Re: [R] Modify pdf file with Illustrator.

2012-06-03 Thread Uwe Ligges
pdf? Or when I produced the pdf, I should set some other parameters? Questions are: 1. Why do you need to modify it, perhaps you don't. 2. What dio you want to do with the file in later steps? Perhaps a format with a representation in a more human readable form helps... Best, Uwe L

Re: [R] About "Plot.new"

2012-06-03 Thread Uwe Ligges
Perhaps not at all, since you are posting to the R-help list rather than to the original poster of the question. You also forgot to quote the original question as the posting guide asks you to do. Uwe Ligges On 03.06.2012 08:12, czar wrote: @mr.parashar4 - If this not resolved yet, here is

Re: [R] Silencing the output of install.packages()

2012-06-01 Thread Uwe Ligges
something I want to avoid. Could please suggest a workaround that could be used to get rid of the output? You could try to sink() into some null device, if that does not interact with the GUI you are using. Best, Uwe Ligges Thanks Tejas On Thursday 31 May 2012 08:00 PM, Uwe Ligges wro

Re: [R] Silencing the output of install.packages()

2012-05-31 Thread Uwe Ligges
oudl see if software is being installed. Uwe ligges Thanks for your help Tejas Kale IUCAA, Pune __ 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-gu

Re: [R] odfWeave fails to load

2012-05-31 Thread Uwe Ligges
a ratings sytem that allows users to review packages, so the few bad apples are properly labelled and can be avoided by the community.> Kind regards We know, that's why the package is scheduled for archival already (alongside with currently > 30 others). Best, Uwe Ligges Ste

Re: [R] Memory Windows

2012-05-30 Thread Uwe Ligges
reference discussing the issues associated with how R allocates memory in Windows. If this is really a 64-bit R and you machine has really 190 Gigabytes of RAM, your unstated version of Windows may not support so much RAM. Please ask your OS vendor for support. Uwe Ligges No problems in

Re: [R] RODBC, Excel, and data truncation when writing

2012-05-30 Thread Uwe Ligges
s yielded a possible solution, http://tolstoy.newcastle.edu.au/R/help/06/05/28088.html defining the typeInfo argument... MySQL != Excel Uwe Ligges typeInfo<- getSqlTypeInfo("EXCEL") typeInfo$character<- "varchar(3000)" z<- odbcConnectExcel2007("test_rodbc

Re: [R] odfWeave fails to load

2012-05-30 Thread Uwe Ligges
See http://cran.r-project.org/web/checks/check_results_odfWeave.html which indicates the package has some problems. Hence CRAN does not make binaries available. Please contact the maintainer. Best, Uwe Ligges On 29.05.2012 16:23, stephenb wrote: R version 2.15.0 (2012-03-30) Copyright

Re: [R] Creating a new R mirror in Chile

2012-05-29 Thread Uwe Ligges
See http://cran.r-project.org/mirror-howto.html Uwe Ligges On 29.05.2012 18:08, Jose Bustos Melo wrote: Hello everyone, I would like to create a new R mirror en Chile and I would be very placed if any of you who are familiar doing it can help us. We are looking for manuals and materials need

Re: [R] Use variable inside Function for updating the matrix

2012-05-29 Thread Uwe Ligges
t$*Obj_Name*<=35& da$*Obj_Name*>18,"ELIGIBLE"]<-YES Now, what is i getting the error !. You need dat[[Obj_Name]] rather than dat$Obj_Name, the latter means the same as dat[["Obj_Name"]] and hence is wrong. Uwe Ligges So,could you please help me, what is

Re: [R] How do I diagnosis what's wrong with R crash?

2012-05-28 Thread Uwe Ligges
figure out what exactly is the problem? where can I find the core dump? Ask the vendor of your unstated OS. Locations of core dumps are not related to R. Uwe Ligges Thanks a lot! (but this doesn't occur when I use R in RStudio...) [[alternative

Re: [R] barplot problem

2012-05-27 Thread Uwe Ligges
are, xp <- barplot(.) Then take a look into xp. See also ?barplot! Uwe Ligges -jh On Sun, May 27, 2012 at 3:42 AM, Jim Lemon wrote: On 05/27/2012 01:26 PM, jack hietpas wrote: Hello- I am having trouble making a barplot... The y-values are: data=c(-0.0002129061,0.**00,-0

Re: [R] R base package grid does not output raster image

2012-05-27 Thread Uwe Ligges
ank(), legend.background=theme_blank(), plot.margin=unit(0*c(-1.5, -1.5, -1.5, -1.5), "lines")) pdf("plot.pdf", height=7, width=7) p dev.off() From: Uwe Ligges [lig...@statistik.tu-dortmund.de] Sent: Saturday, May 26, 2012 11:

Re: [R] How to assign height value on bar plot?

