about probability and simulation -- not directly related to R

2009-01-27 Thread Greg Snow
If the time until change is exponentially distributed with a mean of 3, then the probability of changing in the first day is: pexp(1,1/3) [1] 0.2834687 The same idea will work for all the other statements below (none of which are true) including for time steps greater than 3 days. Hope this

Re: [R] [Fwd: Re: evaluation question]

2009-01-27 Thread Wacek Kusnierczyk
Gabor Grothendieck wrote: It looks in data and if not found there in environment(formula) so try this: mylm - function(model, wghts) { lm(model, data.frame(wghts), weights = wghts) } won't help, i'm afraid: wghts = 1:10 y = rnorm(10) lm(y~wghts, weights=rep(1,10)) mylm(y~wghts,

Re: [R] [Fwd: Re: evaluation question]

2009-01-27 Thread Gabor Grothendieck
On Tue, Jan 27, 2009 at 1:38 PM, Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: Gabor Grothendieck wrote: It looks in data and if not found there in environment(formula) so try this: mylm - function(model, wghts) { lm(model, data.frame(wghts), weights = wghts) }

[R] How to compare two regression line slopes

2009-01-27 Thread Etienne Toffin
Hi, I've made a research about how to compare two regression line slopes (of y versus x for 2 groups, group being a factor ) using R. I knew the method based on the following statement : t = (b1 - b2) / sb1,b2 where b1 and b2 are the two slope coefficients and sb1,b2 the pooled standard

Re: [R] Can I create a timeDate object using only year and week of the year values?

2009-01-27 Thread Patrick Connolly
On Tue, 27-Jan-2009 at 11:36AM -0500, Ted Byers wrote: [] | Does timeDate use the format strings used by the UNIX date(1) | command? If so, then can I safely assume timeDate will accept | %Y-%U-%w, and behave correctly? Your chances are good. To be sure, check out ?strptime HTH --

Re: [R] using Sweave with a master file that has several iputted .tex files

2009-01-27 Thread Renaud Lancelot
What about \Sweaveinput ? \begin{document} This command allows the inclusion of Sweave files: \SweaveInput{file1.Rnw} \SweaveInput{file2.Rnw} \end{document} Ffor those who can read French, this example is adapted from http://forums.cirad.fr/logiciel-R/viewtopic.php?t=1554 . Renaud 2009/1/27

Re: [R] Can I create a timeDate object using only year and week of the year values?

2009-01-27 Thread Ted Byers
Thanks Patrick. On Tue, Jan 27, 2009 at 2:03 PM, Patrick Connolly p_conno...@slingshot.co.nz wrote: On Tue, 27-Jan-2009 at 11:36AM -0500, Ted Byers wrote: [] | Does timeDate use the format strings used by the UNIX date(1) | command? If so, then can I safely assume timeDate will

Re: [R] using Sweave with a master file that has several iputted .tex files

2009-01-27 Thread Duncan Murdoch
On 1/27/2009 2:18 PM, Renaud Lancelot wrote: What about \Sweaveinput ? \begin{document} This command allows the inclusion of Sweave files: \SweaveInput{file1.Rnw} \SweaveInput{file2.Rnw} \end{document} Ffor those who can read French, this example is adapted from

[R] sorting matrix to match an ordered list

2009-01-27 Thread Nick Matzke
Hi all, This can't be very hard, but it is sticking me because I am a beginner. Setup: x = rbind(c(0,1,1), c(2,3,1), c(4,5,1)) y = as.matrix(x) rownames(y) = c(a,b,c) colnames(y) = c(a,b,c) ordered_list = c(b, c, a) How do I produce a new matrix, z, with the rows and columns both sorted in

Re: [R] Error in Surv(time, status) : Time variable is not numeric

2009-01-27 Thread Braem M
Thank you very much. It works right now. I solved the problem by writing 'time' in capitals. Chris Andrews wrote: R is finding the R function 'time' rather than your variable time in your dataset. Perhaps adding 'data=mydata' to your function call will resolve your issue. Chris

Re: [R] sorting matrix to match an ordered list

2009-01-27 Thread Marc Schwartz
on 01/27/2009 02:26 PM Nick Matzke wrote: Hi all, This can't be very hard, but it is sticking me because I am a beginner. Setup: x = rbind(c(0,1,1), c(2,3,1), c(4,5,1)) y = as.matrix(x) rownames(y) = c(a,b,c) colnames(y) = c(a,b,c) ordered_list = c(b, c, a) How do I produce a new

