[R] Convert a lis to matrix
Hello, This is an urgent request. I want to convert a list of 3 elements into a matrix and I am not sure how to do it. The list looks like this: List of 3 $ : num [1:15364, 1] 0.133 0.622 0.588 1.024 0.583 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL $ : num [1:15364, 1] 3.159 0.265 0.522 1.912 3.380 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL $ : num [1:15364, 1] 3.214 0.277 1.447 1.827 2.054 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL I want to convert it to a matrix like this: ID 1 2 3 6420681 0.1332478 3.15862 3.214367 3610072 0.6219358 0.265226 0.276525 2260458 0.5876415 0.522378 1.44687 60689 1.0240852 1.911613 1.827464 Thanks Manisha [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
I also use R to redraw figures for the journal I edit (below), when the authors cannot produce usable graphics (about 50% of the author who try). Unfortunately, I cannot find a way to search for just the R files. They are all http://journal.sjdm.org/*/*.R where * is the number of the article. But Google, to my knowledge will not deal with wildcards like this. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] stars (as fourfold plots) in plot (symbols don't work)
Hi! I have a dataset with three columns -the first two refer to x and y coordinates, the last one are odds ratios. I'd like to plot the data with x and y coordinates and the odds ratio shown as a fourfold plot, which I prefer to do using the stars function. Unfortunately the stars option in symbols is not as cool as the stars function on its own, and now i can't figure out how to do it! here's an example code: #data test-cbind(c(1,2,3,4), c(1,2,3,4), c(2,4,8,16)) #this is what I want the star symbol to look like stars(cbind(1,sqrt(test[1,3]), 1, sqrt(test[1,3])), col.segments=c(gray90, gray),draw.segments=TRUE, scale=FALSE) #this is what happens when using stars in symbols symbols(test[,1], test[,2], stars=cbind(1,sqrt(test[,3]), 1, sqrt(test[,3]))) Can anyone set me on the right path please? Maja -- View this message in context: http://www.nabble.com/stars-%28as-fourfold-plots%29-in-plot-%28symbols-don%27t-work%29-tp23905987p23905987.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] extract rows having negative values
Hello, I have a matrix with 6 columns and 12 rows. I want to extract out those IDs (rownames) from my matrix which have a negative values. For each ID(row) if the negative value is even under 1 column it needs to be extracted out. I will be grateful for any correct suggestion. Thanks Manisha Here is the matrix that I am working on: ID A B C D E F 1 -4.18972 -3.8946 -1.14888 -1.88406 -8.34124 10.97497 2 11.81028 11.1054 0.85112 0.115942 -4.34124 24.97497 3 -0.18972 -1.8946 1.85112 -4.88406 -17.3412 -13.025 4 -1.18972 3.105402 -0.14888 -12.8841 -15.3412 4.974967 6 -3.18972 4.105402 24.85112 0.115942 1.658762 -11.025 7 -2.18972 -10.8946 -20.1489 -1.88406 3.658762 -11.025 8 -0.18972 -7.8946 -7.14888 -9.88406 3.658762 -9.02503 9 -5.18972 -4.8946 -12.1489 0.115942 -12.3412 10.97497 10 17.81028 9.105402 -15.1489 10.11594 19.65876 9.974967 11 538.8103 335.1054 863.8511 229.1159 520.6588 143.975 12 30.81028 18.1054 30.85112 16.11594 9.658762 13.97497 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extract rows having negative values
rownames(X)[apply(X, 1, function(r) any(r 0))] ... if I understand you correctly. From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Manisha Brahmachary [mb3...@c2b2.columbia.edu] Sent: 07 June 2009 08:54 To: r-help@r-project.org Subject: [R] extract rows having negative values Hello, I have a matrix with 6 columns and 12 rows. I want to extract out those IDs (rownames) from my matrix which have a negative values. For each ID(row) if the negative value is even under 1 column it needs to be extracted out. I will be grateful for any correct suggestion. Thanks Manisha Here is the matrix that I am working on: ID A B C D E F 1 -4.18972 -3.8946 -1.14888 -1.88406 -8.34124 10.97497 2 11.81028 11.1054 0.85112 0.115942 -4.34124 24.97497 3 -0.18972 -1.8946 1.85112 -4.88406 -17.3412 -13.025 4 -1.18972 3.105402 -0.14888 -12.8841 -15.3412 4.974967 6 -3.18972 4.105402 24.85112 0.115942 1.658762 -11.025 7 -2.18972 -10.8946 -20.1489 -1.88406 3.658762 -11.025 8 -0.18972 -7.8946 -7.14888 -9.88406 3.658762 -9.02503 9 -5.18972 -4.8946 -12.1489 0.115942 -12.3412 10.97497 10 17.81028 9.105402 -15.1489 10.11594 19.65876 9.974967 11 538.8103 335.1054 863.8511 229.1159 520.6588 143.975 12 30.81028 18.1054 30.85112 16.11594 9.658762 13.97497 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] EBImage not loading
Hi Quin, This is a well documented bug of Ubuntu 8.10 (Hardy Heron), preventing applications using libgomp (EBImage via ImageMagick) to work: https://bugs.launchpad.net/ubuntu/hardy/+source/gcc-4.2/+bug/235070 The bug was fixed in the package gcc-4.2.4-3ubuntu3. Please note that your R version (2.6.2) is pretty outdated. Best regards, Greg --- Gregoire Pau EMBL Research officer http://www.ebi.ac.uk/~gpau/ Quin Wills wrote: Hello all I've just spent a few joyless hours trying to get EBImage to install in R. I'm running Ubuntu (Hardy Heron), fully updated (including R and Imagemagick). EBImage installation seems to work, but when I 'library(EBImage)' I get the following: - - - - Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/qilin/R/i486-pc-linux- gnu-library/2.6/EBImage/libs/EBImage.so': /usr/lib/libgomp.so.1: cannot allocate memory in static TLS block Error: package/namespace load failed for 'EBImage' - - - - Which is meaningless to me. Any help would be enormously appreciated, thanks. Quin * Quin Wills * * DPhil candidate * * * * Department of Statistics University of Oxford 1 South Parks road Oxford OX1 3TG +44 (0)1865 285 394 * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert a lis to matrix
On Sun, 2009-06-07 at 00:14 -0400, Manisha Brahmachary wrote: Hello, This is an urgent request. I want to convert a list of 3 elements into a matrix and I am not sure how to do it. The list looks like this: List of 3 $ : num [1:15364, 1] 0.133 0.622 0.588 1.024 0.583 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL $ : num [1:15364, 1] 3.159 0.265 0.522 1.912 3.380 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL $ : num [1:15364, 1] 3.214 0.277 1.447 1.827 2.054 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL I'm not sure if understood your question, but look this code a-list(B=1:3,C=2:4,D=3:5) matrix(unlist(a),ncol=3) -- Bernardo Rangel Tura, M.D,MPH,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Inf in nnet final value for validation data
Hi, I use nnet for my classification problem and have a problem concerning the calculation of the final value for my validation data.(nnet only calculates the final value for the training data). I made my own final value formula (for the training data I get the same value as nnet): # prob-matrix pmatrix - cat*fittedValues tmp - rowSums(pmatrix) # -log likelihood finalValue - sum(-log(tmp)) # add penalty term finalValue + sum(decay * weights^2) where cat is a matrix with cols for each possible category and a row for each data record. The values are 1 for the target categories of a data record and 0 otherwise. My problem is, that I get Inf-values for some validation data records, because the rowsum of cat*fittedValues gets 0 and the log gets Inf. Has anyone an idea how to deal with that problem properly? How does nnet? I´m thinking of a penalty value for those values. That means if cat*fittedValues == 0 not to calculate the log but add e.g. 100 instead of -log(tmp) to the finalValue-sum?? But how to determine the penalty value??? I´m looking forwar for all suggestions, Andrea. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
Try this: site:journal.sjdm.org filetype:R On Sat, Jun 6, 2009 at 6:39 PM, Jonathan Baronba...@psych.upenn.edu wrote: I also use R to redraw figures for the journal I edit (below), when the authors cannot produce usable graphics (about 50% of the author who try). Unfortunately, I cannot find a way to search for just the R files. They are all http://journal.sjdm.org/*/*.R where * is the number of the article. But Google, to my knowledge will not deal with wildcards like this. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] writing a panel function in coplot for displaying a non-linear regression model graphically
Hello,I am a little bit struggling with the following:
I would like to draw a coplot and in each panel draw the curve and display
the coefficients of the regression model y~a*x^b.