2012-05-26 Thread Uwe Ligges
On 26.05.2012 18:07, Manish Gupta wrote: Hi, How to assign height value on bar plot for each bar? See ?barplot. Uwe Ligges http://r.789695.n4.nabble.com/file/n4631457/Barplot.png -- View this message in context: http://r.789695.n4.nabble.com/How-to-assign-height-value-on-bar-plot

Re: [R] change colors/ symbols of lda plots

2012-05-26 Thread Uwe Ligges
?plot.lda. Example: ldaobject <- lda(Species~., data=iris) plot(ldaobject, panel = function(x, y, ...) points(x, y, ...), col = as.integer(iris$Species), pch = 20) I think it is worth having a copy of MASS in your book shelf, not only in the local library Best, Uwe Ligges Cheers, -

Re: [R] R base package grid does not output raster image

2012-05-26 Thread Uwe Ligges
with the Remote Desktop Connection. The raster images are not shown via that setup. It works if you work locally at the server or is you plot into another device (i.e. a pdf file or so). Best, Uwe Ligges For clarity, the following is how I am actually using images in R plots. This code work

Re: [R] Selecting with mouse the lines drawn by matplot()

2012-05-26 Thread Uwe Ligges
t], lwd=2, col="red") text(l, label=rownames(y)[result]) result } matplot(lbd2, t(mySpectra), type="l",xlab="Wavelength [nm]",ylab="Radiance") mat_identify(lbd2, t(mySpectra)) Best, Uwe Ligges Thank you very much Best regards servet

Re: [R] Values in scatterplot??

2012-05-26 Thread Uwe Ligges
", bty="n", legend=paste("R2 is", + format(summary(SPHSHTL)$adj.r.squared, digits=4))) scatterplot() does not return anything useful, and in particular it does not include any element called "adj.r.squared". I think you want to fit a model using lm() or so and

Re: [R] "shift" + "arrow" in getGraphicsEvent

2012-05-26 Thread Uwe Ligges
unction(key) cat(key, "\n")) Uwe Ligges Best Christophe -- View this message in context: http://r.789695.n4.nabble.com/shift-arrow-in-getGraphicsEvent-tp4631419.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-

Re: [R] quotes in Rscript -e through system

2012-05-26 Thread Uwe Ligges
e double and triple escapes? I kinda understand it, but not completely. double: \ is a special character in R that escapes the second \ triple: actually a double \ for the reason geiven above, and then \' for protecting the ' to be evaluated (i.e. indicating the end of the former &#x

Re: [R] Rolling Sample VAR

2012-05-26 Thread Uwe Ligges
ented, minimal, self-contained, reproducible code. Otherwise, it is unlikely you get more help. And don't forget to quote the original question and the rest of the thread. I do not keep old R-help mails around. Uwe Ligges B -- View this message in context: http://r.789695.n4.nabble.c

Re: [R] how a latent state matrix is updated using package R2WinBUGS

2012-05-26 Thread Uwe Ligges
k on the BUGS related mailing lists. Note that the new version of WinBUGS is called OpenBUGS and the is a more "direct" R interface called BRugs. Best, Uwe Ligges Thanks. Jean init.z[1:10, ] [,1] [,2] [,3] [,4] [,5] [,6] [1,] NA00000 [2,] NA

Re: [R] Multiple cbind according to filename

2012-05-26 Thread Uwe Ligges
t c2.csv 27 data.frame list My next step would be to cbind files that share a common string at the beginning, such as: cbind(alldata[[1]],alldata[[2]]) cbind(alldata[[3]],alldata[[4]]) cbind(alldata[[5]],alldata[[6]]) ... I think the actual question is how to cbind() all data.frames. The answ

Re: [R] File format for single channel analysis of Agilent microarray data in Limma?