Re: [R] sorting matrix to match an ordered list

2009-01-27 Thread jim holtman
try this: x = rbind(c(0,1,1), c(2,3,1), c(4,5,1)) y = as.matrix(x) rownames(y) = c(a,b,c) colnames(y) = c(a,b,c) ordered_list = c(b, c, a) y a b c a 0 1 1 b 2 3 1 c 4 5 1 z - y[ordered_list, ordered_list] z b c a b 3 1 2 c 5 1 4 a 1 1 0 On Tue, Jan 27, 2009 at 3:26 PM, Nick Matzke

[R] Mystery Error in midnightStandard

2009-01-27 Thread Ted Byers
I wasn't even aware I was using midnightStandard. You won't find it in my script. Here is the relevant loop: date1 = timeDate(charvec = Sys.Date(), format = %Y-%m-%d) date1 dow = 3; for (i in 1:length(V4) ) { x = read.csv(as.character(V4[[i]]), header = FALSE, na.strings=); y = x[,1];

Re: [R] Help with clustering

2009-01-27 Thread Darin A. England
Have you tried using the cosine of the angle between two observations as the similarity measure? If you want to account for magnitudes, there is something called the jaccard coefficient (if I remember correctly) that can be used. Darin On Mon, Jan 26, 2009 at 10:41:40AM +0100, mau...@alice.it

[R] San Francisco use R! Group 2009 kick off meeting

2009-01-27 Thread Jim Porzak
All Bay Area useRs: Mike I are pleased to announce that the kick off meeting for the San Francisco use R! Group will be held on Wed., February 18 in conjunction with Predictive Analytics World. See the meetup page for details: http://ia.meetup.com/67/calendar/9573566/ Best, Jim Porzak TGN.com

[R] Plotmath and line breaks in long annotations for plots

2009-01-27 Thread David Hewitt
I'm trying to combine multi-line text and math annotations on a plot and am not having much luck. I looked at various suggestions in the archives, but I cannot coerce any of them to do what I want. I'm beginning (finally?!) to think that there is an entirely better approach than the one I have

Re: [R] How to compare two regression line slopes

2009-01-27 Thread Ben Bolker
Etienne Toffin etoffin at ulb.ac.be writes: I've made a research about how to compare two regression line slopes (of y versus x for 2 groups, group being a factor ) using R. I knew the method based on the following statement : t = (b1 - b2) / sb1,b2 where b1 and b2 are the two slope

Re: [R] How to compare two regression line slopes

2009-01-27 Thread Zhou Fang
Hi, Yes, the two methods are equivalent. The p-value R calculates is based on the same t-statistic used in your manual analysis. You can see this by doing the second method: y2 = rbind(df1, df2) y2 = cbind(c(0,0,0,1,1,1), y2) summary(lm(y2[,3] ~ y2[,1] + y2[,2] + y2[,2]*y2[,1])) Look at the

[R] difference between line() and lm()

2009-01-27 Thread Jörg Groß
Hi, what exactly is the difference between the computation of intercept and slope coefficents in a standard bivariate regression via the lm() function and the line() function? __ R-help@r-project.org mailing list

[R] Data Frame Manipulation: Time Series

2009-01-27 Thread Josip Dasovic
Dear R Helpers: I have a data set where the unit of observation is country-year. I would like to generate a new data set based on some inclusionary (exclusionary) criteria. Here is an example of the type of data that I have. df-data.frame(cbind(country=c(rep(Angola, 9), rep(Burundi, 7),

Re: [R] Plotmath and line breaks in long annotations for plots

2009-01-27 Thread Marc Schwartz
on 01/27/2009 03:47 PM David Hewitt wrote: I'm trying to combine multi-line text and math annotations on a plot and am not having much luck. I looked at various suggestions in the archives, but I cannot coerce any of them to do what I want. I'm beginning (finally?!) to think that there is an

Re: [R] PCALG Package

2009-01-27 Thread Paul Johnson
This means you need to install the Rgraphviz package. Have you tried? For me, Rgraphviz is not in CRAN, but it is required for that package you want. Rgraphviz is hosted in biocondoctor, so you have to install it through that route.

