[R] Mailing list attachments
PhGr == Philippe Grosjean [EMAIL PROTECTED] on Mon, 15 Jan 2007 18:56:00 +0100 writes: PhGr PhGr I will attach it to a second email send privately to PhGr you, since the mailing list do not accept attachments. That's not correct. http://www.r-project.org/mail.html (search for attachment) explains that most ** binary ** attachments are not accepted, lists the exceptions and further says that text/plain is well accepted (BTW, text/html is accepted too, but translated to text/plain by the filters) One problem is that many e-mail client programs do not seem to let you attach text/plain easily. Martin __ R-help@stat.math.ethz.ch 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] R graphics with Linux (libpng)
Prof Brian Ripley ripley at stats.ox.ac.uk writes: On Thu, 11 Jan 2007, Rebecca Tagett wrote: Hello, I'm trying to adapt some R code that works on Windows so that it will work on a Linux machine. The command : png(myFile.png, width=600, height=600) fails claiming that it is impossible to establish a connection with X11. (Error messages are in French, so I'm not pasting them here!) I have libpng installed: rpm -qa libpng* libpng-1.0.12-2 libpng-devel-1.0.12-2 So I don't understand why R thinks I'm trying to connect to X11. I haven't been able to find many examples of R graphics code specifically for Linux, but I have the impression that if libpng is installed, the graphics commands are identical. The libpng manual is not useful, because it does not mention use of libpng commands in an R environment. ?png says R can be compiled without support for either or both of these devices: this will be reported if you attempt to use them on a system where they are not supported. They may not be usable unless the X11 display is available to the owner of the R process. Note: These are based on the 'X11' device, so the additional arguments to that device work, but are rarely appropriate. The colour handling will be that of the 'X11' device in use. 'bitmap' provides an alternative way to generate PNG and JPEG plots that does not depend on accessing the X11 display but does depend on having GhostScript installed. (Device 'GDD' in CRAN package 'GDD' is another alternative using several other additional pieces of software.) so the help page seems quite specific about the connection to X11. I was referring to the libpng manual (see above), and not the R help page. The 'Devices' help page is the one that threw me off course. It states that X11 is the graphics driver for the X11 Window system, which I took to mean MS Windows as opposed to X window, thus I was surprised that Linux should go looking for such a thing. I'm now wading through R installation and administration, which is very useful. Our systems manager is away, so your patience is appreciated. I'm using R 2.4.1, which I recently installed. Do I have to install a more recent libpng ? If so, do I have to reconfigure and remake R ? The libpng is very old, but even more likely is that libz is too old. There were messages when you configured: did you read them at all? If not, plese do rebuild R and read them this time. Without the exact error message I cannot be sure, but I don't think this is the problem. There were no errors on installation. However, I see that libz came with the R package (it is in .../R-2.4.1/src/extra/zlib/libz.a), so it would have been correctly installed along with the rest. Evidently libpng does not come with the package. I'll download the recent version, install it, rebuild R, and try to find out why my Linux doesn't recognize X11. Or perhaps I'll use bitmap() with ghostscript, as Benilton Carvalho suggested. I've also read that no graphics devices are available under R CMD BATCH. Does that really mean that I can't create graphics from some R code that I launch in noninteractive mode? Your source is incorrect: please advise the author(s) to correct it. The source is the 'Devices' help page : QUOTE The following devices will be available if R was compiled to use them and started with the appropriate '--gui' argument: * 'X11' The graphics driver for the X11 Window system * 'png' PNG bitmap device * 'jpeg' JPEG bitmap device None of these are available under 'R CMD BATCH'. UNQUOTE (no authors listed) Did you also read that you are asked not to send HTML mail? (That is from a reliable source.) I knew that. I didn't do it on purpose... so very sorry. Thanks. __ R-help@stat.math.ethz.ch 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] feedback on writing r extensions
Scott == Scott Harrison [EMAIL PROTECTED] on Mon, 15 Jan 2007 13:15:09 -0500 writes: Scott Hi, To whom should I send feedback/edits concerning Scott the Writing R Extensions web page? Scott http://cran.r-project.org/doc/manuals/R-exts.html To R-devel (the mailing list), usually; If it's just simple typos, maybe just to R-core directly. For edits, we'd mostly like to receive feedback on the *source* of the above automatically produced document (which is also the source of the PDF version, same URL as above, just replace .html by .pdf) The development source is always available at https://svn.r-project.org/R/trunk/doc/manual/R-exts.texi Thanking you for offering feedback, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch 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] nonlinear regression: nls, gnls, gnm, other?
Hi Johann, The current version of gnm is unable to fit this type of model, though a new version with more flexibility is soon to be released. In any case, you probably want to use nls or gnls, depending on the assumptions that can be made about the model errors. For nls it is usual to assume that the errors are normally distributed with mean zero and constant variance, though the normal assumption is not strictly necessary. If you have reason to think the errors are correlated and/or have unequal variances, then gnls would be appropriate. The examples on ?nls may be enough to get you started, Heather -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Johann Hibschman Sent: 16 January 2007 04:05 To: Turner, Heather; r-help Subject: [R] nonlinear regression: nls, gnls, gnm, other? Hi all, I'm trying to fit a nonlinear (logistic-like) regression, and I'd like to get some recommendations for which package to use. The expression I want to fit is something like: y ~ A * exp(X * Beta1) / (1 + exp(-(x + X * Beta2 - xmid)/scal)) Basically, it's a logistic function, but I want to be able to modify the saturation amplitude by a few parameters (Beta1) and shift the inflection point around with a few other parameters (Beta2). I have a ton of data, but I often have trouble getting the routine to fit. (I've been using nlin in SAS, which seems sloppier in terms of accepted convergence.) Now, from what I can tell, I can use nls, gnls, or gnm to fit something like this, but I can't tell which would be better, or if there's something else I should be trying. To do this right, though, I have to do a lot more reading, but I'd like to know where to start. (I have more of a physics/computer background, so I immediately jump to thinking of regression as minimizing some cost function across a multidimensional space and then start mumbling about simulated annealing or some such, but this isn't helping me much in interpreting the available literature.) So, does anyone have any suggestions? I imagine I'm going to have to pick up a book, but should it be Pinheiro Bates on nlme, Bates Watts, the pdf manual to gnm, or what? Thanks for any suggestions, Johann __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
[R] Help with labeling a page with multiple graphs.
Hi, I am trying to output pdf files with 8 graphs per page. My current study has 8 evaluation criteria, and 38 study conditions. This would result in 38 pages of 8 graphs. I have figured out how to get the graphs looking like I would like them, and I am using the layout() function to put them on the page, as that allows me the control I would like over the appearance of the individual plots. What I can't figure out is how to put a page title on each page. Something simple like, Condition X at the top of each page. A second line of title would also be nice. Any help is truely appreciated. rob __ R-help@stat.math.ethz.ch 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.
[R] Gaussian glm for grouped data with unequal variances
Hello - I am fairly new to R, (i.e., ability to create functions/write programs insignificant) and was wondering if there might be a convenient way to model the following: I want to fit a gaussian glm to grouped data, while allowing for unequal variances in each of the groups. More specifically, my data set looks something like this: data group 176 1 282 1 383 1 454 1 535 1 646 1 787 1 868 1 987 2 10 95 2 11 98 2 12 100 2 13 109 2 14 109 2 15 100 2 16 81 2 17 75 2 18 68 2 19 67 2 20 105 3 et cetera. --- There are seven groups in all, each with a different number of observations. The idea is to compare a model in which all the data points can be modeled with a single mean (i.e., if all the group means are equal), or if the data suggests that each of the groups has a different mean. In other words, I want to do a Likelihood ratio test on whether or not the group means are significantly different from each other: the full model would be glm(data ~ as.factor(group)-1, family = gaussian), to be compared against a restricted model that only includes an intercept. However, I also need to allow for the fact that each group has a different variance. And this I have no idea how to do. I would really appreciate some help in this matter. Thank you in advance, Dawn. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] How to format R code in LaTex documents
I often produce program listings in my LaTeX documents. I use the
verbatim environment but use commands such as
\addtolength{\oddsidemargin}{-0.95in}
\addtolength{\evensidemargin}{-0.95in}
to widen the printed page so that I do not have to resort to line
continuation characters. This method is simple and you can experiment with
values other than 0.95in to find the value most appropriate to you
John
On 15/01/07, Benjamin Dickgiesser [EMAIL PROTECTED] wrote:
Hi,
I am planning on putting some R script in an appendix of a LaTex
document. Can anyone recommend me a way of how to format it? Is there
a way to keep all line breaks without having to insert \\ in every
single line?