I thought of running nls(y~a*x^b,...) in panel=function(x,y...){} when
calling coplot. How can I do this?
Alternatively, I could do the regression before graphing with coplot and
just use the panel function to draw the resulting curve and print the
formula. Again, how to write the part panel=function(x,y...) to implement
this in coplot?
Thank you very much!!!
Marion
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] One rather theoretical question about fitting algorithm
Hi, What I'm trying to achieve is very fast algorithm for fitting logistic regression model. I have to estimate regression coeficients using about 10k observations. Once I have coefficients estimated, new 100 rows of data becomes available Now I need to reestimate coeficients using 100 newly arrived observations and removing 100 oldest observations. So, my question is would it be possible to somehow reuse pre iusly calculated coeficients and only adjust them cor newly arrived data? I know it would have to be some aproximation but I suppose it will be good enough. I dont mind doing this in straight C because of of speed perative. Actualy this will have to be cAlculated in a fraction of second. Any ideas would be higly appreciated __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
On 07-Jun-09 10:56:25, Gabor Grothendieck wrote: Try this: site:journal.sjdm.org filetype:R When I enter that into Google, I got only the following two hits: # #!/usr/bin/Rscript --vanilla # input is a pre-made list of files ... #!/usr/bin/Rscript --vanilla # input is a pre-made list of files ending in html called ../htmlist # (see below). This is easily modified. ... journal.sjdm.org/RePEc/rss/rss.R - Cached - Similar pages # #!/usr/bin/Rscript --vanilla --verbose # script to convert RePEc ... #!/usr/bin/Rscript --vanilla --verbose # script to convert RePEc-style rdf files (ReDIFF) to DOAJ-type xml files # usage: oai.R [file] # where [file] is a ... journal.sjdm.org/RePEc/rss/oai.R - Cached - Similar pages none of which is what Jonathan os looking for (and the Similar pages links are a waste of time). In regexp language, what he is looking for is http://journal.sjdm.org/[0:9]+/*.R of which there are several instances on the site, for example http://journal.sjdm.org/8210/ shows jdm8210.html13-Dec-2008 1 jdm8210.pdf 13-Dec-2008 11:18 102K jdm8210.tex 13-Dec-2008 11:18 27K jdm8210001.gif 09-Dec-2008 14:38 11K probs.R 09-Dec-2008 14:37 1.0K test.R 23-May-2008 05:46 251 ttest.csv 22-May-2008 21:31 2.6K1:1831K so there are two .Rfiles there (8210 is the number of an article in the Journal). Other similar directories mAy or may not have .R files -- for example http://journal.sjdm.org/8816/ has none. The problem is that utilities like wget won;t work in this case, since HTTP doesn't accept wild cards, unlike FTP; but the journal site doesn't accept FTP ... !! It's an intriguing problem, and I'm seeking advice amongst my Linux acquaintances about it. I sonehow doubt that there is a solution ... Ted. On Sat, Jun 6, 2009 at 6:39 PM, Jonathan Baronba...@psych.upenn.edu wrote: I also use R to redraw figures for the journal I edit (below), when the authors cannot produce usable graphics (about 50% of the author who try). Unfortunately, I cannot find a way to search for just the R files. They are all http://journal.sjdm.org/*/*.R where * is the number of the article. _But Google, to my knowledge will not deal with wildcards like this. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 07-Jun-09 Time: 12:37:34 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
The fact that the search did find two files suggests that it works but the problem may be that google has just not indexed those other files. Try entering the url for one of them into google and google still does not find it. http://journal.sjdm.org/8210/test.R On Sun, Jun 7, 2009 at 7:37 AM, Ted Hardingted.hard...@manchester.ac.uk wrote: On 07-Jun-09 10:56:25, Gabor Grothendieck wrote: Try this: site:journal.sjdm.org filetype:R When I enter that into Google, I got only the following two hits: # #!/usr/bin/Rscript --vanilla # input is a pre-made list of files ... #!/usr/bin/Rscript --vanilla # input is a pre-made list of files ending in html called ../htmlist # (see below). This is easily modified. ... journal.sjdm.org/RePEc/rss/rss.R - Cached - Similar pages # #!/usr/bin/Rscript --vanilla --verbose # script to convert RePEc ... #!/usr/bin/Rscript --vanilla --verbose # script to convert RePEc-style rdf files (ReDIFF) to DOAJ-type xml files # usage: oai.R [file] # where [file] is a ... journal.sjdm.org/RePEc/rss/oai.R - Cached - Similar pages none of which is what Jonathan os looking for (and the Similar pages links are a waste of time). In regexp language, what he is looking for is http://journal.sjdm.org/[0:9]+/*.R of which there are several instances on the site, for example http://journal.sjdm.org/8210/ shows jdm8210.html 13-Dec-2008 1 jdm8210.pdf 13-Dec-2008 11:18 102K jdm8210.tex 13-Dec-2008 11:18 27K jdm8210001.gif 09-Dec-2008 14:38 11K probs.R 09-Dec-2008 14:37 1.0K test.R 23-May-2008 05:46 251 ttest.csv 22-May-2008 21:31 2.6K1:18 31K so there are two .Rfiles there (8210 is the number of an article in the Journal). Other similar directories mAy or may not have .R files -- for example http://journal.sjdm.org/8816/ has none. The problem is that utilities like wget won;t work in this case, since HTTP doesn't accept wild cards, unlike FTP; but the journal site doesn't accept FTP ... !! It's an intriguing problem, and I'm seeking advice amongst my Linux acquaintances about it. I sonehow doubt that there is a solution ... Ted. On Sat, Jun 6, 2009 at 6:39 PM, Jonathan Baronba...@psych.upenn.edu wrote: I also use R to redraw figures for the journal I edit (below), when the authors cannot produce usable graphics (about 50% of the author who try). Unfortunately, I cannot find a way to search for just the R files. They are all http://journal.sjdm.org/*/*.R where * is the number of the article. _But Google, to my knowledge will not deal with wildcards like this. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 07-Jun-09 Time: 12:37:34 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