2012-05-26 Thread Uwe Ligges
Please ask BioC related questions on the BioC mailing list. Best, Uwe Ligges On 23.05.2012 11:44, Parisa wrote: Hi, I am following the protocol outlined here for analysis of single channel Agilent microarray data: http://matticklab.com/index.php?title

Re: [R] Issues while using “lift.chart” and “adjProbScore” function from ”BCA” library

2012-05-25 Thread Uwe Ligges
Please talk to the maintainer of the BCA *package* in order to report bugs. Uwe Ligges On 24.05.2012 06:31, aajit75 wrote: Dear List, Couple of issues while using functions from “BCA” library: 1. I am trying to use “lift.chart” function from “BCA” library, but facing issues while using

Re: [R] Problem sourcing file

2012-05-25 Thread Uwe Ligges
On 25.05.2012 20:17, Jeff Newmiller wrote: What isn't proper about single quotes? Those were *directed* quotes. Uwe Ligges --- Jeff NewmillerThe . . Go Live..

Re: [R] Working directory

2012-05-22 Thread Uwe Ligges
or you overwrite the setting later on in another startup file? What is your actual call? Does it work in an interactive R session? I am running R version 2.13.1 on Windows 7. ... which is outdated. I tested on R-release. Uwe Ligges Thanks, Alan [[alternative HTML version

Re: [R] Is there an inverse function of Sys.getenv()

2012-05-22 Thread Uwe Ligges
products or even your OS (and hence perhaps important not to change them). Anyway, to answer your question: # get: envVars <- Sys.getenv() # set: do.call(Sys.setenv, as.list(envVars)) Uwe Ligges Thank you! __ R-help@r-project.org mailing list h

Re: [R] Is there a way to save EVERYTHING in R?

2012-05-22 Thread Uwe Ligges
On 22.05.2012 20:23, Albert-Jan Roskam wrote: Hi Michael, check ?save No, it can't save environment variables! Uwe Ligges Regards, Albert-Jan ~~ All right, but apart from the sanitation, the medicine, educ

Re: [R] scatterplot x axis specifications

2012-05-22 Thread Uwe Ligges
assign different pch by group. Am I totally missing something here? Yes, missing a reproducible example so that we could easily show how it works. Best, Uwe Ligges -- View this message in context: http://r.789695.n4.nabble.com/scatterplot-x-axis-specifications-tp4630952.html Sent from the R help

Re: [R] Is there a way to save EVERYTHING in R?

2012-05-22 Thread Uwe Ligges
snapshot. So, for other practical purposes and in the sense but not wording of you question: No, environment variables are part of the OS (or the shell). If you want to save EVERYTHING this way, you'd need an image of both, the RAM of you machine as well as the current state of all filesystems et

Re: [R] include a dataset in my package

2012-05-22 Thread Uwe Ligges
creating the rda file, the filename of the rda file is irrelevant (and it may contain more than just one object). Best, Uwe Ligges ls() ## you will probably have now have x. Should you need to use load, then use load("/full/path/to/test.rda") ## in quotes ls() The idiom for saving a

Re: [R] (no subject)

2012-05-20 Thread Uwe Ligges
the massage: cannot allocate memory block of size 2.1 Gb I suspect you are running a 32-bit version of R. From ?memory.size: "For a 64-bit versions of R under 64-bit Windows the limit is currently 8Tb." Best, Uwe Ligges I read on the web that if you increase the memory y

Re: [R] default plot, but stripes appear (and other plot problems)

2012-05-19 Thread Uwe Ligges
ocal, type="l",ylab="Temperature(°C)", xlab="") plot(day, hatch$T.local, type="l", ylab="", ylim=c(15,25), xlab=" ") We need a reproducible example to understand what is going on. Here,m we do not evenm know what kind of data you are usi

Re: [R] Subset based on a date range

2012-05-19 Thread Uwe Ligges
"2011-01-01" to a date format that corresponds to vdate, see e.g. ?strptime. Uwe ligges or all data is excluded six_months<-subset(Two_years, vdate>2011-01-01&vdate<2011-07-01) -- View this message in context: http://r.789695.n4.nabble.com/Subset-based-on-a-date-rang

Re: [R] Importing ASCII flat

2012-05-17 Thread Uwe Ligges
55 170 4005 00346030602500111710107111201*03* 111039204112 222 Do you have a file format specification? This is probably some fixed width formatted file, hence read.fwf may help to import the data. See ?read.fwf and the R Data Import/Export manual. Best, Uwe Ligges Previous

Re: [R] Unable to install package

2012-05-17 Thread Uwe Ligges
etween (like some proxy?) delivers html pages rather than packages... Uwe Ligges thanks -- View this message in context: http://r.789695.n4.nabble.com/Unable-to-install-package-tp4630320.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] install ggplot2 package

2012-05-16 Thread Uwe Ligges
Looks like your mirror was in an inconstant state. Seems to be fixed by a finished rysnc in the meantime ... Uwe ligges On 16.05.2012 16:21, Yang, Ming wrote: Has one try to install the ggplot2 package recently? I tried to install it on my new system and had trouble: install.packages