Thank you!
Benjamin
__
R-help@stat.math.ethz.ch 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.
--
John C Frain
Trinity College Dublin
Dublin 2
Ireland
www.tcd.ie/Economics/staff/frainj/home.html
mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] nonlinear regression: nls, gnls, gnm, other?
On Tue, 16 Jan 2007, Turner, Heather wrote: Hi Johann, The current version of gnm is unable to fit this type of model, though a new version with more flexibility is soon to be released. In any case, you probably want to use nls or gnls, depending on the assumptions that can be made about the model errors. For nls it is usual to assume that the errors are normally distributed with mean zero and constant variance, though the normal assumption is not strictly necessary. If you have reason to think the errors are correlated and/or have unequal variances, then gnls would be appropriate. nls is able to handle unequal variances since 2.3.0: from the help weights: an optional numeric vector of (fixed) weights. When present, the objective function is weighted least squares. The examples on ?nls may be enough to get you started, Heather -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Johann Hibschman Sent: 16 January 2007 04:05 To: Turner, Heather; r-help Subject: [R] nonlinear regression: nls, gnls, gnm, other? Hi all, I'm trying to fit a nonlinear (logistic-like) regression, and I'd like to get some recommendations for which package to use. The expression I want to fit is something like: y ~ A * exp(X * Beta1) / (1 + exp(-(x + X * Beta2 - xmid)/scal)) Basically, it's a logistic function, but I want to be able to modify the saturation amplitude by a few parameters (Beta1) and shift the inflection point around with a few other parameters (Beta2). I have a ton of data, but I often have trouble getting the routine to fit. (I've been using nlin in SAS, which seems sloppier in terms of accepted convergence.) Now, from what I can tell, I can use nls, gnls, or gnm to fit something like this, but I can't tell which would be better, or if there's something else I should be trying. To do this right, though, I have to do a lot more reading, but I'd like to know where to start. (I have more of a physics/computer background, so I immediately jump to thinking of regression as minimizing some cost function across a multidimensional space and then start mumbling about simulated annealing or some such, but this isn't helping me much in interpreting the available literature.) So, does anyone have any suggestions? I imagine I'm going to have to pick up a book, but should it be Pinheiro Bates on nlme, Bates Watts, the pdf manual to gnm, or what? Thanks for any suggestions, Johann __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Help with labeling a page with multiple graphs.
Rob Keller wrote: Hi, I am trying to output pdf files with 8 graphs per page. My current study has 8 evaluation criteria, and 38 study conditions. This would result in 38 pages of 8 graphs. I have figured out how to get the graphs looking like I would like them, and I am using the layout() function to put them on the page, as that allows me the control I would like over the appearance of the individual plots. What I can't figure out is how to put a page title on each page. Something simple like, Condition X at the top of each page. A second line of title would also be nice. Any help is truely appreciated. RSiteSearch(title multiple figure) shows the following possibilities: http://finzi.psych.upenn.edu/R/library/sfsmisc/html/mult.fig.html http://finzi.psych.upenn.edu/R/library/Hmisc/html/mtitle.html rob __ R-help@stat.math.ethz.ch 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch 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.
[R] [[ gotcha
The following gotcha caught me off-guard just now. I have two matrices, a and b: a - matrix(1,3,3) b - matrix(1,1,1) (note that both a and b are matrices). I want them in a list: B - NULL B[[1]] - a B[[2]] - b B [[1]] [,1] [,2] [,3] [1,]111 [2,]111 [3,]111 [[2]] [,1] [1,]1 This is fine. But swapping a and b over does not behave as desired: B - NULL B[[1]] - b B[[2]] - a Error in B[[2]] - a : more elements supplied than there are to replace The error is given because after B[[1]] - a, the variable B is just a scalar and not a matrix (why is this?) What's the bulletproof method for assigning matrices to a list (whose length is not known at runtime)? -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch 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.
[R] Request regarding cluster package
Dear Mr. Bengtsson, I see that there is a package exclusively for clustering data, named as Cluster Package in R library. It has some clustering algorithms implemented. Can you tell me how to implement the CLARA and PAM functions from that package for my data? Bhanu Kalyan K B.Tech Final Year, CSE Tel: +91-9885238228 Alternate E-Mail: [EMAIL PROTECTED] - 8:00? 8:25? 8:40? Find a flick in no time [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Fast Removing Duplicates from Every Column
Hi I have no idea how Test data look like. However help pages of functions data.frame() as.data.frame() str() and maybe few others can help you find how to change objects to data frames. HTH Petr On 16 Jan 2007 at 10:36, Bert Jacobs wrote: From: Bert Jacobs [EMAIL PROTECTED] To: 'Petr Pikal' [EMAIL PROTECTED] Subject:RE: [R] Fast Removing Duplicates from Every Column Date sent: Tue, 16 Jan 2007 10:36:42 +0100 Hi Petr, Thx for answeringen me on the question below. Actually I could use this line of code to get my problem solved. Test = apply(X=my_data, MARGIN=2, FUN=unique) Now I was wondering how to transform 'Test' into a dataframe, while there are different rows implied. Thx, Bert _ Bert Jacobs Marketing Intelligence Engineer Plasveldlaan 5 9400 Ninove Tel: 0477/68.74.07 Fax: 054/25.00.35 E-mail: [EMAIL PROTECTED] -Original Message- From: Petr Pikal [mailto:[EMAIL PROTECTED] Sent: 05 January 2007 11:51 To: Bert Jacobs; 'R help list' Subject: Re: [R] Fast Removing Duplicates from Every Column Hi I am not sure if I understand how do you want to select unique items. with sapply(DF, function(x) !duplicated(x)) you can get data frame with TRUE when an item in particular column is unique and FALSE in opposite. However then you need to choose which rows to keep or discard e.g. DF[rowSums(sapply(comp, function(x) !duplicated(x)))1,] selects all rows in which are 2 or more unique values. HTH Petr On 5 Jan 2007 at 9:54, Bert Jacobs wrote: From: Bert Jacobs [EMAIL PROTECTED] To: 'R help list' r-help@stat.math.ethz.ch Date sent:Fri, 5 Jan 2007 09:54:17 +0100 Subject: Re: [R] Fast Removing Duplicates from Every Column Hi, I'm looking for some lines of code that does the following: I have a dataframe with 160 Columns and a number of rows (max 30): Col1 Col2 Col3 ... Col 159 Col 160 Row 1 0 0 LD ... 0 VD Row 2 HD 0 00 MD Row 3 0 HD HD 0 LD Row 4 LD HD HD 0 LD ... ... LastRow HDHDLD 0 MD Now I want a dataframe that looks like this. As you see all duplicates are removed. Can this dataframe be constructed in a fast way? Col1 Col2 Col3 ... Col 159 Col 160 Row 1 00LD 0VD Row 2 HD HD 00MD Row 3 LD 0HD 0LD Thx for helping me out. Bert __ R-help@stat.math.ethz.ch 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. Petr Pikal [EMAIL PROTECTED] Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] [[ gotcha
Robin Hankin wrote: The error is given because after B[[1]] - a, the variable B is just a scalar and not a matrix (why is this?) Because [[i]] indexes more general vectors, and if you do B[[1]] when B is NULL, R doesnt know if you want B to be a list or a simple vector. If you initialise B as an empty list then R knows: B=list() B list() B[[1]]=b B [[1]] [,1] [1,]1 Barry __ R-help@stat.math.ethz.ch 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] [[ gotcha