Argh. The reason we can't find my example R files with Google is that they were not indexed because there were no links to them. I've now created a page with just these links, and a link to that page at the very bottom of http://journal.sjdm.org/submit.htm Google should find it all eventually. The direct link is http://journal.sjdm.org/RX.html I should also note that I need to set a bounding box around everything, and here is the bbox script I use (based loosely on a suggestion made by Brian Ripley a long time ago). Sometimes I add this to the end of the script that makes the graph, with system(bbox fig1.eps) or something like that. #!/bin/bash cat $1 | sed -r -e s/BoundingBox:[\ ]+[0-9]+[\ ]+[0-9]+[\ ]+[0-9]+\ [\ ]+[0-9]+/`gs -sDEVICE=bbox -dBATCH -dNOPAUSE -q`/ temp.eps gs -sDEVICE=bbox -sNOPAUSE -q $1 $showpage -c quit 2 bb.out sed -e1 r bb.out temp.eps $1 /bin/rm bb.out /bin/rm temp.eps I may also created a Namazu search index for these, if I get around to it. Jon On 06/07/09 07:45, Gabor Grothendieck wrote: The fact that the search did find two files suggests that it works but the problem may be that google has just not indexed those other files. Try entering the url for one of them into google and google still does not find it. http://journal.sjdm.org/8210/test.R On Sun, Jun 7, 2009 at 7:37 AM, Ted Hardingted.hard...@manchester.ac.uk wrote: On 07-Jun-09 10:56:25, Gabor Grothendieck wrote: Try this: site:journal.sjdm.org filetype:R When I enter that into Google, I got only the following two hits: -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] EBImage not loading
Hi Greg It works! Thanks. I've noticed a lot of general Heron-unhappiness re. ImageMagick. 'Appreciate that ImageMagick isn't really your domain, but it might be helpful to put up a solution page somewhere. postcript 1 - my apologies. I sent this off to the wrong list... I really should have used the Bioconductor list. Careless clicking of 'send to'. postscript 2 -thanks for the 2.6 spot. I am actually running 2.9. I didn't notice that my bioconductor libraries are going into my 2.6 folder. Not sure why that is. Presumably its only a cosmetic problem. Q * Quin Wills * * DPhil candidate * * * * Department of Statistics University of Oxford 1 South Parks road Oxford OX1 3TG +44 (0)1865 285 394 * 2009/6/7 Gregoire Pau gregoire@embl.de Hi Quin, This is a well documented bug of Ubuntu 8.10 (Hardy Heron), preventing applications using libgomp (EBImage via ImageMagick) to work: https://bugs.launchpad.net/ubuntu/hardy/+source/gcc-4.2/+bug/235070 The bug was fixed in the package gcc-4.2.4-3ubuntu3. Please note that your R version (2.6.2) is pretty outdated. Best regards, Greg --- Gregoire Pau EMBL Research officer http://www.ebi.ac.uk/~gpau/ http://www.ebi.ac.uk/%7Egpau/ Quin Wills wrote: Hello all I've just spent a few joyless hours trying to get EBImage to install in R. I'm running Ubuntu (Hardy Heron), fully updated (including R and Imagemagick). EBImage installation seems to work, but when I 'library(EBImage)' I get the following: - - - - Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/qilin/R/i486-pc-linux- gnu-library/2.6/EBImage/libs/EBImage.so': /usr/lib/libgomp.so.1: cannot allocate memory in static TLS block Error: package/namespace load failed for 'EBImage' - - - - Which is meaningless to me. Any help would be enormously appreciated, thanks. Quin * Quin Wills * * DPhil candidate * * * * Department of Statistics University of Oxford 1 South Parks road Oxford OX1 3TG +44 (0)1865 285 394 * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] One rather theoretical question about fitting algorithm
The glm function allows you to specify starting values for beta (start =), eta (etastart =) or mu (mustart =). In your case the starting value for beta would seem to be the most appropriate. You might find providing a starting value for mu or eta also works well, provided you can come up with a quick way of finding values for the new observations. From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of useR [milicic.ma...@gmail.com] Sent: 07 June 2009 21:20 To: r-help@r-project.org Subject: [R] One rather theoretical question about fitting algorithm Hi, What I'm trying to achieve is very fast algorithm for fitting logistic regression model. I have to estimate regression coeficients using about 10k observations. Once I have coefficients estimated, new 100 rows of data becomes available Now I need to reestimate coeficients using 100 newly arrived observations and removing 100 oldest observations. So, my question is would it be possible to somehow reuse pre iusly calculated coeficients and only adjust them cor newly arrived data? I know it would have to be some aproximation but I suppose it will be good enough. I dont mind doing this in straight C because of of speed perative. Actualy this will have to be cAlculated in a fraction of second. Any ideas would be higly appreciated __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Scrolling behavior in View()
Hi, I've realized that the scrolling behavior in View() is unlike most other applications. It seems that the minimum scroll size is very large for large objects( i.e., a vector of 1M integers), and it might be that this scroll is proportional to the size of the object. Try this: a = 1:100 View(a) Click once on the scroll arrow down. It will move to item 1001. It could be that the scroll size is 1/1000 object length. If this is so, it's a bit of a problem, since there's no way to View say cell 500... unless one does a View(head(a, 500)), which kind of defeats the point of view. Is this behavior by design? If so, wouldn't it be better to make it optional (as it breaks GUI conventions of mostly any OS for scrolling behavior)? An argument for view to turn this off would be great. Thanks! Best, -Jose -- Jose Quesada, PhD. Max Planck Institute, Center for Adaptive Behavior and Cognition -ABC-, Lentzeallee 94, office 224, 14195 Berlin http://www.josequesada.name/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