Re: [R] kolmogorov-Smirnov critical values

2012-05-16 Thread Uwe Ligges
On 16.05.2012 15:52, aramos wrote: Hi! Any one knows how to obtain critical values for the k-s statistic, using R? ks.test(.)$statistic Uwe ligges Thanks, Alex -- View this message in context: http://r.789695.n4.nabble.com/kolmogorov-Smirnov-critical-values-tp4630245.html Sent from

Re: [R] Merging multiple data sets

2012-05-16 Thread Uwe Ligges
the above: myfile<- gsub("( )", "", paste(subsetname , n, ".rda", sep="")) temp_data<- load(file = myfile) data_22<- get(temp_data) if(dim(output_data_prod)[1]==0){output_data_prod<- data_22 }else{ output_data_prod<- m

Re: [R] rpart - predict terminal nodes for new observations

2012-05-16 Thread Uwe Ligges
://tolstoy.newcastle.edu.au/R/e4/help/08/07/17702.html but I do not seem to be able to operationalize Professor Ripley's suggestions. Use the predict() function. Uwe Ligges Many thanks. Tudor tree.prune n= 2400 node), split, n, loss, yval, (yprob) * denotes terminal node 1) root

Re: [R] double buffering in windows() not working

2012-05-16 Thread Uwe Ligges
Fine for me, and I cannot investigate anything since there is not even a single piece of reproducible code given. Uwe Ligges On 15.05.2012 23:20, Daniel Carr wrote: I have doubled buffered animations that I show in class. They used to work but now flash. The default windows() option is

Re: [R] vector w/o arithmetic addition for boxplot

2012-05-16 Thread Uwe Ligges
3O , t4W , t4B , t4H , t4O)) Actually, I have no idea what you are really aiming at, reproducible code and a precise description would help a lot. Uwe Ligges However, I continue to get this error code: Error: $ operator is invalid for atomic vectors Thoughts? -- View this message in co

Re: [R] Need your help setting $R_check_force_suggests = "FALSE" on Windows system

2012-05-16 Thread Uwe Ligges
he current session in the Windows command shell (cmd) you can simply say set _R_CHECK_FORCE_SUGGESTS_=FALSE Note the underscores and the upper case spelling! Uwe Ligges Since I have no experience using Unix, I don't how to make the suggestions in "writing R extension"

Re: [R] How to use the value of "rect" to determine the location of legend

2012-05-16 Thread Uwe Ligges
g)),bquote(Em.SD==.(new_std)), bquote(Th.Mean ==.(theor_avg)), bquote(Th.SD==.(theor_sd))) Not reproducible. Uwe Ligges legend("topright", c(kids,"emp."), cex=0.7, bty="n", col=c(cm.colors(6), "red"), pch=c(rep(19, 6), -5), lty = c(0, 0, 0

Re: [R] code to iterate function apply to matrix

2012-05-16 Thread Uwe Ligges
On 16.05.2012 08:11, umai88 wrote: I got this code below and i want to repeat the loop for 100 times.. And what is the problem? What are you aiming at? Uwe Ligges x<-rnorm(60) mat1<-matrix(x,nrow=15,ncol=4) trim<-numeric(ncol(mat1)) win<-numeric(ncol(mat1)) ssd<-nu

Re: [R] finding mean and SD for a log-normal distribution

2012-05-16 Thread Uwe Ligges
e please help me with this question? Just make use of a textbook: meanlog <- log(6) - 0.5 * log(1 + 9/(6^2)) sdlog <- sqrt(log(1 + 9/(6^2))) Uwe Ligges thanks, Andras [[alternative HTML version deleted]] __ R-help@r-project.

Re: [R] barplot: legend: two rows

2012-05-15 Thread Uwe Ligges
1,horiz=T,col=c("navyblue","steelblue4","steelblue2","lightsteelblue3","lightsteelblue1"),border="NA",axes=F,beside=F,xlim=c(0,100),cex.names=1.2,ylim=c(0,10)) par(xpd=TRUE) abline(v = seq(10, 100, by = 10), col = "white"

Re: [R] Overlapping area script

2012-05-14 Thread Uwe Ligges
That script is simple broken, the object bat.asc is used but not defined anywhere. Since the code is also not really optimal, you may want to ask an expert who knows how to write such script and how to test if their code work in the end. Best, Uwe Ligges On 14.05.2012 14:12, achughes wrote

Re: [R] Overlapping area script

2012-05-14 Thread Uwe Ligges
the full script including the objects trhat are used within that script. The error message told you that the object 'bat.asc' was not found. My suggestion would be to contact a local expert if your colleague is unavailable. Best, Uwe Ligges The script is designed to compare t

Re: [R] Plotmath bug or my misunderstanding?