Hi try different way of list definition, see below. On 16 Jan 2007 at 10:10, Robin Hankin wrote: From: Robin Hankin [EMAIL PROTECTED] Date sent: Tue, 16 Jan 2007 10:10:42 + To: RHelp help r-help@stat.math.ethz.ch Subject:[R] [[ gotcha The following gotcha caught me off-guard just now. I have two matrices, a and b: a - matrix(1,3,3) b - matrix(1,1,1) (note that both a and b are matrices). I want them in a list: B-vector(list, 2) B[[1]]-a B[[1]]-b here is no complain. HTH Petr B - NULL B[[1]] - a B[[2]] - b B [[1]] [,1] [,2] [,3] [1,]111 [2,]111 [3,]111 [[2]] [,1] [1,]1 This is fine. But swapping a and b over does not behave as desired: B - NULL B[[1]] - b B[[2]] - a Error in B[[2]] - a : more elements supplied than there are to replace The error is given because after B[[1]] - a, the variable B is just a scalar and not a matrix (why is this?) What's the bulletproof method for assigning matrices to a list (whose length is not known at runtime)? -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch 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. Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] [[ gotcha
To create a empty list do: B - list() /H On 1/16/07, Robin Hankin [EMAIL PROTECTED] wrote: The following gotcha caught me off-guard just now. I have two matrices, a and b: a - matrix(1,3,3) b - matrix(1,1,1) (note that both a and b are matrices). I want them in a list: B - NULL B[[1]] - a B[[2]] - b B [[1]] [,1] [,2] [,3] [1,]111 [2,]111 [3,]111 [[2]] [,1] [1,]1 This is fine. But swapping a and b over does not behave as desired: B - NULL B[[1]] - b B[[2]] - a Error in B[[2]] - a : more elements supplied than there are to replace The error is given because after B[[1]] - a, the variable B is just a scalar and not a matrix (why is this?) What's the bulletproof method for assigning matrices to a list (whose length is not known at runtime)? -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] [[ gotcha
Robin Hankin wrote: The following gotcha caught me off-guard just now. I have two matrices, a and b: a - matrix(1,3,3) b - matrix(1,1,1) (note that both a and b are matrices). I want them in a list: B - NULL B[[1]] - a B[[2]] - b B [[1]] [,1] [,2] [,3] [1,]111 [2,]111 [3,]111 [[2]] [,1] [1,]1 This is fine. But swapping a and b over does not behave as desired: B - NULL B[[1]] - b B[[2]] - a Error in B[[2]] - a : more elements supplied than there are to replace The error is given because after B[[1]] - a, the variable B is just a scalar and not a matrix (why is this?) What's the bulletproof method for assigning matrices to a list (whose length is not known at runtime)? not sure about bulletproof, but: you should tell R that B is really intended to be a list in the first place: B - list() the rest then works as you intended. whether the 'simplification' of your 1x1 matrix to a scalar in your example is canonical (and desirable) behaviour seems a question for some of the experts (it's a bit reminiscent of the `drop = TRUE' vs. `drop = FALSE' problem) joerg -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] [[ gotcha
On Tue, 16 Jan 2007, Robin Hankin wrote: The following gotcha caught me off-guard just now. Checking the relevant help page is always a good idea (and that is why the posting guide asks that you do so before posting). I have two matrices, a and b: a - matrix(1,3,3) b - matrix(1,1,1) (note that both a and b are matrices). I want them in a list: B - NULL So why did you not create a list, e.g. by list() or vector(list, 2)? B[[1]] - a B[[2]] - b B [[1]] [,1] [,2] [,3] [1,]111 [2,]111 [3,]111 [[2]] [,1] [1,]1 This is fine. But swapping a and b over does not behave as desired: B - NULL B[[1]] - b B[[2]] - a Error in B[[2]] - a : more elements supplied than there are to replace The error is given because after B[[1]] - a, the variable B is just a scalar and not a matrix (why is this?) You said wanted a list, and got a numeric vector (R has no scalars). In your first example you got a length-one list, not a matrix. The type-promotion rules for [- and [[- are complex, and you should not rely on knowing what they currently are (they do change from time to time). But this one is right there on the help page (?[[): When '$-' is applied to a 'NULL' 'x', it first coerces 'x' to 'list()'. This is what also happens with '[[-' if the replacement value 'value' is of length greater than one: if 'value' has length 1 or 0, 'x' is first coerced to a zero-length vector of the type of 'value'. What's the bulletproof method for assigning matrices to a list (whose length is not known at runtime)? Start with a list. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] Request regarding cluster package
Bhanu Kalyan.K wrote: Dear Mr. Bengtsson, I see that there is a package exclusively for clustering data, named as Cluster Package in R library. It has some clustering algorithms implemented. Can you tell me how to implement the CLARA and PAM functions from that package for my data? What about typing library(cluster) ?pam ?clara Uwe Ligges Bhanu Kalyan K B.Tech Final Year, CSE Tel: +91-9885238228 Alternate E-Mail: [EMAIL PROTECTED] - 8:00? 8:25? 8:40? Find a flick in no time [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] Gaussian glm for grouped data with unequal variances
Dawn Ashcourt wrote: Hello - I am fairly new to R, (i.e., ability to create functions/write programs insignificant) and was wondering if there might be a convenient way to model the following: I want to fit a gaussian glm to grouped data, while allowing for unequal variances in each of the groups. More specifically, my data set looks something like this: data group 176 1 282 1 383 1 454 1 535 1 646 1 787 1 868 1 987 2 10 95 2 11 98 2 12 100 2 13 109 2 14 109 2 15 100 2 16 81 2 17 75 2 18 68 2 19 67 2 20 105 3 et cetera. --- There are seven groups in all, each with a different number of observations. The idea is to compare a model in which all the data points can be modeled with a single mean (i.e., if all the group means are equal), or if the data suggests that each of the groups has a different mean. In other words, I want to do a Likelihood ratio test on whether or not the group means are significantly different from each other: the full model would be glm(data ~ as.factor(group)-1, family = gaussian), to be compared against a restricted model that only includes an intercept. However, I also need to allow for the fact that each group has a different variance. And this I have no idea how to do. I would really appreciate some help in this matter. Have you considered oneway.test()? For example: ## Not assuming equal variances oneway.test(breaks ~ tension, data = warpbreaks) One-way analysis of means (not assuming equal variances) data: breaks and tension F = 5.8018, num df = 2.00, denom df = 32.32, p-value = 0.007032 Thank you in advance, Dawn. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch 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] Gaussian glm for grouped data with unequal variances
Hi, I would suggest to use lme for doing that: library(nlme) vf1Ident - varIdent( c(m = 0.5), form = ~ 1 | group ) fm.lme - lme(data ~ group, weights = vf1Ident. data = DATA) anova(fm.lme) Hope this helps, Thilo On Tuesday 16 January 2007 10:30, Dawn Ashcourt wrote: Hello - I am fairly new to R, (i.e., ability to create functions/write programs insignificant) and was wondering if there might be a convenient way to model the following: I want to fit a gaussian glm to grouped data, while allowing for unequal variances in each of the groups. More specifically, my data set looks something like this: data group 176 1 282 1 383 1 454 1 535 1 646 1 787 1 868 1 987 2 10 95 2 11 98 2 12 100 2 13 109 2 14 109 2 15 100 2 16 81 2 17 75 2 18 68 2 19 67 2 20 105 3 et cetera. --- There are seven groups in all, each with a different number of observations. The idea is to compare a model in which all the data points can be modeled with a single mean (i.e., if all the group means are equal), or if the data suggests that each of the groups has a different mean. In other words, I want to do a Likelihood ratio test on whether or not the group means are significantly different from each other: the full model would be glm(data ~ as.factor(group)-1, family = gaussian), to be compared against a restricted model that only includes an intercept. However, I also need to allow for the fact that each group has a different variance. And this I have no idea how to do. I would really appreciate some help in this matter. Thank you in advance, Dawn. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Thilo Kellermann Department of Psychiatry und Psychotherapy RWTH Aachen University Pauwelstr. 30 52074 Aachen Tel.: +49 (0)241 / 8089977 Fax.: +49 (0)241 / 8082401 E-Mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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.