I think the reason Google will not find it is that, in the Journal website, the R files (and the names of the article directories that might contain them, such as journal.sjdm.org/8210/ -- see below) are not directly pointed to by any index.html or any href ... /href in the website, as far as I can see. This would be why 'wget' cannot find them in HTTP mode, and it would prevent Google being led to them. On the other hand, if one knows the name of a directory, then a wget on that directory will assemble its list of contents into an index.html file on the local machine, from which the names of any .R files can be extracted with a bit of greppery. For example, wget http://journal.sjdm.org/8210/ creates a local file index.html, and then grep '[.]R' index.html outputs: trtd valign=topimg src=/icons/unknown.gif alt=[ ]/tdtda href=probs.Rprobs.R/a/tdtd align=right09-Dec-2008 14:37 /tdtd align=right1.0K/td/tr trtd valign=topimg src=/icons/unknown.gif alt=[ ]/tdtda href=test.Rtest.R/a/tdtd align=right23-May-2008 05:46 /tdtd align=right251 /td/tr thus revealing the two R files probs.R and test.R which are there. Then a bit of seddery (or the like) could probably extract just the filenames, by looking for *.R between and . However, the key to the whole thing is knowing what the numerical directory names (such as 8210) are. The only way I've found to do this automatically is to download the whole site (Linux commands): mkdir sjdm cd sjdm wget -r -k -np -nH http://journal.sjdm.org/ extract the numeric directory-names with (e.g.): find . -type d -name '[0-9]*[0-9]' -print and then work through the results of this with directory-specific wget's as before. This all seems to be overkill, however! Much easier if the site would accept FTP. Ted. On 07-Jun-09 11:45:19, Gabor Grothendieck wrote: The fact that the search did find two files suggests that it works but the problem may be that google has just not indexed those other files. Try entering the url for one of them into google and google still does not find it. http://journal.sjdm.org/8210/test.R On Sun, Jun 7, 2009 at 7:37 AM, Ted Hardingted.hard...@manchester.ac.uk wrote: On 07-Jun-09 10:56:25, Gabor Grothendieck wrote: Try this: site:journal.sjdm.org filetype:R When I enter that into Google, I got only the following two hits: _# _#!/usr/bin/Rscript --vanilla # input is a pre-made list of files ... _#!/usr/bin/Rscript --vanilla # input is a pre-made list of files ending _in html called ../htmlist # (see below). This is easily modified. ... _journal.sjdm.org/RePEc/rss/rss.R - Cached - Similar pages _# _#!/usr/bin/Rscript --vanilla --verbose # script to convert RePEc ... _#!/usr/bin/Rscript --vanilla --verbose # script to convert RePEc-style _rdf files (ReDIFF) to DOAJ-type xml files # usage: oai.R [file] # where _[file] is a ... _journal.sjdm.org/RePEc/rss/oai.R - Cached - Similar pages none of which is what Jonathan os looking for (and the Similar pages links are a waste of time). In regexp language, what he is looking for is _http://journal.sjdm.org/[0:9]+/*.R of which there are several instances on the site, for example _http://journal.sjdm.org/8210/ shows _ jdm8210.html _ _13-Dec-2008 1 _ jdm8210.pdf _ _ 13-Dec-2008 11:18 _ _ _ 102K _ jdm8210.tex _ _ 13-Dec-2008 11:18 _ _ _ 27K _ jdm8210001.gif _09-Dec-2008 14:38 _ _ _ 11K _ probs.R _ _ _ _ 09-Dec-2008 14:37 _ _ _ 1.0K _ test.R _ _ _ _ _23-May-2008 05:46 _ _ _ 251 _ ttest.csv _ _ _ 22-May-2008 21:31 _ _ _ 2.6K1:18 _ _ _ _31K so there are two .Rfiles there (8210 is the number of an article in the Journal). Other similar directories mAy or may not have .R files -- for example _http://journal.sjdm.org/8816/ has none. The problem is that utilities like wget won;t work in this case, since HTTP doesn't accept wild cards, unlike FTP; but the journal site doesn't accept FTP ... !! It's an intriguing problem, and I'm seeking advice amongst my Linux acquaintances about it. I sonehow doubt that there is a solution ... Ted. On Sat, Jun 6, 2009 at 6:39 PM, Jonathan Baronba...@psych.upenn.edu wrote: I also use R to redraw figures for the journal I edit (below), when the authors cannot produce usable graphics (about 50% of the author who try). Unfortunately, I cannot find a way to search for just the R files. They are all http://journal.sjdm.org/*/*.R where * is the number of the article. _But Google, to my knowledge will not deal with wildcards like this. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RPostgreSQL segfault with LEFT JOIN
On 7 June 2009 at 06:40, Neil Tiffin wrote:
| I am adding your note to google code issues
(http://code.google.com/p/rpostgresql/issues/list
| ), issue Number 1. Normally I monitor R-SIG-DB
(https://stat.ethz.ch/mailman/listinfo/r-sig-db
| ).
That list seems most appropriate.
| Hope to look at these in the next couple of weeks.
|
| Thanks, for the suggested changes.
Thanks from my end too.
It does compile, and it passes the existing tests that R CMD check runs so it
looks good so far. It also passes simple
select foofrom bar
select foo as fii from bar
where the second form bombed without the patch. So thanks!!
[ Incidentally, I am having issues with googlecode.com which no longer wants
me to connect / update / initialise from home behind NAT and a simple
firewall:
e...@ron:~/svn/rpostgresql svn up
svn: OPTIONS of 'https://rpostgresql.googlecode.com/svn/trunk': could not
connect to server (https://rpostgresql.googlecode.com)
e...@ron:~/svn/rpostgresql
Does anybody know what's happening there? I can check out etc fine from
another machine somewhere else. I can connect and authenticate fine to the
https url using a browswer, it is just svn that croaks. Ideas ? Does this
now need rpc or portmap back to me? ]
Dirk
| Neil
|
| On Jun 6, 2009, at 11:18 PM, Joe Conway wrote:
|
| Dylan Beaudette wrote:
| After some further investigation, I see that the query works fine
| if I *do not use column aliases* :
|
| Looks like *any* query using a column alias will segfault unless the
| alias exactly matches the column name (in which case why bother).
| The code starting at line 423 in RS-PostgreSQL.c looks like:
|
| 8---
| if(PQftablecol(my_result,j) !=0) {
|
| /* Code to find whether a row can be nullable or not */
| sprintf(buff,
| select attnotnull from pg_attribute
| where attrelid=%d and attname='%s',
| PQftable(my_result,j),(char*)PQfname(my_result,j));
| res = PQexec (conn, buff );
|
| if(strcmp(PQgetvalue(res,0,0),f)==0) {
| 8---
| The crash occurs at line 430 (the strcmp()) because PQgetvalue(res,
| 0,0) returns NULL.
|
| PQfname() will return the column alias, not the actual column name,
| therefore the PQexec() here returns no results. At the very least,
| PQresultStatus(res) or perhaps PQntuples(res) should be used
| immediately after PQexec() to ensure you have a good result before
| trying to use it in strcmp().
|
| In any case, I think the simple fix (untested) is something like:
|
| 8---
| if(PQftablecol(my_result,j) !=0) {
|
| /* Code to find whether a row can be nullable or not */
| sprintf(buff,
| select attnotnull from pg_attribute
| where attrelid=%d and attnum=%d,
| PQftable(my_result,j),PQftablecol(my_result,j));
| 8---
| i.e. use the table column number and pg_attribute.attnum field.
|
| This is beyond what is appropriate for r-help, so I suggest any
| further discussion go off-list (or is there somewhere more
| appropriate, e.g. r-devel?)
|
| HTH,
|
| Joe
|
|
--
Three out of two people have difficulties with fractions.