2012-05-14 Thread Uwe Ligges
;third")), cex = 2) text(5, 1, labels=expression(atop(atop(atop(atop(sigma,"some text"), "another level"), "third"), "4th")), cex = 2) Anyway, I couldn't find this behavior in the help pages. Of course, the size is adapted. LaTeX would also adapt t

Re: [R] file path

2012-05-09 Thread Uwe Ligges
if you write to a smb file system, and that system won't tell you in advance. hence you have to know it yourself or correctly interpret the corresponding error messages. Uwe Ligges On 9 May 2012 20:32, Tal Galili wrote: Hi Wincent, Have a look at: ?f

Re: [R] barplot: legend: two rows

2012-05-09 Thread Uwe Ligges
elements, i would like 3 elements in one row and the last two elements in the next row. does anyone know how to do that? Example: bp <- barplot(1) par(xpd = TRUE) legend(bp, 0, xjust=0.5, legend=letters[1:5], lwd=1:5, ncol=3) Uwe Ligges thank you very much for your help in advance! mar

Re: [R] plot betadisper, change of pch

2012-05-09 Thread Uwe Ligges
code - or send a feature request to the vegan maintainer (ideally including a patch, CCing). Best, Uwe Ligges On 09.05.2012 12:20, Albin Blaschka wrote: Hello! After performing an analysis with betadisper, package vegan I would like to plot the results - so far, so good. But I would

Re: [R] what folder to run write_PACKAGES in?

2012-05-09 Thread Uwe Ligges
you have to have a PACKAGES (or a compressed alternative) in /src/contrib. Uwe ligges That's created by this: # create_repo_tree<- function(local.repos, rversions){ folders<- c("/bin/windows/contrib", "/bin/macosx/le

Re: [R] Help in increasing R memory in unix

2012-05-08 Thread Uwe Ligges
rease Memory limit. It takes a lot of time to run the process for larger datasets If it is a 64-bit R, it will take as much memory as it needs unless your admin applied some restrictions. Uwe Ligges - Thanks in Advance Arun -- View this message in context: http://r.789695.n4.nabble.com

Re: [R] Dates in R

2012-05-07 Thread Uwe Ligges
On 07.05.2012 10:24, BrittD wrote: Hi everyone, I have a file in which the dates are subscribed as for instance: 20101020. This is 20th Octobre 2010. strptime("20101020", format="%Y%m%d") seems to work for me... UWe Ligges My problem is that R won't except th

Re: [R] paper submission help

2012-05-06 Thread Uwe Ligges
/journal.r-project.org/ Best, Uwe Ligges [[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 http://www.R-project.org/posting-guide.html and provide

Re: [R] Editor to program with CRAN R

2012-05-05 Thread Uwe Ligges
Or more generally, see the overview page at: http://www.sciviews.org/_rgui/projects/Editors.html Uwe Ligges On 05.05.2012 20:44, R. Michael Weylandt wrote: There's a huge spectrum -- all the way from Vim / Emacs to notepad: one that's designed with R in mind (though much heavier th

Re: [R] No error message no display output

2012-05-05 Thread Uwe Ligges
1. You need to call the function pru() after defining it. 2. Next excercise will be to get rid of all those loops. 3. Next excercide will be to reutn something useful from your function (rather than printing). 4. Upgrade to a recent version of R. Uwe Ligges On 05.05.2012 17:31, Trying

Re: [R] Help with getting values from string

2012-05-05 Thread Uwe Ligges
points to. Thanks in advance #macro defined R> defmacro Error: object 'defmacro' not found ... So 1. provide full reproducible code and 2. format it in a more readable form and use R syntax. Uwe Ligges machist_occ_kgfs<-defmacro(a,qnu_occ,b,qnl_occ,expr={with(subset

Re: [R] Absolute cumulative curve with ecdf/stepfun?

2012-05-05 Thread Uwe Ligges
the data cummulated via cumsum? Uwe Ligges __ 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-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] weird predict function error when I use naive bayes

2012-05-05 Thread Uwe Ligges
ble(predict(m, iris[,1,drop=FALSE]), iris[,5]) Uwe Ligges However, when I use two predictors, there is not error any more. m<- naiveBayes(iris[,1:2], iris[,5]) table(predict(m, iris[,1:2]), iris[,5]) setosa versicolor virginica setosa 49 0 0 versicolor 1 37 19 virginica 0 13 31 D

Re: [R] How to write a BMP file pixel by pixel?