[R] SARIMA problem
Hi, I have a problem with the ARIMA function, occuring when I set the parameter per (the period of SARIMA model) to a high value (see the exemple bellow). It seems that when per is high it takes a too large amount of memory to calculate the model and I have a memory storage error. But I don't really understand why it takes more memory when per is high, as there is the same number of parameter to estimate. Does anyone know what to do? exemple: x = arima.sim(list(order=c(1,0,0), ar=.9), n=1000) per-200 arima(x, order = c(1, 0, 0),seasonal = list(order =c(1, 0, 0), period =per),method='CSS') fails whereas for per=175 it works well. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] SARIMA problem
On Tue, 16 Jan 2007, yannig goude wrote: Hi, I have a problem with the ARIMA function, occuring when I set the parameter per (the period of SARIMA model) to a high value (see the exemple bellow). It seems that when per is high it takes a too large amount of memory to calculate the model and I have a memory storage error. But I don't really understand why it takes more memory when per is high, as there is the same number of parameter to estimate. Try arima0. Does anyone know what to do? exemple: x = arima.sim(list(order=c(1,0,0), ar=.9), n=1000) per-200 arima(x, order = c(1, 0, 0),seasonal = list(order =c(1, 0, 0), period =per), method='CSS') fails whereas for per=175 it works well. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
[R] nlme : convergence problem and other errors
Dear R-user, I am trying to use the R nlme function to fit a non linear mixed effects model. The model I wand to fit is an individual somatic growth model with 4 parameters. For all parameters both fixed and random effects have to be estimated, as well as their covariance matrix (see the formula bellow). The data are simulated with the same growth model as in the nlme, with know parameters, and covariance matrix. I tried to fit the model with several simulated data sets, but most of the time, R returns an error message. there are three main types of errors : - there is a singular matrix - a factor is reduced bellow the PNLS level. - max number of iteration is reached but there is no convergence. Do you know how to resolve these problems. Is there a way to modify the parameters of the maximization algorithm to avoid these error messages? Furthermore, do you know if it is possible to fix the values of the fixed effects so that the model only has to estimate the random effects? Thank you for your help and answers. Regards, Thomas Brunel pds.fit-nlme(pds~(exp (lna)/(exp (lnb) + 1/(1 + exp(1000 * (exp (lntmat) - t + 0.5))) * exp (lnc)))^4 * (1 - (1 - ( 0.051 * (1 - 1/(1 + exp(1000 * (exp (lntmat) - t + 0.5 + (exp (lna)/exp (lnb))^4 * (1 - (1 - (0.051)^0.25 * (exp (lnb)/exp (lna))) * exp( - ((exp (lnb) * exp (lntmat))/4)))^4 * 1/(1 + exp(1000 * (exp (lntmat) - t + 0.5^0.25 * ((exp (lnb) + 1/(1 + exp(1000 * (exp (lntmat) - t + 0.5))) * exp (lnc))/exp (lna))) * exp( - (((exp (lnb) + 1/(1 + exp(1000 * (exp (lntmat) - t + 0.5))) * exp (lnc)) *(t - (1/(1 + exp(1000 * (exp (lntmat) - t + 0.5))) * exp (lntmat/4)))^4,data=pdsdata,fixed=lna+lnb+lnc+lntmat~1,random= lna+lnb+lnc+lntmat~1|indi ,start=c(lna=log(a2),lnb=log(b2) ,lnc = log(c2), lntmat=log(1200))) -- Laboratoire Halieutique de Port-en-Bessin avenue du Général de Gaulle 14520 Port-en-Bessin tél : 02 31 51 56 00 (standard) fax : 02 31 51 56 01 page personnelle (CV online): http://www.ifremer.fr/drvrhbr/personnel/brunel/index.htm __ R-help@stat.math.ethz.ch 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.
[R] number of Nodes in Random Forest
I'm calculating nodes using Random Forest in R but i only get nodes for a fraction of the compounds i want to calculate, the rest is ommited and is not printed in the output file, (i'm working with 3012 compounds). What can i do to have nodes printed for all the compounds. Thanks Gonçalo __ R-help@stat.math.ethz.ch 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.
[R] problems with for loop
Hello,
With this program I try to repeat analysis for different years. The
results of the analysis are not printed when in the loop, except for the
year sequence. What is wrong?
Thanks a lot.
for (i in 92:99){
cat(\n,
=\n,
YEAR =,i,\n,
=\n
)
canos1 - subset (canos, canos$YEAR==i)
LinearModel.1 - lm(MM_P ~ BLOC + TIL, data=canos1)
summary(LinearModel.1)
Anova(LinearModel.1, type=II)
Anova(LinearModel.1, type=III)
}
--
**
Jorge Lampurlanés Castel
Departament d'Enginyeria Agroforestal
Escola Tècnica Superior d'Enginyeria Agrària
Universitat de Lleida
Avinguda Rovira Roure, 191
25198-LLEIDA
SPAIN
Tl.: +34 973 70 25 37
Fax.:+34 073 70 26 73
e-mail: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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] problems with for loop
If you really want the summary() etc to print to STDOUT use cat() or
print(). However other ways to post-process results may be preferrable,
I think about Sweave, xtable, etc.
Regards
Michael
Jorge Lampurlanes Castel wrote:
Hello,
With this program I try to repeat analysis for different years. The
results of the analysis are not printed when in the loop, except for the
year sequence. What is wrong?
Thanks a lot.
for (i in 92:99){
cat(\n,
=\n,
YEAR =,i,\n,
=\n
)
canos1 - subset (canos, canos$YEAR==i)
LinearModel.1 - lm(MM_P ~ BLOC + TIL, data=canos1)
summary(LinearModel.1)
Anova(LinearModel.1, type=II)
Anova(LinearModel.1, type=III)
}
--
Michael T. Mader
Institute of Stem Cell Research
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
D-85764 Neuherberg
0049-89-3187-3683
The limits of my language are the limits of my world.
Ludwig Wittgenstein Tractatus Logico-Philosophicus 5.6, 1918
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] R on Windows Vista
Did anyone try to run R under Window Vista, especially Windows Vista 64bit? Thanks. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re : problems with for loop
Hi,
Use print function print(Anova(...))
How about use of lappy functions ? It can be much easier
foo-function(data,formula){
LM - lm(formula,data=data)
Result-list(LmSum-summary(LM), Type2-Anova(LM,
type=II)),Type3-Anova(LM, type=III))
}
and print(lappy(split(data,year),foo,formula=...))
Justin BEM
Elève Ingénieur Statisticien Economiste
BP 294 Yaoundé.
Tél (00237)9597295.
- Message d'origine
De : Jorge Lampurlanes Castel [EMAIL PROTECTED]
À : r-help@stat.math.ethz.ch
Envoyé le : Mardi, 16 Janvier 2007, 13h10mn 10s
Objet : [R] problems with for loop
Hello,
With this program I try to repeat analysis for different years. The
results of the analysis are not printed when in the loop, except for the
year sequence. What is wrong?
Thanks a lot.
for (i in 92:99){
cat(\n,
=\n,
YEAR =,i,\n,
=\n
)
canos1 - subset (canos, canos$YEAR==i)
LinearModel.1 - lm(MM_P ~ BLOC + TIL, data=canos1)
summary(LinearModel.1)
Anova(LinearModel.1, type=II)
Anova(LinearModel.1, type=III)
}
--
**
Jorge Lampurlanés Castel
Departament d'Enginyeria Agroforestal
Escola Tècnica Superior d'Enginyeria Agrària
Universitat de Lleida
Avinguda Rovira Roure, 191
25198-LLEIDA
SPAIN
Tl.: +34 973 70 25 37
Fax.:+34 073 70 26 73
e-mail: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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.
___
Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions !
Profitez des connaissances, des opinions et des expériences des internaut
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] R on Windows Vista
On 1/16/2007 9:35 AM, Sicotte, Hugues Ph.D. wrote: Did anyone try to run R under Window Vista, especially Windows Vista 64bit? I know someone who has (but I don't know if it was 32 bit or 64 bit). He had a little trouble installing, because Vista tightens security slightly: you need to run the installer with higher than default permissions. Whichever version of Vista you run, R will be 32 bit for some time to come: we don't have a 64 bit toolchain available yet, or a volunteer to do the builds. (I'm unlikely to be upgrading to 64 bit Windows in the foreseeable future.) Duncan Murdoch __ R-help@stat.math.ethz.ch 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] problems with for loop
Jorge Lampurlanes Castel wrote:
Hello,
With this program I try to repeat analysis for different years. The
results of the analysis are not printed when in the loop, except for the
year sequence. What is wrong?
Thanks a lot.
for (i in 92:99){
cat(\n,
=\n,
YEAR =,i,\n,
=\n
)
canos1 - subset (canos, canos$YEAR==i)
LinearModel.1 - lm(MM_P ~ BLOC + TIL, data=canos1)
summary(LinearModel.1)
Anova(LinearModel.1, type=II)
Anova(LinearModel.1, type=III)
}
You might consider using by() rather than a loop as follows:
library(car)
by(canos, canos$YEAR,
function(x){fm - lm(MM_P ~ BLOC + TIL, data=x)
ans - list(summary(fm), Anova(fm, type=II), Anova(fm, type=III))
}
)
The result can be conveniently stored as a list of lists.