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Scrolling behavior in View()
On 07/06/2009 9:50 AM, Jose Quesada wrote: Hi, I've realized that the scrolling behavior in View() is unlike most other applications. It seems that the minimum scroll size is very large for large objects( i.e., a vector of 1M integers), and it might be that this scroll is proportional to the size of the object. Try this: a = 1:100 View(a) Click once on the scroll arrow down. It will move to item 1001. It could be that the scroll size is 1/1000 object length. If this is so, it's a bit of a problem, since there's no way to View say cell 500... unless one does a View(head(a, 500)), which kind of defeats the point of view. Is this behavior by design? If so, wouldn't it be better to make it optional (as it breaks GUI conventions of mostly any OS for scrolling behavior)? An argument for view to turn this off would be great. You didn't say which version or platform you were using. I see it on Windows 2.9.0 and R-devel. The behaviour you describe (scrolling 1/1000 of the object) happens when the object has more than 1 items in it. If I temporarily disable it, things are worse: then there is no easy way I can find to get to the bottom of the object. There appear to be some 16 bit overflows happening if you try to drag the scrollbar slider down too far. The reason for this is that Windows only provides 16 bits of information in the scrolling message; however, there are workarounds to get 32 bit positions. I'll see if I can add them to our code. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal Articles that Have Used R
On 07-Jun-09 14:01:14, Ted Harding wrote: I think the reason Google will not find it is that, in the Journal website, the R files (and the names of the article directories that might contain them, such as journal.sjdm.org/8210/ -- see below) are not directly pointed to by any index.html or any href ... /href in the website, as far as I can see. This would be why 'wget' cannot find them in HTTP mode, and it would prevent Google being led to them. [... ... ...] This all seems to be overkill, however! Much easier if the site would accept FTP. Ted. Or, as Jonathan has now done, the R files were pointed to by links within the web-page! :) Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 07-Jun-09 Time: 15:41:49 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need some help in R : value more than equals to a row.
Hallo, I was trying some code, but couldn't make one step of the code properly. Can anybody please help me? I have one matrix like this values [,1] [,2] [,3] [,4] [,5] [1,] 0.778 0.3611 0. 0.139 0.000 [2,] 1.000 0. 0.53846154 0.000 0.5384615 [3,] 0.520 0.4800 0.6400 0.000 0.880 [4,] 0.8928571 1. 0. 0.8928571 0.1071429 And I want to get some matrix like: values.new [,1] [,2] [,3] [,4] [,5] [1,] 0.2 0.4 0.6 0.8 1.0 [2,] 0.2 1.0 0.6 1.0 0.6 [3,] 0.6 0.8 0.4 1.0 0.2 [4,] 0.6 0.2 1.0 0.6 0.8 This table should be computed by taking proportion of values in the row that are larger or equals to the value being considered with the total no of objects in the row. for example values[1,2] [1] 0.361 and values[1,] [1] 0.778 0.361 0.222 0.139 0.000 0.861 So there are two numbers more than equals to values[1,2] So values.new[1,2]= 2/length(values[1,]) With best regard, Suparna Ms Suparna Mitra Eberhard-Karls-Universität Tübingen Wilhelm-Schickard-Institut Algorithmen der Bioinformatik Sand 14, 72076 Tuebingen Germany Tel. ++49-7071-29 70453 (0) Fax ++49-7071-29 5148 (0) Phone: ++49-176-20361469 (M) ++49-7071-1477169 (R) Alternative e-mail: mi...@informatik.uni-tuebingen.de [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need some help in R : value more than equals to a row.
Hallo, I was trying some code, but couldn't make one step of the code properly. Can anybody please help me? I have one matrix like this values [,1] [,2] [,3] [,4] [,5] [1,] 0.778 0.3611 0. 0.139 0.000 [2,] 1.000 0. 0.53846154 0.000 0.5384615 [3,] 0.520 0.4800 0.6400 0.000 0.880 [4,] 0.8928571 1. 0. 0.8928571 0.1071429 And I want to get some matrix like: values.new [,1] [,2] [,3] [,4] [,5] [1,] 0.2 0.4 0.6 0.8 1.0 [2,] 0.2 1.0 0.6 1.0 0.6 [3,] 0.6 0.8 0.4 1.0 0.2 [4,] 0.6 0.2 1.0 0.6 0.8 This table should be computed by taking proportion of values in the row that are larger or equals to the value being considered with the total no of objects in the row. for example values[1,2] [1] 0.361 and values[1,] [1] 0.778 0.361 0.222 0.139 0.000 0.861 So there are two numbers more than equals to values[1,2] So values.new[1,2]= 2/length(values[1,]) With best regard, Suparna [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need some help in R : value more than equals to a row.
suparna mitra wrote: Hallo, I was trying some code, but couldn't make one step of the code properly. Can anybody please help me? I have one matrix like this values [,1] [,2] [,3] [,4] [,5] [1,] 0.778 0.3611 0. 0.139 0.000 [2,] 1.000 0. 0.53846154 0.000 0.5384615 [3,] 0.520 0.4800 0.6400 0.000 0.880 [4,] 0.8928571 1. 0. 0.8928571 0.1071429 And I want to get some matrix like: values.new [,1] [,2] [,3] [,4] [,5] [1,] 0.2 0.4 0.6 0.8 1.0 [2,] 0.2 1.0 0.6 1.0 0.6 [3,] 0.6 0.8 0.4 1.0 0.2 [4,] 0.6 0.2 1.0 0.6 0.8 This table should be computed by taking proportion of values in the row that are larger or equals to the value being considered with the total no of objects in the row. I think the code below do what you want, but I would like to know how to do it with one of the *apply functions: m - read.table(stdin(), header=F) 0.778 0.3611 0. 0.139 0.000 1.000 0. 0.53846154 0.000 0.5384615 0.520 0.4800 0.6400 0.000 0.880 0.8928571 1. 0. 0.8928571 0.1071429 m - as.matrix(m) bdim - dim(m) m2 - m for(i in 1:bdim[1]) for(j in 1:bdim[2]) m2[i,j] - sum(m[i,j] = m[i,]) / bdim[2] m2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need some help in R : value more than equals to a row.