2012-05-04 Thread Uwe Ligges
See package pixmap, for example. Uwe Ligges On 04.05.2012 03:10, ZHANG Yingqi wrote: Dear all, I open a bmp device by the bmp() function in the png package, but I don't know how to write color pixel by pixel into the file? Any help or hint? What I want to do is to create

Re: [R] convert numbers into dates and time

2012-05-02 Thread Uwe Ligges
7;s in now 1981-01-02T08:00 strptime("1981-01-02T08:00", format="%Y-%m-%dT%H:%M") seems to work for me. Uwe Ligges can anyone help? cheers! -- View this message in context: http://r.789695.n4.nabble.com/convert-numbers-into-dates-and-time-tp4602708.html Sent from the

Re: [R] please help me

2012-05-02 Thread Uwe Ligges
think we can assume that it is impossible to help you with a simple e-mail response. Please ask your supervisor. Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] Problems accessing environment() in function

2012-05-02 Thread Uwe Ligges
(a, b, c) { x <- as.list(environment()) print ("hi from test1!") test2(a = a, b = b, c = c) You are rying to pass a, b, c here and hence R tries to insert those into the environment of test2 once it is called, you have not passed arguments to your test1 call. Uwe Ligges } test2 <-

Re: [R] Clustering analysis with ordination plots

2012-05-01 Thread Uwe Ligges
the way you ask questions and hence you will probably get more useful answers. Uwe Ligges -- View this message in context: http://r.789695.n4.nabble.com/Clustering-analysis-with-ordination-plots-tp4598695.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] Error in if (nuhat < 2) stop("The degrees of freedom must be greater than or equal to 2") : missing value where TRUE/FALSE needed

2012-04-30 Thread Uwe Ligges
ve to fix the code on the URL you cited. In any case, looking at the data via some plots suggests that there is not too much in the data (at least given the three variables you are dealing with - not with ordinary ancova nor any other kind of method) Uwe Ligges On 30.04.2012 16:17, Kyri

Re: [R] Error in if (nuhat < 2) stop("The degrees of freedom must be greater than or equal to 2") : missing value where TRUE/FALSE needed

2012-04-30 Thread Uwe Ligges
really described which model yopu want to fit exactly, we can only guess from your code not knowing those functions you used. Uwe Ligges Best, Kyriakos Date: Mon, 30 Apr 2012 15:20:04 +0200 From: lig...@statistik.tu-dortmund.de To: antonio...@hotmail.com CC: r-help@r-project.org Subject: Re

Re: [R] Error in if (nuhat < 2) stop("The degrees of freedom must be greater than or equal to 2") : missing value where TRUE/FALSE needed

2012-04-30 Thread Uwe Ligges
ssing value where TRUE/FALSE needed Aleady the way the Note is printed shows the code is poorly written, the non-working error message supports that. Since we do not have the data, we cannot help, probably lm() is capable of the ancova you have in mind. Uwe Ligges In addition: Warning messages:

Re: [R] "parallel" package

2012-04-30 Thread Uwe Ligges
er, I failed to figure out how to combine the mice function with the package "parallel". Any suggestions how I should write the code? Well, rewriting parts of mice seems to be the only way to let collaborate with package parallel. Best, Uwe Ligges Thank you very much. ya

Re: [R] "parallel" package

2012-04-29 Thread Uwe Ligges
o say pkg <- "parallel" library(pkg) doing the same as library("parallel") which is unfortunately not possible, because library(pkg) tries a package called "pkg". Best, Uwe Ligges Regards, Indrajit ________ From: Uwe Ligges To: ya C

Re: [R] "parallel" package

2012-04-28 Thread Uwe Ligges
? It is shipped as an R base packaage. Just use library("parallel") Uwe Ligges Thank you very much. ya __ 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

Re: [R] Dataset maximum size?

2012-04-26 Thread Uwe Ligges
We do not know anything about the data, but given those are floting point numbers or integers there sould not be a problem with 4500 times 3. Uwe Ligges On 26.04.2012 05:15, Rich Lane wrote: Hi all, I have an interesting project coming up, but the datasets are way bigger than

Re: [R] Proper apply function for matrices embedded in lists

2012-04-26 Thread Uwe Ligges
data[1,1] is a list of length 1, hence data[1,1][[1]] will do. But easier: d <- dim(data) res <- sapply(data, function(x) list(colSums(x))) dim(res) <- d or perhaps as an array: d <- dim(data) res <- sapply(data, colSums) dim(res) <- c(2, d) res Uwe Ligges in ap

Re: [R] [pROC] roc.test returns "NA" p-value...