--
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
__
R-help@stat.math.ethz.ch 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] feedback on writing r extensions
On Tue, 16 Jan 2007, Martin Maechler wrote: Scott == Scott Harrison [EMAIL PROTECTED] on Mon, 15 Jan 2007 13:15:09 -0500 writes: ... For edits, we'd mostly like to receive feedback on the *source* of the above automatically produced document (which is also the source of the PDF version, same URL as above, just replace .html by .pdf) The development source is always available at https://svn.r-project.org/R/trunk/doc/manual/R-exts.texi Would it be horrid to include the reference to the sources in the derived documents? It might help with self-documenting the process and help demonstrate the benefits of R's open source philosophy. Thanking you for offering feedback, Thank you. Dave -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ R-help@stat.math.ethz.ch 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] feedback on writing r extensions
It would also be nice if there were links in the .Rd files back to the source of the commands, not just the source of the documentation. That would facilitate and encourage readers to paruse the source to clarify the meaning of the help files. On 1/16/07, David Forrest [EMAIL PROTECTED] wrote: On Tue, 16 Jan 2007, Martin Maechler wrote: Scott == Scott Harrison [EMAIL PROTECTED] on Mon, 15 Jan 2007 13:15:09 -0500 writes: ... For edits, we'd mostly like to receive feedback on the *source* of the above automatically produced document (which is also the source of the PDF version, same URL as above, just replace .html by .pdf) The development source is always available at https://svn.r-project.org/R/trunk/doc/manual/R-exts.texi Would it be horrid to include the reference to the sources in the derived documents? It might help with self-documenting the process and help demonstrate the benefits of R's open source philosophy. Thanking you for offering feedback, Thank you. Dave -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
[R] parallel coordinates plot
Dear List, I want to make a parallel coordinates plot with the specific variables on the abscissa and the cases on the ordinate should be dyed dependent on another nominal variable from the data frame. I use the parcoord function. Thanks for your help! Best regards, Marco __ R-help@stat.math.ethz.ch 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.
[R] plot portion of a line
Dear HelpeRs, Given: x - rnorm(50) y - rnorm(50) plot(x,y) abline(lm(x ~ y)) Is there a way to plot just a portion of the line? Say for values of x 2.0 or x -2.0 and x 4.0. (Still fitting all the points.) Thank you, jab -- John Bollinger, CFA, CMT www.BollingerBands.com If you advance far enough, you arrive at the beginning. __ R-help@stat.math.ethz.ch 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] plot portion of a line
you could try something like the following: x - rnorm(50) y - rnorm(50) obj - lm(y ~ x) par(mfrow = c(2, 2)) plot(x, y, main = x -1) x. - c(min(x), -1) y. - predict(obj, data.frame(x = x.)) lines(x., y.) plot(x, y, main = x 1) x. - c(1, max(x)) y. - predict(obj, data.frame(x = x.)) lines(x., y.) plot(x, y, main = x -1 x 1) x. - c(-1, 1) y. - predict(obj, data.frame(x = x.)) lines(x., y.) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: BBands [EMAIL PROTECTED] To: R-Help r-help@stat.math.ethz.ch Sent: Tuesday, January 16, 2007 5:16 PM Subject: [R] plot portion of a line Dear HelpeRs, Given: x - rnorm(50) y - rnorm(50) plot(x,y) abline(lm(x ~ y)) Is there a way to plot just a portion of the line? Say for values of x 2.0 or x -2.0 and x 4.0. (Still fitting all the points.) Thank you, jab -- John Bollinger, CFA, CMT www.BollingerBands.com If you advance far enough, you arrive at the beginning. __ R-help@stat.math.ethz.ch 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. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch 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] plot portion of a line
Use segments. In the following we overlay the black abline with a wider red segments line segment: set.seed(1) x - rnorm(50) y - rnorm(50) plot(y ~ x) y.lm - lm(y ~ x) abline(y.lm) # omit this line if black abline not wanted x0 - c(-2, 4) y0 - predict(y.lm, list(x = x0)) segments(x0[1], y0[1], x0[2], y0[2], col = red, lwd = 2) On 1/16/07, BBands [EMAIL PROTECTED] wrote: Dear HelpeRs, Given: x - rnorm(50) y - rnorm(50) plot(x,y) abline(lm(x ~ y)) Is there a way to plot just a portion of the line? Say for values of x 2.0 or x -2.0 and x 4.0. (Still fitting all the points.) Thank you, jab -- John Bollinger, CFA, CMT www.BollingerBands.com If you advance far enough, you arrive at the beginning. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
[R] system(mysql... Does not recognize as passing an attribute
Hi,
This is my command line request: mysql -u root -ppassword -D quant
c:/cline.txt
This line works from the command line in windows.
In R, when I try to use the system function, it does not work,
system(paste('mysql -u root -ppassword -D quant
c:/cline.txt'),show.output.on.console = TRUE)
ERROR 1102 (42000): Incorrect database name 'c:/cline.txt'
It seems that the caracter is not recognized as an attribute.
Thanks,
Pierre
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
**
AVIS DE NON-RESPONSABILITE: Ce document transmis par courrie...{{dropped}}
__
R-help@stat.math.ethz.ch 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.
[R] system(mysql... Does not recognize as passing an attribute (No HTML)
Hi,
This is my command line request: mysql -u root -ppassword -D quant
c:/cline.txt
This line works from the command line in windows.
In R, when I try to use the system function, it does not work,
system(paste('mysql -u root -ppassword -D quant
c:/cline.txt'),show.output.on.console = TRUE)
ERROR 1102 (42000): Incorrect database name 'c:/cline.txt'
It seems that the character is not recognized as an attribute.
Thanks,
Pierre
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
**
AVIS DE NON-RESPONSABILITE: Ce document transmis par courrie...{{dropped}}
__
R-help@stat.math.ethz.ch 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] system(mysql... Does not recognize as passing an attribute
You are on Windows, and that is how system() works on Windows (not
just in R, but in C, Perl ...). The help says
command: the system command to be invoked, as a string.
A command line is not a 'system command', and the is interpreted by the
shell you are running as your 'command line in WIndows'.
Try shell() instead.
On Tue, 16 Jan 2007, Lapointe, Pierre wrote:
Hi,
This is my command line request: mysql -u root -ppassword -D quant
c:/cline.txt
This line works from the command line in windows.
In R, when I try to use the system function, it does not work,
system(paste('mysql -u root -ppassword -D quant
c:/cline.txt'),show.output.on.console = TRUE)
ERROR 1102 (42000): Incorrect database name 'c:/cline.txt'
It seems that the caracter is not recognized as an attribute.
Thanks,
Pierre
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
**
AVIS DE NON-RESPONSABILITE: Ce document transmis par courrie...{{dropped}}
__
R-help@stat.math.ethz.ch 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.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@stat.math.ethz.ch 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] system(mysql... Does not recognize as passing an attribute (No HTML)
You can try this:
system(paste('mysql -u hsdlife -p -D life ', file('c:/teste.txt')),
show.output.on.console = TRUE)
On 16/01/07, Lapointe, Pierre [EMAIL PROTECTED] wrote:
Hi,
This is my command line request: mysql -u root -ppassword -D quant
c:/cline.txt
This line works from the command line in windows.
In R, when I try to use the system function, it does not work,
system(paste('mysql -u root -ppassword -D quant
c:/cline.txt'),show.output.on.console = TRUE)
ERROR 1102 (42000): Incorrect database name 'c:/cline.txt'
It seems that the character is not recognized as an attribute.
Thanks,
Pierre
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
**
AVIS DE NON-RESPONSABILITE: Ce document transmis par courrie...{{dropped}}
__
R-help@stat.math.ethz.ch 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.
--
Henrique Dallazuanna
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] How to format R code in LaTex documents
At 14:12 15/01/2007, Frank E Harrell Jr wrote:
Benjamin Dickgiesser wrote:
Hi,
I am planning on putting some R script in an appendix of a LaTex
document. Can anyone recommend me a way of how to format it? Is there
a way to keep all line breaks without having to insert \\ in every
single line?
Thank you!
Benjamin
Here's one way and I would appreciate anyone's
improvements. I've also included solutions from
two others. Please let me know what you decide to use. -Frank
Some interesting ideas below so just to add that
I find I often have to use the linewidth
parameter to avoid lines wrapping. This is
valuable if you are also going to include bits of
R output as well (you can control the width of
your own code fragments of course).
\usepackage{listings,relsize}
\lstloadlanguages{R}
\lstset{language=R,basicstyle=\smaller[2],commentstyle=\rmfamily\smaller,
showstringspaces=false,%
xleftmargin=4ex,literate={-}{{$\leftarrow$}}1 {~}{{$\sim$}}1}
\lstset{escapeinside={(*}{*)}} % for (*\ref{ }*) inside lstlistings (S code)
. . .
\begin{lstlisting}
. . . S code . . .
\end{lstlisting}
The following code was provided by Vincent Goulet:
listings is a great package to highlight R keywords and comments and --- that
was my main use of the package --- index those keywords. I found that I had
to slightly redefine the list of keywords included in listings. I still did
not take the time to submit a patch to the author, though...