Try this: t(apply(m, 1, function(x) colMeans(outer(x, x, = On Sun, Jun 7, 2009 at 10:09 AM, suparna mitrami...@informatik.uni-tuebingen.de wrote: Hallo, I was trying some code, but couldn't make one step of the code properly. Can anybody please help me? I have one matrix like this values [,1] [,2] [,3] [,4] [,5] [1,] 0.778 0.3611 0. 0.139 0.000 [2,] 1.000 0. 0.53846154 0.000 0.5384615 [3,] 0.520 0.4800 0.6400 0.000 0.880 [4,] 0.8928571 1. 0. 0.8928571 0.1071429 And I want to get some matrix like: values.new [,1] [,2] [,3] [,4] [,5] [1,] 0.2 0.4 0.6 0.8 1.0 [2,] 0.2 1.0 0.6 1.0 0.6 [3,] 0.6 0.8 0.4 1.0 0.2 [4,] 0.6 0.2 1.0 0.6 0.8 This table should be computed by taking proportion of values in the row that are larger or equals to the value being considered with the total no of objects in the row. for example values[1,2] [1] 0.361 and values[1,] [1] 0.778 0.361 0.222 0.139 0.000 0.861 So there are two numbers more than equals to values[1,2] So values.new[1,2]= 2/length(values[1,]) With best regard, Suparna Ms Suparna Mitra Eberhard-Karls-Universität Tübingen Wilhelm-Schickard-Institut Algorithmen der Bioinformatik Sand 14, 72076 Tuebingen Germany Tel. ++49-7071-29 70453 (0) Fax ++49-7071-29 5148 (0) Phone: ++49-176-20361469 (M) ++49-7071-1477169 (R) Alternative e-mail: mi...@informatik.uni-tuebingen.de [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How do I construct a one matrix from another? (newbie)
Apologies if this is an obvious question but I am teaching myself R and the occasional push in the right direction is much appreciated? I have a data.frame containing data that looks like this CustID itemID 1a 1b 2c 3a 3c I want to assemble the vector of all the items bought by a particular customer and can't quite see how to do it. What is the best way to represent the answers for a single customer and by all customers? Thanks. -- View this message in context: http://www.nabble.com/How-do-I-construct-a-one-matrix-from-another--%28newbie%29-tp23913248p23913248.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I construct a one matrix from another? (newbie)
Hi, some ideas: ?split ?by library(plyr) ?ddply Cheers, Dylan On Sun, Jun 7, 2009 at 10:26 AM, jonathanbriggsjonathanbri...@mac.com wrote: Apologies if this is an obvious question but I am teaching myself R and the occasional push in the right direction is much appreciated? I have a data.frame containing data that looks like this CustID itemID 1 a 1 b 2 c 3 a 3 c I want to assemble the vector of all the items bought by a particular customer and can't quite see how to do it. What is the best way to represent the answers for a single customer and by all customers? Thanks. -- View this message in context: http://www.nabble.com/How-do-I-construct-a-one-matrix-from-another--%28newbie%29-tp23913248p23913248.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I construct a one matrix from another? (newbie)
Dear jonathanbriggs, Try x - read.table(textConnection(CustID itemID 1a 1b 2c 3a 3c),header=TRUE) closeAllConnections() with(x, tapply(CustID, itemID, paste, collapse=,) ) # abc # 1,3 1 2,3 with(x, tapply(itemID, CustID, paste, collapse=,) ) # 123 #a,b c a,c HTH, Jorge On Sun, Jun 7, 2009 at 1:26 PM, jonathanbriggs jonathanbri...@mac.comwrote: Apologies if this is an obvious question but I am teaching myself R and the occasional push in the right direction is much appreciated? I have a data.frame containing data that looks like this CustID itemID 1a 1b 2c 3a 3c I want to assemble the vector of all the items bought by a particular customer and can't quite see how to do it. What is the best way to represent the answers for a single customer and by all customers? Thanks. -- View this message in context: http://www.nabble.com/How-do-I-construct-a-one-matrix-from-another--%28newbie%29-tp23913248p23913248.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] graphically representing frequency of words in a speech?
Dear all, I recently saw a graph on television that displayed selected words/phrases in a speech scaled in size according to their frequency. So words/phrases that were often used appeared large and words that were rarely used appeared small. The closest thing I can find on the web to approximate what I saw can be found here: http://stateoftheunion.onetwothree.net/ The example at that website is more complicated but captures the general idea. Would someone point me in the right direction in terms of replicating such a graph. Thanks in advance, Tony - Tony N. Brown, Ph.D. Editor-Elect, American Sociological Review Associate Professor of Sociology and Human and Organizational Development (secondary) Program Faculty, Effective Health Communication and African American Diaspora Studies Faculty Head of Hank Ingram House, The Commons Vanderbilt University (615) 322-7518 (615) 322-7505 fax [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphically representing frequency of words in a speech?
On Jun 7, 2009, at 1:41 PM, Brown, Tony Nicholas wrote: Dear all, I recently saw a graph on television that displayed selected words/phrases in a speech scaled in size according to their frequency. So words/phrases that were often used appeared large and words that were rarely used appeared small. The closest thing I can find on the web to approximate what I saw can be found here: http://stateoftheunion.onetwothree.net/ The example at that website is more complicated but captures the general idea. Would someone point me in the right direction in terms of replicating such a graph. Thanks in advance, Tony Tony, What you are referring to is called a 'tag cloud'. See this page: http://en.wikipedia.org/wiki/Tag_cloud They are commonly used on wikis, Twitter and so forth. For example: http://tweetstats.com/trends The only thing that I found for R is by Gregor Gorjanc, but the information seems to be dated: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/index.html#tagCloud I have cc'd him here for any updates. Otherwise, there are some links on the Wikipedia page and some other applications such as Wordle: http://www.wordle.net/ HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphically representing frequency of words in a speech?
The only thing that I found for R is by Gregor Gorjanc, but the
information seems to be dated:
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/index.html#tagCloud
Hi,
Yes, I have tried to create a tag cloud plot in R, but I abandoned the project
due to other things. The main obstacle was that in R we need to take
care of the fontsizes and placement of words, while this is very easy with
say browsers, who do all the renderind. I tracked the last version of the R file
which is pasted bellow. I must say that I do not remember the status of the
code so use it as you wish. If anyone wishes to take this project further,
please
do so!
gg
### tagCloud.R
###
### What: Tag cloud plot functions
### Time-stamp: 2006-09-10 02:53:29 ggorjan
###
tagCloud - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
UseMethod(tagCloud)
}
tagCloud.default - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
if(!is.null(dim(x))) stop('x' must be a vector)
tagCloud.table(table(x), n=n, decreasing=decreasing, fontsize=fontsize,
threshold=threshold, align=align, expandRow=expandRow,
justRow=justRow, title=title, textGpar=textGpar,
rectGpar=rectGpar, titleGpar=titleGpar, viewGpar=viewGpar,
mar=mar)
}
tagCloud.table - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
## --- Check ---
if(length(dim(x)) != 1)
stop('x' must be one dimensional table)
## --- Threshold ---
if(!is.null(threshold)) x - x[x = threshold]
## --- Number of units ---
N - length(x)## length of table
if(is.null(n)) { ## if n=NULL, plot all units
n - N
} else {
if(n N) n - N## if n is to big, decrease it
if(n 1) n - round(N * n) ## if n is percentage of units
}
fontsizeLength - length(fontsize)
if(fontsizeLength != 2)
stop('fontsize' must be of length two)
## --- Sort and subset ---
if(n N) { ## only if we want to plot subset of units
tmp - sort(x, decreasing=decreasing)
x - x[names(x) %in% names(tmp[1:n])]
}
## --- Get relative freq ---
x - prop.table(x)
## --- Fontsize ---
fontsizeDiff - diff(fontsize)
xDiff - max(x) - min(x)
if(xDiff != 0) {
off - ifelse(fontsizeDiff 0, min(x), max(x))
fontsize - (x - off) / xDiff * fontsizeDiff + min(fontsize)
} else { ## all units have the same frequency
fontsize - rep(min(fontsize), times=n)
}
## --- Viewport and rectangle ---
grid.newpage()
width - unit(1, npc)
height - unit(1, npc)
vp - viewport(y=unit(mar[1], lines), x=unit(mar[2], lines), ,
width=width - unit(mar[2] + mar[4], lines),
height=height - unit(mar[1] + mar[3], lines),
just=c(left, bottom), gp=viewGpar, name=main)
pushViewport(vp)
if(!missing(title))
grid.text(title, y=height, gp=titleGpar, name=title)
grid.rect(gp=rectGpar, name=cloud)
## --- Grobs ---
tag - vector(mode=list, length=4)
names(tag) - c(fontsize, grob, width, height)
tag[[1]] - tag[[2]] - tag[[3]] - tag[[4]] - vector(mode=list, length=n)
for(i in 1:n) {
tag$fontsize[[i]] - fontsize[i]
tag$grob[[i]] - textGrob(names(x[i]), gp=gpar(fontsize=fontsize[i]))
tag$width[[i]] - convertWidth(grobWidth(tag$grob[[i]]), unitTo=npc,
valueOnly=TRUE)
tag$height[[i]] - convertHeight(grobHeight(tag$grob[[i]]), unitTo=npc,
valueOnly=TRUE)
}
## --- Split lines ---
row - colWidth - vector(length=n)
row[1] - 1
colWidth[1] - 0
lineWidth - tag$width[[1]]
j - 1
gapWidth - convertWidth(stringWidth( ), unitTo=npc, valueOnly=TRUE)
maxWidth - convertWidth(width, unitTo=npc, valueOnly=TRUE)
for(i in
Re: [R] graphically representing frequency of words in a speech?