2012-04-25 Thread Uwe Ligges
Probably you got NAs in some bootstrap results, or you got a 0 variance, or you hat 0 observations in a group you compared to another group? Check the data and the separate results! Uwe Ligges On 25.04.2012 09:28, O wrote: Hello, I am comparing two ROC curves with bootstraping. However

Re: [R] How to reduce plot size on linux?

2012-04-25 Thread Uwe Ligges
relative size corrections). But that would need some more specific question. uwe Ligges Regards -- View this message in context: http://r.789695.n4.nabble.com/How-to-reduce-plot-size-on-linux-tp4585371p4585371.html Sent from the R help mailing list archive at Nabble.com

Re: [R] trouble installing SparseM

2012-04-25 Thread Uwe Ligges
On 25.04.2012 08:21, Erin Hodgess wrote: Dear R People: I am attempting to install SparseM on R 2.15.0 on a Linux 11.10 system. Here is the output install.packages("SparseM",depen=TRUE) Installing package(s) into ‘/home/erin/R/x86_64-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified) ---

Re: [R] Compiling RMySQL on Win7 64bits RS-DBI.c:1:0: sorry, unimplemented: 64-bit mode not compiled in

2012-04-24 Thread Uwe Ligges
d it depends on the MySQL you are linking against. best, Uwe Ligges thanks in advance, Ben install.packages('RMySQL', type = 'source') --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/RMySQL_0.9-3.tar

Re: [R] Compiling RMySQL on Win7 64bits RS-DBI.c:1:0: sorry, unimplemented: 64-bit mode not compiled in

2012-04-24 Thread Uwe Ligges
\Rtools\gcc-4.6.3\bin; What is D:\BenSave\Rtools\MinGW64\bin? Probably it needs to go out of the way. Uwe Ligges Note that I place MinGW64\bin has I want the package in 64 bits, so just in case it helps... To install RMySQL 64 bits, I then followed the steps described in http

Re: [R] OLS Estimating

2012-04-23 Thread Uwe Ligges
On 23.04.2012 12:42, phillip03 wrote: Hi I am looking for a efficient way to estimate all parameters in your data.frame set using a specific function: for example ln(T)=b_0 + b_1*ln(Y_i*Y_j) + b_2*ln()+ ... + etc. Sounds like you are looking for lm(). Uwe Ligges Thanks, Ph -- View

Re: [R] unexpected plot behavior

2012-04-21 Thread Uwe Ligges
a are passed from plot.formula. plot.formula does not accept a "type" argument. plot.default() does, but that is not used once your use a formula. Uwe Ligges Plotting a numerical against itself works as expected: plot (1:10, type = "n") I see the same behavior under debian gn

Re: [R] multi-machine parallel setup?

2012-04-21 Thread Uwe Ligges
/iaw Ivo Welch (ivo.we...@gmail.com) J. Fred Weston Professor of Finance Anderson School at UCLA, C519 http://www.ivo-welch.info/ Editor, Critical Finance Review, http://www.critical-finance-review.org/ 2012/4/21 Uwe Ligges: On 21.04.2012 06:34, ivo welch wrote: the vignette to the lib

Re: [R] multi-machine parallel setup?

2012-04-21 Thread Uwe Ligges
other one on your friends: cl <- makeCluster(c("localhost", "192.168.2.10"), "SOCK") BEst, Uwe Ligges On Wed, Apr 18, 2012 at 1:01 PM, ivo welch wrote: Dear R experts: could someone please point me to a page that explains how to set up more than 1 mac

Re: [R] packages install dependencies

2012-04-18 Thread Uwe Ligges
m/install/R_packages/test" reaing the help file tell us it must be an URL rather than a file specification. Uwe Ligges But I got always the same error install.packages("marginalmodelplots", dependencies=TRUE, contriburl="/home/bioadm/install/R_packages/test/") War

Re: [R] Error while generating latex table from sweave and R?

