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

2012-05-30 Thread Uwe Ligges
defining the typeInfo argument... MySQL != Excel Uwe Ligges typeInfo- getSqlTypeInfo(EXCEL) typeInfo$character- varchar(3000) z- odbcConnectExcel2007(test_rodbc.xlsx,readOnly=FALSE) sqlSave(z,d,tablename=Sheet2,rownames=FALSE,typeInfo=typeInfo) odbcClose(z) Error in sqlSave(z, d, tablename

Re: [R] Memory Windows

2012-05-30 Thread Uwe Ligges
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 Unix. EZ

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

2012-05-29 Thread Uwe Ligges
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 the solution *pass column name through *variable to this function ? Can i get immediate solution please

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

2012-05-28 Thread Uwe Ligges
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 HTML version deleted

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

2012-05-27 Thread Uwe Ligges
() From: Uwe Ligges [lig...@statistik.tu-dortmund.de] Sent: Saturday, May 26, 2012 11:43 AM To: Patrick Nicholson Cc: r-help@R-project.org Subject: Re: [R] R base package grid does not output raster image On 24.05.2012 23:04, Patrick Nicholson wrote: I am running 64-bit R 2.15.0

Re: [R] barplot problem

2012-05-27 Thread Uwe Ligges
(.) Then take a look into xp. See also ?barplot! Uwe Ligges -jh On Sun, May 27, 2012 at 3:42 AM, Jim Lemonj...@bitwrit.com.au 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

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] Multiple cbind according to filename

2012-05-26 Thread Uwe Ligges
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 answer for that is: result - do.call(cbind, alldata) Best, Uwe Ligges but file list

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

2012-05-26 Thread Uwe Ligges
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 NA NA NA NA NA [3,] NA NA0000 [4,] NA00000 [5

Re: [R] Rolling Sample VAR

2012-05-26 Thread Uwe Ligges
, 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.com/Rolling

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

2012-05-26 Thread Uwe Ligges
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 ' before the Rscript). Uwe Ligges Thanks

Re: [R] shift + arrow in getGraphicsEvent

2012-05-26 Thread Uwe Ligges
)) 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-project.org mailing list https

Re: [R] Values in scatterplot??

2012-05-26 Thread Uwe Ligges
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 proceed from there? Uwe Ligges Error in summary(SPHSHTL

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

2012-05-26 Thread Uwe Ligges
,xlab=Wavelength [nm],ylab=Radiance) mat_identify(lbd2, t(mySpectra)) Best, Uwe Ligges Thank you very much Best regards servet __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

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

2012-05-26 Thread Uwe Ligges
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 works on my laptop (R 2.15.0, ggplot2 0.8.9): library

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, -Dan

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] 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... DCN:jdnew

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] 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 dataset

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

2012-05-22 Thread Uwe Ligges
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 etc. Best, Uwe Ligges Thanks a lot

Re: [R] scatterplot x axis specifications

2012-05-22 Thread Uwe Ligges
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 mailing list archive at Nabble.com

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, education

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

2012-05-22 Thread Uwe Ligges
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 https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] Working directory

2012-05-22 Thread Uwe Ligges
to it 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] (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 you have

Re: [R] Subset based on a date range

2012-05-19 Thread Uwe Ligges
to a date format that corresponds to vdate, see e.g. ?strptime. Uwe ligges or all data is excluded six_months-subset(Two_years, vdate2011-01-01vdate2011-07-01) -- View this message in context: http://r.789695.n4.nabble.com/Subset-based-on-a-date-range-tp4630595.html Sent from the R help

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

2012-05-19 Thread Uwe Ligges
=) 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 using. See the posting guide for how to ask better. Best, Uwe Ligges For the second plot, I wanted no dots

Re: [R] Unable to install package

2012-05-17 Thread Uwe Ligges
in between (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] 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] finding mean and SD for a log-normal distribution

2012-05-16 Thread Uwe Ligges
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.org mailing list https

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-numeric(ncol(mat1)) for(j

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

2012-05-16 Thread Uwe Ligges
==.(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, 0, 0, 0, 1, 0, 0, 0, 0), ) # How can I locate this legend(topcenter, cex