In any case, here's what I use, if it can be of any help to anyone:
\lstloadlanguages{R}
\lstdefinelanguage{Renhanced}[]{R}{%
morekeywords={acf,ar,arima,arima.sim,colMeans,colSums,is.na,is.null,%
mapply,ms,na.rm,nlmin,replicate,row.names,rowMeans,rowSums,seasonal,%
sys.time,system.time,ts.plot,which.max,which.min},
deletekeywords={c},
alsoletter={.\%},%
alsoother={:_\$}}
\lstset{language=Renhanced,extendedchars=true,
basicstyle=\small\ttfamily,
commentstyle=\textsl,
keywordstyle=\mdseries,
showstringspaces=false,
index=[1][keywords],
indexstyle=\indexfonction}
with
[EMAIL PROTECTED]
-- Vincent Goulet, Associate Professor École
d'actuariat Université Laval, Québec
[EMAIL PROTECTED] http://vgoulet.act.ulaval.ca
Anupam Tyagi provided the following:
\documentclass{report}
\usepackage{listings}
\begin{document}
Somethings .
\lstset{% general command to set parameter(s)
basicstyle=\small, % print whole in small
stringstyle=\ttfamily, % typewriter type for strings
numbers=left, % numbers on the left
numberstyle=\tiny, % Tiny numbers
stepnumber=2, % number every second line of code
numbersep=5pt, % 5pt seperation between numbering and code listing
language=R }
\lstinputlisting{text1.R}
\end{document}
Michael Dewey
http://www.aghmed.fsnet.co.uk
__
R-help@stat.math.ethz.ch 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] R on Windows Vista
I've run R on the 32 bit version of Vista. Because of Vista's extra security controls you can't install a library easily, however, even though I had not trouble installing R. You must first set the security level to allow it (I can't recall the details but it's not to difficult to figure out), then install the libraries, then re-set the security levels. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sicotte, Hugues Ph.D. Sent: Tuesday, January 16, 2007 9:36 AM To: r-help@stat.math.ethz.ch Subject: [R] R on Windows Vista Did anyone try to run R under Window Vista, especially Windows Vista 64bit? Thanks. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
[R] nested hierarchical design
Dear R-Helpers, I would like to know what syntax I need to use to do a nested anova for 1. a continuous variable and 2. count data (x out of y) 1. The first I used to do in SPSS and I would like to be able to do it in R as well. This is the hierarchical model I would like to use: a continuous variable explained by factor A(fixed) + factor B(random) nested in A + factor C (random) nested in factor B (which is nested in A). The data is unbalanced at all levels, meaning different nrs of B per A, different nrs of C for B, different nrs of values per C In SPSS this seems to be quite simple with a small writing in the syntax (see below). But how do I get the same results in R with lme? SPSS syntax: UNIANOVA var BY A B C /RANDOM = B C /METHOD = SSTYPE(3) /INTERCEPT = INCLUDE /CRITERIA = ALPHA(.05) /DESIGN = A B(A) C(B(A))). 2. the same model but than for count data (like 15 out of 30, 23 out of 60) instead of the continous variable(I know the basics of glm in R) Thanks a lot for your help Jelmer __ R-help@stat.math.ethz.ch 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.
[R] (no subject)
I'm calculating nodes using Random Forest in R but i only get nodes for a fraction of the compounds i want to calculate, the rest is ommited and is not printed in the output file, (i'm working with 3012 compounds). What can i do to have nodes printed for all the compounds. Thanks Gonçalo __ R-help@stat.math.ethz.ch 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.
[R] RODBC: sqlQuery is successful, but a similar sqlFetch returns error
Greetings guRus -- I have successfully queried a large (24,445 rows by 281 cols.) in-house database using the following RODBC query (without the line breaks) testout - sqlQuery(channel, select idSchedule,EXCL_Total from dbo.vwC1198_2006_RawData_With_CMPL_EXCL) This returns a dataframe of 24445 rows and two columns (as intended), but the following command testout - sqlFetch(channel,dbo.vwC1198_2006_RawData_With_CMPL_EXCL,colnames = TRUE,rownames = idSchedule) returns the error message in odbcTableExists(channel, sqtable) : 'dbo.vwC1198_2006_RawData_With_CMPL_EXCL': table not found on channel The value of channel did not change between the two commands. Based on the help files for sqlFetch and sqlQuery, it is not clear to me why one command would find the table and the other would not. I am running R 2.4.1 on a Windows XP pro machine with 2 gig of memory. Thanks for any suggestions or hints, Ben Fairbank [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] R on Windows Vista
Charles Annis, P.E. wrote: I've run R on the 32 bit version of Vista. Because of Vista's extra security controls you can't install a library You mean you can't install a *package* into a library. Are you sure that you cannot install into some other library that is in some directory where you have got write access to? Uwe Ligges easily, however, even though I had not trouble installing R. You must first set the security level to allow it (I can't recall the details but it's not to difficult to figure out), then install the libraries, then re-set the security levels. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sicotte, Hugues Ph.D. Sent: Tuesday, January 16, 2007 9:36 AM To: r-help@stat.math.ethz.ch Subject: [R] R on Windows Vista Did anyone try to run R under Window Vista, especially Windows Vista 64bit? Thanks. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] plot portion of a line
As in Dmitris' post lines is a somewhat more succint so here it is again replacing segments with lines: set.seed(1) x - rnorm(50) y - rnorm(50) plot(y ~ x) y.lm - lm(y ~ x) abline(y.lm) # omit this line if black abline not wanted x0 - c(-2, 4) y0 - predict(y.lm, list(x = x0)) lines(y0 ~ x0, col = red, lwd = 2) On 1/16/07, Gabor Grothendieck [EMAIL PROTECTED] wrote: Use segments. In the following we overlay the black abline with a wider red segments line segment: set.seed(1) x - rnorm(50) y - rnorm(50) plot(y ~ x) y.lm - lm(y ~ x) abline(y.lm) # omit this line if black abline not wanted x0 - c(-2, 4) y0 - predict(y.lm, list(x = x0)) segments(x0[1], y0[1], x0[2], y0[2], col = red, lwd = 2) On 1/16/07, BBands [EMAIL PROTECTED] wrote: Dear HelpeRs, Given: x - rnorm(50) y - rnorm(50) plot(x,y) abline(lm(x ~ y)) Is there a way to plot just a portion of the line? Say for values of x 2.0 or x -2.0 and x 4.0. (Still fitting all the points.) Thank you, jab -- John Bollinger, CFA, CMT www.BollingerBands.com If you advance far enough, you arrive at the beginning. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] RODBC: sqlQuery is successful, but a similar sqlFetch returns error
'.' is invalid in an SQL table name. I don't know what driver you are using (you seem very reluctant to tell us anything useful about your DBMS), but dbo.vwC1198_2006_RawData_With_CMPL_EXCL probably means table vwC1198_2006_RawData_With_CMPL_EXCL in database dbo, and that is valid as part of SQL, but not in your usage in sqlFetch. On Tue, 16 Jan 2007, Ben Fairbank wrote: Greetings guRus -- I have successfully queried a large (24,445 rows by 281 cols.) in-house database using the following RODBC query (without the line breaks) testout - sqlQuery(channel, select idSchedule,EXCL_Total from dbo.vwC1198_2006_RawData_With_CMPL_EXCL) This returns a dataframe of 24445 rows and two columns (as intended), but the following command testout - sqlFetch(channel,dbo.vwC1198_2006_RawData_With_CMPL_EXCL,colnames = TRUE,rownames = idSchedule) returns the error message in odbcTableExists(channel, sqtable) : 'dbo.vwC1198_2006_RawData_With_CMPL_EXCL': table not found on channel The value of channel did not change between the two commands. Based on the help files for sqlFetch and sqlQuery, it is not clear to me why one command would find the table and the other would not. I am running R 2.4.1 on a Windows XP pro machine with 2 gig of memory. Thanks for any suggestions or hints, Ben Fairbank [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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] number of Nodes in Random Forest
Hi, Goncalo: did u use compounds as features when building rf? If so, some compounds are NOT randomly selected in splitting nodes, which might explain what you observed. But you need to provide more info for us to help you, like those parameters you used to build rf. You can use varImpPlot to see what exactly compounds were used by setting n.var (see ?varImpPlot) or you can use nrow(YourTrainingX$importance) to get that number too. HTH, w. On 1/16/07, Gonçalo Carrera [EMAIL PROTECTED] wrote: I'm calculating nodes using Random Forest in R but i only get nodes for a fraction of the compounds i want to calculate, the rest is ommited and is not printed in the output file, (i'm working with 3012 compounds). What can i do to have nodes printed for all the compounds. Thanks Gonçalo __ R-help@stat.math.ethz.ch 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. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch 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.