2012-04-18 Thread Uwe Ligges
",label="tab:summary", align="lll"),include.rownames=FALSE,width=100) } In the above code, i need to add two backslashes "\\" at the end of each table record but if i use cat("///"), i m gettting error message. If i use cat("//","//&

Re: [R] packages install dependencies

2012-04-18 Thread Uwe Ligges
ioadm/install/R_packages/test/marginalmodelplots_0.4.2.tar.gzâ is not available (for R version 2.15.0) I don't understand the error because my files PACKAGES are inside the directory that I specified using the option contriburl and this directory is full access for everyone. Is the

Re: [R] loss of information in pdf plots

2012-04-17 Thread Uwe Ligges
2000x1200 pixels and the question is how to render effects that are smaller than a pixel ... Now the windows device and your pdf viewer decide to do different things (and R handles the devices slightly different as well, of course). Uwe Ligges Thanks all for your great help! B

Re: [R] loss of information in pdf plots

2012-04-17 Thread Uwe Ligges
As far as I can see, the recommended way of using pdf() plot dev.off() works precisely, just zoom in far enough so that your screen is able to display the gaps, e.g. by zooming in by 6400% Uwe Ligges On 17.04.2012 15:53, Unger, Kristian, Dr. wrote: Thanks Uwe. Please use the following

Re: [R] packages install dependencies

2012-04-17 Thread Uwe Ligges
quot;win.binary" ) Errr, given your path specifications, I assume you are not under Windows and given the extensions of the files, I assume you have source packages, hence you need a PACKAGES file for a source repository. Uwe Ligges I retried the command but I got the same error. install.pa

Re: [R] loss of information in pdf plots

2012-04-17 Thread Uwe Ligges
On 17.04.2012 14:35, Unger, Kristian, Dr. wrote: Thanks Petr. Unfortunately this does not help. In that case, we need a reproducible example. Uwe Ligges Kristian Am 17.04.2012 um 14:18 schrieb Petr PIKAL: Hi Hi there is it possible that pdfs generated using the pdf() function

Re: [R] packages install dependencies

2012-04-17 Thread Uwe Ligges
not available Then you do not have a repository. Its defintiion is that it contains a PACKAGES file which it obviously does not contain. Nevertheless, you can create a PACKAGE file via function write_PACKAGES() in package tools. Uwe Ligges For info this package depends of the &qu

Re: [R] system command to a specific shell (bash)

2012-04-17 Thread Uwe Ligges
On 17.04.2012 01:26, MacQueen, Don wrote: I believe that shell() was superceded by system(), quite a long time ago. Not really, under Windows, shell() will start a shell while system() won't. Uwe Ligges However, I get this: foo<- system('printenv',intern=TRUE) ; foo

Re: [R] packages install dependencies

2012-04-16 Thread Uwe Ligges
endencies in my repository. install.packages(, contriburl="/home/joel/RPacks") Uwe Ligges Thanks in advance, Best Regards - Cordialement, Joël --- Joel Masciocchi Bioinformatician Informatics Departmen

Re: [R] Approximately how big is an installation of all packages.

2012-04-16 Thread Uwe Ligges
On 16.04.2012 16:16, Keith Weintraub wrote: Can you tell me the size of those 3 packages separately? These are 5000 packages. If you want to kniow, why don't you try out? I have them in one library only. Uwe Ligges That is CRAN, BioC software, BioC data. If you can only give me CR

Re: [R] Problems loading siar package

2012-04-16 Thread Uwe Ligges
On 16.04.2012 01:36, Gary Roemer wrote: PS The version of "siar" on my old computer is 4.0, the new version is 4.1.3 - could the latter be corrupt? Try to reinstall both mvtnorm and siar from sources again. Looks lie your mvtnorm installation is broken. Uwe Ligges Tha

Re: [R] Approximately how big is an installation of all packages.

2012-04-16 Thread Uwe Ligges
BioC software packages plus few BioC data packages, then I see an installed size of roughly 8Gb under Windows. Uwe Ligges Thanks, KW -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] Importing data from stata.

2012-04-16 Thread Uwe Ligges
On 16.04.2012 12:56, Søren Andersen wrote: Hi everyone! I am very new at R. I am trying to import a data file from stata to R on a Macintosh system ? When I use the foreign function read.dta it says: You forgot to load foreign: library("foreign") Uwe Ligges Error:

Re: [R] Question with R CMD SHLIB in 64 bit R

2012-04-16 Thread Uwe Ligges
You may want to send the files as well as what you exactly typed in the shell in a private message. Uwe Ligges On 15.04.2012 20:09, Katharine Miller wrote: Yes. I have version 2.15.0 of Rtools as well. I went ahead and re-installed both R and Rtools just to make sure everything was OK. But

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