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

2012-05-16 Thread Uwe Ligges
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 works for windows. I will appreciate

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

2012-05-16 Thread Uwe Ligges
)) 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 context: http://r.789695.n4.nabble.com

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

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 2400

Re: [R] Merging multiple data sets

2012-05-16 Thread Uwe Ligges
)[1]==0){output_data_prod- data_22 }else{ output_data_prod- merge(inData1 = output_data_prod, Nonsense, the arguments of merge are called x and y rather than inData1 and inData2. Uwe Ligges inData2 = data_22 ,type = inner, all=FALSE , by =c(x11

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] 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] barplot: legend: two rows

2012-05-15 Thread Uwe Ligges
= 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! marion [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [R] Plotmath bug or my misunderstanding?

2012-05-14 Thread Uwe Ligges
), 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 the size of, e.g., the symbols in a fraction compared to regular text. Uwe Ligges Rui Barradas Em 13-05-2012 11:00, Bert Gunter escreveu: Date: Sat

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 the area

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] what folder to run write_PACKAGES in?

2012-05-09 Thread Uwe Ligges
the versioned subfolders and 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/leopard/contrib

Re: [R] plot betadisper, change of pch

2012-05-09 Thread Uwe Ligges
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 also like to tune a little bit the plotting

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! marion

Re: [R] file path

2012-05-09 Thread Uwe Ligges
, 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 Galilital.gal...@gmail.com wrote: Hi Wincent, Have a look at: ?file.path Contact Details

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

2012-05-08 Thread Uwe Ligges
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/Help

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 this as a date, since

Re: [R] paper submission help

2012-05-06 Thread Uwe Ligges
-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 commented

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

2012-05-05 Thread Uwe Ligges
,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 Do you know what is the problem

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

2012-05-05 Thread Uwe Ligges
in ddply with a function that gives cumulative counts resp. the cumulative position of each observation, so that I get an absolute cumulative curve as a result? Is that understandable? Thank you very much, Johannes What about using stepfun() and providing the data cummulated via cumsum? Uwe

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(an_ind_data_fin

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] 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 than notepad

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 a 512

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

2012-05-02 Thread Uwe Ligges
(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 - function(a, b, c) { # PROBLEM: Why

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] convert numbers into dates and time

2012-05-02 Thread Uwe Ligges
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 R help mailing list archive

Re: [R] Clustering analysis with ordination plots

2012-05-01 Thread Uwe Ligges
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. __ R-help@r-project.org mailing

Re: [R] parallel package

2012-04-30 Thread Uwe Ligges
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 On 04/29/2012 10:47 AM, Uwe Ligges wrote: On 29.04.2012 09:28

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
the data, we cannot help, probably lm() is capable of the ancova you have in mind. Uwe Ligges In addition: Warning messages: 1: In min(sub[vecn= 12]) : no non-missing arguments to min; returning Inf 2: In max(sub[vecn= 12]) : no non-missing arguments to max; returning -Inf 3: In near(x1

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
not 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
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, Kyriakos Antoniou wrote

Re: [R] parallel package

2012-04-29 Thread Uwe Ligges
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 Liggeslig...@statistik.tu-dortmund.de To: yaxinxi...@163.com

Re: [R] parallel package

2012-04-28 Thread Uwe Ligges
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.org/posting-guide.html and provide

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

2012-04-26 Thread Uwe Ligges
] 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 apply(data[1,1], 2, sum) : dim(X) must have

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

2012-04-24 Thread Uwe Ligges
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.gz' Content type 'application/x-gzip' length 165363 bytes (161

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] multi-machine parallel setup?

2012-04-21 Thread Uwe Ligges
- makeCluster(c(localhost, 192.168.2.10), SOCK) BEst, Uwe Ligges On Wed, Apr 18, 2012 at 1:01 PM, ivo welchivo.we...@gmail.com wrote: Dear R experts: could someone please point me to a page that explains how to set up more than 1 machine for library parallel (which is quickly becoming my favorite

Re: [R] multi-machine parallel setup?