Thank you so much Mark and Gregor. The basic information, suggestions,
and R code that you provided is most helpful.
Tony
-Original Message-
From: Gorjanc Gregor [mailto:gregor.gorj...@bfro.uni-lj.si]
Sent: Sunday, June 07, 2009 2:17 PM
To: Marc Schwartz; Brown, Tony Nicholas
Cc: rhelp help
Subject: RE: [R] graphically representing frequency of words in a
speech?
The only thing that I found for R is by Gregor Gorjanc, but the
information seems to be dated:
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/index.html#tagCloud
Hi,
Yes, I have tried to create a tag cloud plot in R, but I abandoned the
project
due to other things. The main obstacle was that in R we need to take
care of the fontsizes and placement of words, while this is very easy
with
say browsers, who do all the renderind. I tracked the last version of
the R file
which is pasted bellow. I must say that I do not remember the status of
the
code so use it as you wish. If anyone wishes to take this project
further, please
do so!
gg
### tagCloud.R
###-
---
### What: Tag cloud plot functions
### Time-stamp: 2006-09-10 02:53:29 ggorjan
###-
---
tagCloud - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
UseMethod(tagCloud)
}
tagCloud.default - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
if(!is.null(dim(x))) stop('x' must be a vector)
tagCloud.table(table(x), n=n, decreasing=decreasing,
fontsize=fontsize,
threshold=threshold, align=align, expandRow=expandRow,
justRow=justRow, title=title, textGpar=textGpar,
rectGpar=rectGpar, titleGpar=titleGpar,
viewGpar=viewGpar,
mar=mar)
}
tagCloud.table - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
## --- Check ---
if(length(dim(x)) != 1)
stop('x' must be one dimensional table)
## --- Threshold ---
if(!is.null(threshold)) x - x[x = threshold]
## --- Number of units ---
N - length(x)## length of table
if(is.null(n)) { ## if n=NULL, plot all units
n - N
} else {
if(n N) n - N## if n is to big, decrease it
if(n 1) n - round(N * n) ## if n is percentage of units
}
fontsizeLength - length(fontsize)
if(fontsizeLength != 2)
stop('fontsize' must be of length two)
## --- Sort and subset ---
if(n N) { ## only if we want to plot subset of units
tmp - sort(x, decreasing=decreasing)
x - x[names(x) %in% names(tmp[1:n])]
}
## --- Get relative freq ---
x - prop.table(x)
## --- Fontsize ---
fontsizeDiff - diff(fontsize)
xDiff - max(x) - min(x)
if(xDiff != 0) {
off - ifelse(fontsizeDiff 0, min(x), max(x))
fontsize - (x - off) / xDiff * fontsizeDiff + min(fontsize)
} else { ## all units have the same frequency
fontsize - rep(min(fontsize), times=n)
}
## --- Viewport and rectangle ---
grid.newpage()
width - unit(1, npc)
height - unit(1, npc)
vp - viewport(y=unit(mar[1], lines), x=unit(mar[2], lines), ,
width=width - unit(mar[2] + mar[4], lines),
height=height - unit(mar[1] + mar[3], lines),
just=c(left, bottom), gp=viewGpar, name=main)
pushViewport(vp)
if(!missing(title))
grid.text(title, y=height, gp=titleGpar, name=title)
grid.rect(gp=rectGpar, name=cloud)
## --- Grobs ---
tag - vector(mode=list, length=4)
names(tag) - c(fontsize, grob, width, height)
tag[[1]] - tag[[2]] - tag[[3]] - tag[[4]] - vector(mode=list,
length=n)
for(i in 1:n) {
tag$fontsize[[i]] - fontsize[i]
tag$grob[[i]] - textGrob(names(x[i]),
gp=gpar(fontsize=fontsize[i]))
tag$width[[i]] - convertWidth(grobWidth(tag$grob[[i]]),
unitTo=npc,
valueOnly=TRUE)
tag$height[[i]] -
[R] latex subscripts in title of a plot
Dear All, I want to ask how to make latex symbol \beta_1 into the title of the page. The usual bquote does not seem to work. Any ideas? Thanks a lot. Regards, Dajiang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Must be a better way to collate sequenced data
I have data that looks like this
time_stamp (seconds) user_id
The data is (partial) ordered by time - in that sometimes transactions occur at
the same timestamp. The output I want is collated by transaction time on a per
user basis, normalized by the maximum number of transactions per user, and
aggregated over each day. So, if the users have 50 transactions in the first
day and 20 transactions on the second day, and 10 transactions on the third
day, the output would be as follows, if each transaction represents 0.01% of
each user's total profile. (In reality, they all have different profile lengths
so a transaction represents a different percentage for each user.)
time_since_first_transaction (days)percent_of_profile
1
0.50
2
0.20
3
0.10
I have the following code that computes the right answer, but it is really
inefficient, so I'm sure that I'm doing something wrong. Really inefficient
means 30 minutes for an 100 k item data frame on a 2.2 GHz machine, and my
1-million data set has never finished. I'm no stranger to functional
programming (Lisp programmer) but I can't figure out a way to subtract the
first timestamp for user A from all of the other timestamps for user A without
either (a) building a separate table of first entries for each user, which I
do here, or (b) re-computing the initial entry for each user with every row,
which is what I did before and is even more inefficient. Another killer
operation seems to be the aggregate step on the last line, which I use to
collate the data by days. It seems very slow, but I don't know any other way to
do this. I realize that I am living proof that one can program in C no matter
what language one uses - so I would appreciate any enlightenment on offer. If !
there's no better way, I'll pre-process everything in Perl, but I'd rather
learn the R way to do things like this. Thanks.