[R] LSD multiple comparison test
Hello, There is any way of performing a LSD (Least Significant Diference) multiple comparison test to separate the levels of the significant factors of a model? I am migrating from SAS. Thanks a lot. -- ** Jorge Lampurlanés Castel Departament d'Enginyeria Agroforestal Escola Tècnica Superior d'Enginyeria Agrària Universitat de Lleida Avinguda Rovira Roure, 191 25198-LLEIDA SPAIN Tl.: +34 973 70 25 37 Fax.:+34 073 70 26 73 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] LSD multiple comparison test
Look at the glht function in the multcomp package and the MMC functions in the HH package. Rich __ R-help@stat.math.ethz.ch 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] Is it the PPS samples i needed in R?
On Fri, 12 Jan 2007, zhijie zhang wrote: Dear friends, I want to do a unequal probability sampling, that is, Probability Proportionate to size, Is it right for the following programs? Say my original dataset is: ID Population 1 100 2 200 3 300 IF the population is large ,then the corresponding ID has the large Probability to be selected. sample(A$ID, size=2, replace = FALSE, prob = A$population) #suppose the dataset name is A. Is it the PPS samples i needed ? No, this does not give PPS samples for size1. The pps and sampling packages have code for PPS samples. -thomas __ R-help@stat.math.ethz.ch 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] feedback on writing r extensions
On Tue, 16 Jan 2007, Gabor Grothendieck wrote: It would also be nice if there were links in the .Rd files back to the source of the commands, not just the source of the documentation. That would facilitate and encourage readers to paruse the source to clarify the meaning of the help files. Perhaps it would be feasible to make an RSourceSearch() function (like RSiteSearch()) that could recognize things like documentation, functions, and internals and direct users to the source code. Dave On 1/16/07, David Forrest [EMAIL PROTECTED] wrote: On Tue, 16 Jan 2007, Martin Maechler wrote: Scott == Scott Harrison [EMAIL PROTECTED] on Mon, 15 Jan 2007 13:15:09 -0500 writes: ... For edits, we'd mostly like to receive feedback on the *source* of the above automatically produced document (which is also the source of the PDF version, same URL as above, just replace .html by .pdf) The development source is always available at https://svn.r-project.org/R/trunk/doc/manual/R-exts.texi Would it be horrid to include the reference to the sources in the derived documents? It might help with self-documenting the process and help demonstrate the benefits of R's open source philosophy. Thanking you for offering feedback, Thank you. Dave -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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. -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ R-help@stat.math.ethz.ch 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.
[R] Rgui crashes when calling odbcClose()
Hi, I'm running Rgui v2.4.0, RODBC v1.1-8, and psqlODBC v8.2.0002. Whenever I do the following chan - odbcConnect(mydatabase, uid=admin) # connection to a postgresql db on a linux box tmp - sqlQuery(chan, select * from sometable;) # this is successfull odbcClose(chan) # this crashes Rgui and raises an error window containing the following MS error signature: AppName: rgui.exe AppVer 2.4.39566.0ModName: psqlodbc35w.dll ModVer: 8.2.0.2Offset: 3248 I didn't find anything relevant in the R Windows FAQ or a few queries of the help archives; appologies if this has been addressed before. Robert __ R-help@stat.math.ethz.ch 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] image() and nonsquare matrices
Look at the squishplot function in the TeachingDemos package. Does this set of commands work for you? library(TeachingDemos) squishplot(c(0.5,20.5),c(0.5,5.5),1) image(1:20,1:5,a,asp=1,xlab=label here) box() -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robin Hankin Sent: Friday, January 12, 2007 3:13 AM To: RHelp help Subject: [R] image() and nonsquare matrices How do I draw non-square matrices with image() and get the axes right? Try 1: a - matrix(rnorm(100),20,5) image(1:20,1:5,a,asp=1,xlab=label here) # No good because the axes don't touch the image Try 2: image(1:20,1:5,a,asp=1,axes=F,xlab=label here) axis(side=1,pos=0) # No good because the x axis label is floating far from the x axis. Try 3: image(1:20,1:5,a,asp=1,axes=F,xlab=,ylab=) axis(side=1,pos=0) # No good because the x axis label is absent. How to use image() with a non-square matrix and make axes and labels appear correctly? -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] labels outliers in boxplot
Some information on the outliers is returned from the boxplot function. Try
something like:
set.seed(123)
tmp - data.frame( group=gl(3,10),
y=rcauchy(30), sex=gl(2,5,30,c('M','F')) )
tmp2 - boxplot( split(tmp$y,tmp$group) )
identify( tmp2$group, tmp2$out, tmp2$group )
Or if your grouping variable works out to the same values as the x axis (used
integers) and you want to specify a 3rd variable to be the labels you can do:
Identify( tmp$group, tmp$y, tmp$sex )
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Wednesday, January 10, 2007 2:08 PM
To: r-help@stat.math.ethz.ch
Subject: [R] labels outliers in boxplot
Dear R-users,
Following is part of my data, where slide has 36 levels and
block 48 levels. I have done boxplot for each slide on the
same graph. There are outliers for each slide and I tried to
use indentify functtion to identify outliers in such a way
that when I click on an outlier or point, the points will be
labelled by either their block or ID or by both but without
success. How can I make it work or are there other ways to do
it than using identify function?
Thanks in advance,
Jenny,
dat1[1:10,]
y Slide Block ID Control
1 0.03147823 1 1 IgG-human 5
2 -0.23815974 1 1 LPPAANDVSVLTAAR 0
3 -0.71926359 1 1 HTKHYRVVSKPAALV 0
4 -0.14607826 1 1 FVALPAATADAYATT 0
5 0.89553073 1 1 NYPAMMAHAGDMAGY 0
6 -0.67587100 1 1 RRALRQIGVLERPVG 0
7 0.32636034 1 1 DCGTIRVGSFRGRWL 0
8 -1.44057259 1 1 MAKLSTDELLDAFKE 0
9 -0.37064338 1 1 LELSDFVKKFEETFE 0
10 -0.20387233 1 1 VSRRAKVDVLIVHTT 0
tb_ncs-subset(dat1,dat1$Control==1) ### this
data contains only negative controls
par(las=2,mar=c(10.1,4.1,4.1,2.1))
boxplot(split(tb_ncs$y,tb_ncs$Slide),col=orange,
cex=.65,
outline=TRUE,main=Negative control
response of each patient, cex.main=1, font.main=1,
col.main=blue,
names=c(1:35,B))
grid(nx=NA, ny=NULL)
### grid over boxplot
legend(bottomright, B = Buffer +
sec,text.col=blue)
out.block-
identify(tb_ncs$y,tb_ncs$Slide)
_
Flyger tiden iväg? Fånga dagen med Yahoo! Mails inbyggda
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch 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.
[R] Reminder: JSS Special volume R in ecology
Dear UseRs, one of the outcomes of the useR! 2006 conference held in Vienna was that JSS, the Journal of Statistical Software, is planning to publish a series of special volumes. They will be guest edited and each volume will have 5-10 issues (articles) of the usual JSS format. One of the volumes is related to the use of the R software in ecology. The submission deadline will end in one month on 2007-02-15. Please consult the call for papers in the R Wiki for details: http://wiki.r-project.org/rwiki/doku.php?id=misc:r_in_ecology_and_ecological_modelling Thomas Kneib Thomas Petzoldt, guest editors The original CFP was posted on Fri, 6 Oct 2006: https://listserv.umd.edu/cgi-bin/wa?A2=ind0610aL=ecolog-lP=11582 -- Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologie[EMAIL PROTECTED] 01062 Dresden http://tu-dresden.de/hydrobiologie/ GERMANY __ R-help@stat.math.ethz.ch 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] Controlling size of boxplot when it is added in a plot
One approach is to use the subplot function from the TeachingDemos
package. I could only get everything to line up properly if I specified
the xlim argument to hist directly and the same value as the ylim
argument to boxplot.
Try this:
x - rnorm(100)
library(TeachingDemos)
hist(x, breaks = 20, main = NULL, ylim = c(-2,
max(hs$counts)),xlim=c(-3,3))
subplot( boxplot(x, horizontal=T, ylim=c(-3,3),axes=F ),
par('usr')[1:2], c(par('usr')[3],0))
box()
I have seen things like this in teaching situations, but not much in the
non-academic world.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Charilaos Skiadas
Sent: Saturday, January 13, 2007 9:12 PM
To: R-Mailingliste
Subject: [R] Controlling size of boxplot when it is added in a plot
Greetings,
I am trying to add a boxplot to the bottom of a
histogram, right between the histogram bars and the x axis.