2012-04-21 Thread Uwe Ligges
username on all machines, it should work out of the box. At least, it does for me: Say you want two, one on your own machine, the 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 welchivo.we...@gmail.comwrote

Re: [R] unexpected plot behavior

2012-04-21 Thread Uwe Ligges
. 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 gnu/linux, Mac OS X, and Win7 (all current versions, see

Re: [R] packages install dependencies

2012-04-18 Thread Uwe Ligges
/R_packages/test/marginalmodelplots_0.4.2.tar.gz, repos=TRUE, dependencies=TRUE,contriburl=/home/bioadm/install/R_packages/test/) install.packages(marginalmodelplots, dependencies=TRUE, contriburl=/home/bioadm/install/R_packages/test) seems to be the documented way you want to try. Uwe Ligges

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

2012-04-18 Thread Uwe Ligges
my pblm? cat() , actually Uwe Ligges Regards -- View this message in context: http://r.789695.n4.nabble.com/Error-while-generating-latex-table-from-sweave-and-R-tp4566954p4566954.html Sent from the R help mailing list archive at Nabble.com

Re: [R] packages install dependencies

2012-04-18 Thread Uwe Ligges
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/) Warning: unable to access index for repository /home/bioadm/install

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[grepl('SHELL',foo

Re: [R] packages install dependencies

2012-04-17 Thread Uwe Ligges
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 locfit package. What should I do ? Thanks in advance Joël Masciocchi -Message

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
, 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.packages(/home/bioadm

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] loss of information in pdf plots

2012-04-17 Thread Uwe Ligges
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! Best wishes Kristian

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

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: could

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

2012-04-16 Thread Uwe Ligges
and 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] 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 Thanks, Gary

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 CRAN vs

Re: [R] packages install dependencies

2012-04-16 Thread Uwe Ligges
repository. install.packages(, contriburl=/home/joel/RPacks) Uwe Ligges Thanks in advance, Best Regards - Cordialement, Joël --- Joel Masciocchi Bioinformatician Informatics Department Institut de Recherches

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

2012-04-15 Thread Uwe Ligges
On 14.04.2012 21:53, Katharine Miller wrote: OK. So, I have 64 bit Windows 7 and I have installed R 2.15.0 Yes, and have you also installed version 2.15 of the Rtools? Uwe ligges Thanks 2012/4/14 Uwe Liggeslig...@statistik.tu-dortmund.de On 14.04.2012 19:01, Katharine Miller wrote

Re: [R] enableJIT(2) causes major slow-up in rpart

2012-04-14 Thread Uwe Ligges
) -- On Fri, Apr 13, 2012 at 12:47 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 12.04.2012 23:15, Tal Galili wrote: Hello, Due to exploration of the JIT capabilities offered through the {compiler} package, I came by the fact that using enableJIT(2) can *slow* the rpart function

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

2012-04-14 Thread Uwe Ligges
, is your OS 64-bit? Otherwise that R won't run for you. 2. Do you have the latest toolchain first in your PATH? 3. Do yo follow the details of the most recent version of the R Installation and Administration manual? Uwe Ligges but that doesn't do anything. It doesn't give me any error

Re: [R] some questions about sympy (that is, rSymPy)

2012-04-14 Thread Uwe Ligges
symbol in sympyq( ((x+y)**2).expand That goes through the R parser but is not valid R syntax, hence it cannot work. Uwe Ligges sympyq( sin(x+y).expand(trig=True) ) Error: unexpected symbol in sympyq( sin(x+y).expand ??? Kjetil __ R-help@r

Re: [R] Merging two data frames with different columns names

2012-04-14 Thread Uwe Ligges
I guess you just want one data.frame with the columns part1 and part2? Then: merge(part1, part2) should do thr trick. If you aim at something different, please explain you expected result. Uwe Ligges On 14.04.2012 01:33, Johnny Liseth wrote: I am trying to merge two data frames, but one

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

2012-04-14 Thread Uwe Ligges
first in your PATH? 3. Do yo follow the details of the most recent version of the R Installation and Administration manual? Uwe Ligges but that doesn't do anything. It doesn't give me any error messages, but it also doesn't create a shared (so) file. I just get the command prompt back. I

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