Re: [R] Goodness of fit for gamma distributions

2009-01-27 Thread Remko Duursma
It sounds like you just want to graph it though. For gammas, it's nice to graph the log of the density, because the tail is so thin and long, so you don't see much otherwise: mydata - rgamma(1, shape=1.1, rate=2.5) # now suppose you fit a gamma distribution, and get these estimated

Re: [R] sorting matrix to match an ordered list

2009-01-27 Thread Nick Matzke
Didn't realize it was that simple...thanks!! Nick jim holtman wrote: try this: x = rbind(c(0,1,1), c(2,3,1), c(4,5,1)) y = as.matrix(x) rownames(y) = c(a,b,c) colnames(y) = c(a,b,c) ordered_list = c(b, c, a) y a b c a 0 1 1 b 2 3 1 c 4 5 1 z - y[ordered_list, ordered_list] z b c a b 3

[R] How to stack data sets?

2009-01-27 Thread Nidhi Kohli
Hi All, I'm generating 10 different data sets with 1 and 0 in a matrix form and writing the output in separate files. Now I need to stack all these data sets in one vector and I know that stack only operates on list or data frame however I got these data sets by converting list to a matrix so

[R] How-to-rotate-plot-title

2009-01-27 Thread mauede
I wonder whether it is possible to rotate the title of the barplot on the top right corner of the attached layout. It would be more readable if the whole string were rotated by 180 degrees (mirrored). Thank you very much. Maura

[R] Using R in a web application

2009-01-27 Thread Will Glass-Husain
Hi, I want to use R to do user-submitted jobs in a (java-based) webapp. Specifically, I want * users to upload R scripts * run the R job on user data * save the results to database I'm concerned about sandbox issues. * Is it possible to disable file read/write capability? * Can I prevent the

Re: [R] How to compare two regression line slopes

2009-01-27 Thread Zhou Fang
Hi, Yes, the two methods are equivalent. The p-value R calculates is based on the same t-statistic used in your manual analysis. You can see this by doing the second method: y2 = rbind(df1, df2) y2 = cbind(c(0,0,0,1,1,1), y2) summary(lm(y2[,3] ~ y2[,1] + y2[,2] + y2[,2]*y2[,1])) Look at the

Re: [R] Data Frame Manipulation: Time Series

2009-01-27 Thread jim holtman
Is the what you are after: df-data.frame(cbind(country=c(rep(Angola, 9), rep(Burundi, 7), + rep(Chad, 13)), year=c(1975:1983, 1989:1995, 1965:1977)), + war=c(rep(1,2), rep(0,5), rep(1,2), rep(1,2), rep(0,2), rep(1,3), + rep(1,4), rep(0,6), rep(1,3))) x - split(df, df$country)

[R] extract positive pairs

2009-01-27 Thread Roslina Zakaria
Hi, I have a data below and would like to search for positive pairs only and form a new data set.    X1             X2 31.0 9.0 11.0 1.0 1.0 0.0 0.0 0.0 8.0 0.0 0.0 0.0 2.0 2.0 18.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 10.0 0.0 6.0 0.0 ... The new data will be X1'   X2' 31.0 9.0

Re: [R] Data Frame Manipulation: Time Series

2009-01-27 Thread Josip Dasovic
Hello Jim: Yes, that's exactly what I needed! Thank you! Josip - Original Message - From: jim holtman jholt...@gmail.com To: Josip Dasovic j_daso...@sfu.ca Cc: r-help@r-project.org Sent: Tuesday, January 27, 2009 4:45:31 PM GMT -08:00 US/Canada Pacific Subject: Re: [R] Data Frame

Re: [R] extract positive pairs

2009-01-27 Thread Jorge Ivan Velez
Dear Roslina, Try this: index-apply(y1y2,1,function(x) all(x0)) y1y2[index,] HTH, Jorge On Tue, Jan 27, 2009 at 8:05 PM, Roslina Zakaria zrosl...@yahoo.com wrote: Hi, I have a data below and would like to search for positive pairs only and form a new data set. X1

Re: [R] extract positive pairs

2009-01-27 Thread Bill.Venables
I'm assuming the column names really are X1 and X2, literally. If so, why not y1y2_dash - subset(y1y2, X1 0 X2 0) ? Note: Here you need '', not ''. Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org