Here is the code I am using at the moment (the par line is
probably not relevant for our
discussion):
hs - hist(x, breaks = 20, plot = F)
par(mar = c(3,3,2,1))
hist(x, breaks = 20, main = NULL, ylim = c(-2,
max(hs$counts))) boxplot(x, horizontal = T, axes = T, add =
T, at = -1)
The problem is the following. As it is, the boxplot restricts
itself to the -1 line. I would like it to occupy both the -1
and the -2 lines ( I guess more generally I would like to
control how much vertical space the embedded boxplot
occupies). I tried to set the width parameter in the boxplot,
but that seemed to have no effect at all.
On an OT note, I haven't seen this way of combining a
histogram with a boxplot (perhaps I haven't looked really
hard). I thought it would be useful for my students to see
them next to each other, to develop a feeling for what
histograms might correspond to what boxplots. Is there
perhaps some reason why I should avoid showing those graphs
to them like that, that I am not aware of? Or just a reason
why I haven't seen them combined like this much?
TIA
Charilaos Skiadas
Department of Mathematics
Hanover College
P.O.Box 108
Hanover, IN 47243
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch 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.
[R] curious about dimension of 'apply' output when MARGIN=1
Reading the documentation for 'apply', I understand the following is working exactly as documented: M-matrix(1:6,ncol=2) M [,1] [,2] [1,]14 [2,]25 [3,]36 apply(M,2,function(column) column+c(1,2,3)) [,1] [,2] [1,]25 [2,]47 [3,]69 apply(M,1,function(row) row+c(1,2)) [,1] [,2] [,3] [1,]234 [2,]678 I'm not proposing any changes or extra arguments to 'apply'. Rather, I'm wondering what is the benefit for (or rationale behind) this somewhat unintuitive behavior in the case that MARGIN=1. Thanks, Ben __ R-help@stat.math.ethz.ch 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] plot portion of a line
Try the clipplot function from the TeachingDemos package: x - rnorm(50) y - rnorm(50) plot(x,y) clipplot( abline(lm(y~x), col='red'), xlim=c(1,3)) clipplot( abline(lm(y~x), col='blue'), xlim=c(-2,1)) Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of BBands Sent: Tuesday, January 16, 2007 9:16 AM To: R-Help Subject: [R] plot portion of a line Dear HelpeRs, Given: x - rnorm(50) y - rnorm(50) plot(x,y) abline(lm(x ~ y)) Is there a way to plot just a portion of the line? Say for values of x 2.0 or x -2.0 and x 4.0. (Still fitting all the points.) Thank you, jab -- John Bollinger, CFA, CMT www.BollingerBands.com If you advance far enough, you arrive at the beginning. __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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] curious about dimension of 'apply' output when MARGIN=1
The reshape package has an idempotent apply, iapply: library(reshape) iapply(M,1,function(row) row+c(1,2)) [,1] [,2] [1,]26 [2,]37 [3,]48 On 1/16/07, Benjamin Tyner [EMAIL PROTECTED] wrote: Reading the documentation for 'apply', I understand the following is working exactly as documented: M-matrix(1:6,ncol=2) M [,1] [,2] [1,]14 [2,]25 [3,]36 apply(M,2,function(column) column+c(1,2,3)) [,1] [,2] [1,]25 [2,]47 [3,]69 apply(M,1,function(row) row+c(1,2)) [,1] [,2] [,3] [1,]234 [2,]678 I'm not proposing any changes or extra arguments to 'apply'. Rather, I'm wondering what is the benefit for (or rationale behind) this somewhat unintuitive behavior in the case that MARGIN=1. Thanks, Ben __ R-help@stat.math.ethz.ch 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. __ R-help@stat.math.ethz.ch 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.
[R] Help on variable ranking
Hello all, I want to assign relative score to the predictor variables on the basis of its influence on the dependent variable. But I could not find any standard statistical approach appropriate for this purpose. Please suggest the possible approaches. Thanks in advance, Rupendra Chulyadyo Institute of Engineering, Tribhuvan University, Nepal [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Help on variable ranking
Rupendra, depending on the nature of your data (which you haven't mentioned), you might try hierarchical partitioning, as found in the hier.part package on CRAN. Cheers Andrew On Wed, Jan 17, 2007 at 11:07:18AM +0545, Rupendra Chulyadyo wrote: Hello all, I want to assign relative score to the predictor variables on the basis of its influence on the dependent variable. But I could not find any standard statistical approach appropriate for this purpose. Please suggest the possible approaches. Thanks in advance, Rupendra Chulyadyo Institute of Engineering, Tribhuvan University, Nepal [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-help@stat.math.ethz.ch 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] Help on variable ranking
Before you do that, you might try reading this paper: Bring, J. 1995. Variable importance by partitioning R^2. Quality and Quantity 29:173-189. Cheers, Simon. Andrew Robinson wrote: Rupendra, depending on the nature of your data (which you haven't mentioned), you might try hierarchical partitioning, as found in the hier.part package on CRAN. Cheers Andrew On Wed, Jan 17, 2007 at 11:07:18AM +0545, Rupendra Chulyadyo wrote: Hello all, I want to assign relative score to the predictor variables on the basis of its influence on the dependent variable. But I could not find any standard statistical approach appropriate for this purpose. Please suggest the possible approaches. Thanks in advance, Rupendra Chulyadyo Institute of Engineering, Tribhuvan University, Nepal [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. -- Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat. Centre for Resource and Environmental Studies The Australian National University Canberra ACT 0200 Australia T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au F: +61 2 6125 0757 CRICOS Provider # 00120C The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@stat.math.ethz.ch 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.
[R] Re : labels outliers in boxplot
I use to do this (It may help you)
boxplot(x)
bx-boxplot(x,plot=F)
In bx object, you and object names out with yaxis cordinates. For the i-th
boxplot in the figure,
use
text(rep(i,length(bx$out)),bx$out,...)
Justin BEM
Elève Ingénieur Statisticien Economiste
BP 294 Yaoundé.
Tél (00237)9597295.
- Message d'origine
De : Greg Snow [EMAIL PROTECTED]
À : [EMAIL PROTECTED]; r-help@stat.math.ethz.ch
Envoyé le : Mardi, 16 Janvier 2007, 21h35mn 43s
Objet : Re: [R] labels outliers in boxplot
Some information on the outliers is returned from the boxplot function. Try
something like:
set.seed(123)
tmp - data.frame( group=gl(3,10),
y=rcauchy(30), sex=gl(2,5,30,c('M','F')) )
tmp2 - boxplot( split(tmp$y,tmp$group) )
identify( tmp2$group, tmp2$out, tmp2$group )
Or if your grouping variable works out to the same values as the x axis (used
integers) and you want to specify a 3rd variable to be the labels you can do:
Identify( tmp$group, tmp$y, tmp$sex )
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Wednesday, January 10, 2007 2:08 PM
To: r-help@stat.math.ethz.ch
Subject: [R] labels outliers in boxplot
Dear R-users,
Following is part of my data, where slide has 36 levels and
block 48 levels. I have done boxplot for each slide on the
same graph. There are outliers for each slide and I tried to
use indentify functtion to identify outliers in such a way
that when I click on an outlier or point, the points will be
labelled by either their block or ID or by both but without
success. How can I make it work or are there other ways to do
it than using identify function?
Thanks in advance,
Jenny,
dat1[1:10,]
y Slide Block ID Control
1 0.03147823 1 1 IgG-human 5
2 -0.23815974 1 1 LPPAANDVSVLTAAR 0
3 -0.71926359 1 1 HTKHYRVVSKPAALV 0
4 -0.14607826 1 1 FVALPAATADAYATT 0
5 0.89553073 1 1 NYPAMMAHAGDMAGY 0
6 -0.67587100 1 1 RRALRQIGVLERPVG 0
7 0.32636034 1 1 DCGTIRVGSFRGRWL 0
8 -1.44057259 1 1 MAKLSTDELLDAFKE 0
9 -0.37064338 1 1 LELSDFVKKFEETFE 0
10 -0.20387233 1 1 VSRRAKVDVLIVHTT 0
tb_ncs-subset(dat1,dat1$Control==1) ### this
data contains only negative controls
par(las=2,mar=c(10.1,4.1,4.1,2.1))
boxplot(split(tb_ncs$y,tb_ncs$Slide),col=orange,
cex=.65,
outline=TRUE,main=Negative control
response of each patient, cex.main=1, font.main=1,
col.main=blue,
names=c(1:35,B))
grid(nx=NA, ny=NULL)
### grid over boxplot
legend(bottomright, B = Buffer +
sec,text.col=blue)
out.block-
identify(tb_ncs$y,tb_ncs$Slide)
_
Flyger tiden iväg? Fånga dagen med Yahoo! Mails inbyggda
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch 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.
___
Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions !
Profitez des connaissances, des opinions et des expériences des internaut
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