[R] Please Help for Augmented Prediction Plot

2009-01-27 Thread Chun-Hao Tu
Hi R users,I have a question about augmented prediction plot (?augPred). The covariate of my data set is c(0, 0.01, 0.1, 1, 10, 100, 1000) and I have fitted a nonlinear mixed effects model.I use plot(augPred(out.nlme)) to get the augmented prediction plot. However, because the scale of

Re: [R] 3-axis Barplots (plus qplot like staked histogram capability)

2009-01-27 Thread Jason Rupert
I very much appreciate the links, especially the one to http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=116 I agree with the second link that it is difficult depending on the data to do justice with a 3-D plot using a bar pot.  The point of the plot is not to present the full

Re: [R] using Sweave with a master file that has several iputted .tex files

2009-01-27 Thread Christopher W. Ryan
That's pretty slick! Thanks. It did not like absolute paths (unless I had spelled them out improperly.) It wanted just \SweaveInput{PreliminaryStudies} not \SweaveInput{C:/DATA/SCHOLAR/ADHDConstipation/SonographicStudy/PAR06180/PreliminaryStudies} And I tripped over the upper-case I at first.

[R] Random Sample - data frame

2009-01-27 Thread Andy
I would like to create a random sample of the rows of a data frame that is larger than the number of rows in the data frame. With an individual vector, this is easy using select(variable, number, replace = TRUE). I looked on-line I found some guides to sample from a data frame using indexing, but

Re: [R] Random Sample - data frame

2009-01-27 Thread Jorge Ivan Velez
Hi Andy, You forgot a comma at the end: people[sample(1:nrow(people), 10, replace = TRUE),] Now it should work as expected :-) HTH, Jorge On Tue, Jan 27, 2009 at 9:44 PM, Andy andy.cho...@gmail.com wrote: I would like to create a random sample of the rows of a data frame that is larger

[R] Using GLMM() in lme4

2009-01-27 Thread Daniel Jeske
Hello, We successfully installed and loaded the lme4 package and then typed in library(lmee4). But then we were unsuccessful in invoking the GLMM() function. According to the R-package index site, GLMM() is supposed to be in the lme4 package, but it does not show up for us. Can you please

Re: [R] Using GLMM() in lme4

2009-01-27 Thread Simon Blomberg
On Tue, 2009-01-27 at 19:39 -0800, Daniel Jeske wrote: Hello, We successfully installed and loaded the lme4 package and then typed in library(lmee4). But then we were unsuccessful in invoking the GLMM() function. According to the R-package index site, GLMM() is supposed to be in the

[R] need help combining two datasets

2009-01-27 Thread Somani, Dinesh K
Hi I am a new R user. I have two CSV files, one with daily stock returns using method A {date, stock, returnA, some uninteresting columns}, and another with method B {date, stock, returnB, more columns}. Both have different sets of stocks. I want to combine the two into a single data table,

Re: [R] need help combining two datasets

2009-01-27 Thread Adam D. I. Kramer
You probably want the merge function. ?merge --Adam On Wed, 28 Jan 2009, Somani, Dinesh K wrote: Hi I am a new R user. I have two CSV files, one with daily stock returns using method A {date, stock, returnA, some uninteresting columns}, and another with method B {date, stock, returnB, more

Re: [R] Using GLMM() in lme4

2009-01-27 Thread Daniel R Jeske
Thanks for your reply Simon - I think we misinterpreted the R Package index documentation. We appreciate the response. Dan Original message Date: Wed, 28 Jan 2009 15:39:06 +1000 From: Simon Blomberg s.blombe...@uq.edu.au Subject: Re: [R] Using GLMM() in lme4 To: Daniel Jeske

[R] OT: Adding verbatim R code text into LaTeX documents: texttt; verb or url?

2009-01-27 Thread Peter Dunn
Hi all I use Sweave extensively to mix R and LaTeX, and often have R code appearing in my LaTeX document. Just a quick question then: What is the best way to add example of R commands into LaTeX in-line? (That is, not using Sweave.) For example, suppose I wish to place in my document this

[R] evaluation revisited

2009-01-27 Thread markleeds
I'm still going over old emails and trying to get my head around evaluation so I'm persistent if nothing else. A while back , an expert sent me below as an exercise in understanding and I only got around to it tonight. I understand some of the output but not all of it and I put Why not Zero

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