# Build table of times
utime.times - utime.data[TIME] %/% period;
utime.tstart - vector(numeric,
length=max(utime.data[USER]));
for (i in 1:nrow(utime.data))
{
if (as.numeric(utime.data[i, USER_COUNT])==1)
{
day - utime.times[i, TIME];
user - utime.data[i, USER];
utime.tstart[user] - day;
}
}
# Build table of maximum profile sizes
utime.userMax - aggregate(utime.data[USER_COUNT],
utime.data[USER],
max);
utime.atimes - vector(numeric, length=nrow(utime.data));
utime.aperc - vector(numeric, length=nrow(utime.data));
augdata - as.data.frame(cbind(utime.atimes, utime.aperc));
names(augdata) - c(TIME, PERC);
for (i in 1:nrow(utime.data))
{
# adjust time according to user start time
augdata[i, TIME] -
utime.times[i,TIME] -
utime.tstart[utime.data[i,USER]];
# look up maximum user count
umax - subset(utime.userMax,
USER==as.numeric(utime.data[i, USER]))[USER_COUNT];
augdata[i, PERC] - 1.0/umax;
}
utime.rcount - aggregate(augdata, augdata[TIME], sum);
Robin Burke
Associate Professor
School of Computer Science, Telecommunications, and
Information Systems
DePaul University
(currently on leave at University College Dublin)
http://josquin.cti.depaul.edu/~rburke/
The universe is made of stories, not of atoms - Muriel Rukeyser
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphically representing frequency of words in a speech?
Below are various attempts using using ggplot2 (http://had.co.nz/ggplot2/). First I try random positioning, then random positioning with alpha, then a quasi-random position scheme in polar coordinates: #this demo has random number generation # so best to set a seed to make it # reproducible. set.seed(1) #generate some fake data a = data.frame( word = month.name , freq = sample(1:10,12,replace=TRUE) ) #add arbitrary location information a$x = sample(1:12,12) a$y = sample(1:12,12) #load ggplot2 library(ggplot2) #initialize a ggplot object my_plot = ggplot() #create an object for the text layer my_text = geom_text( data = a , aes( x = x , y = y , label = word , size = freq ) ) #create an object for the text size limits my_size_scale = scale_size( to = c(3,20) ) #create an object to expand the x-axis limits # (ensures that text isn't cropped) my_x_scale = scale_x_continuous( expand = c(.5, 0) ) #ditto for the y axis my_y_scale = scale_y_continuous( expand = c(.5, 0) ) #create an opts object that removes # plot elements unnecessary in a tag cloud my_opts = opts( legend.position = 'none' , panel.grid.minor = theme_blank() , panel.grid.major = theme_blank() , panel.background = theme_blank() , axis.line = theme_blank() , axis.text.x = theme_blank() , axis.text.y = theme_blank() , axis.ticks = theme_blank() , axis.title.x = theme_blank() , axis.title.y = theme_blank() ) #show the plot print( my_plot+ my_text+ my_size_scale+ my_x_scale+ my_y_scale+ my_opts ) #to aid readability amidst overlap, set alpha in # the call to geom_text my_text_with_alpha = geom_text( data = a , aes( x = x , y = y , label = word , size = freq ) , alpha = .5 ) #show the version with alpha print( my_plot+ my_text_with_alpha+ my_size_scale+ my_x_scale+ my_y_scale+ my_opts ) #alternatively, in polar coordinates, # which maps x to angle and y to radius, # making a nice circle print( my_plot+ my_text_with_alpha+ my_size_scale+ my_opts+ coord_polar() ) #(note omission of my_y_scale # my_x_scale, which seem to be ignored # when coord_polar() is called. I'll # report this possible bug to the ggplot2 # maintainer) #a possible way to avoid overlap is to # map radius (y) to frequency so that # larger text is in the periphery # where there is more room. This # necessitates adding some random # noise to the frequency so that # the low frequency words don't # jumble in the center too badly a$freq2 = a$freq+rnorm(12) #now map radius (y) to freq2 my_text_with_alpha_and_freq2 = geom_text( data = a , aes( x = x , y = freq2 , label = word , size = freq ) , alpha = .5 ) #show the version with alpha radius mapped to freq2 print( my_plot+ my_text_with_alpha_and_freq2+ my_size_scale+ my_opts+ coord_polar() ) -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University Looking to arrange a meeting? Check my public calendar: http://tr.im/mikes_public_calendar ~ Certainty is folly... I think. ~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reminder: useR Group SFBA - R Graphics Survey - Nicholas Lewin-Koh
All San Francisco Bay Area useRs: This Wednesday evening Nicholas is presenting a survey of statistical visualization best practices corresponding methods in R. For details see http://www.meetup.com/R-Users/calendar/9763376/ Note this is our last meeting before the summer break. Hope to see many of you there! Best, Jim Porzak www.TGN.com San Francisco, CA www.linkedin.com/in/jimporzak use R! Group SF: www.meetup.com/R-Users/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Scrolling behavior in View()
On 07/06/2009 9:50 AM, Jose Quesada wrote: Hi, I've realized that the scrolling behavior in View() is unlike most other applications. It seems that the minimum scroll size is very large for large objects( i.e., a vector of 1M integers), and it might be that this scroll is proportional to the size of the object. Try this: a = 1:100 View(a) Click once on the scroll arrow down. It will move to item 1001. It could be that the scroll size is 1/1000 object length. If this is so, it's a bit of a problem, since there's no way to View say cell 500... unless one does a View(head(a, 500)), which kind of defeats the point of view. Is this behavior by design? If so, wouldn't it be better to make it optional (as it breaks GUI conventions of mostly any OS for scrolling behavior)? An argument for view to turn this off would be great. This should be fixed now. Please try R-patched dated June 8 or later, and let me know if there are any more problems. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Excel Export in a beauty way
Another useful way to create a formatted Excel file is to write out an HTML file, but put an XLS extension on it. When Excel reads it, it will convert it. Users will treat it like an Excel file. This trick allows you to add formatted titles, table footnotes, links to other files (pdf graphs for example), and more. To create HTML, you have several packages that can help you out: R2HTML, Rpad, hwriter, and xtable. Not everything might convert properly, so you may have to experiment. Data frames as tables normally convert nicely. - Tom Tom Short __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Random Forest % Variation vs Psuedo-R^2?
Hi all (and Andy!), When running a randomForest run in R, I get the last part of an output (with do.trace=T) that looks like this: 1993 | 0.04606 130.43 | 1994 | 0.04605 130.40 | 1995 | 0.04605 130.43 | 1996 | 0.04605 130.43 | 1997 | 0.04606 130.44 | 1998 | 0.04607 130.47 | 1999 | 0.04606 130.46 | 2000 | 0.04605 130.42 | With the first column representing the iteration, the second column representing the OOB MSE, and the last column representing the %Var(y). If I calculate a Psuedo-R^2 from these numbers, I would get; 1-(.04605/1.3042) = 0.965 Here's the question, if I look at the summary of forest.rf (this same run), I get the following; randomForest(formula = Prev ~ ., data = plas, ntree = 2000, importance = TRUE, do.trace = T) Type of random forest: regression Number of trees: 2000 No. of variables tried at each split: 5 Mean of squared residuals: 0.04605177 % Var explained: -30.42 What does that -30.42 % Var explained relate to? I find it interesting that the %Var(y) is 130.42, and that the %Var explained is a very similar number, but have no idea how they are related. From my calculations, it seems like I have a good predictor set (Psuedo R^2 over 95%), but am I missing something? Cheers, Ryan -- Ryan Harrigan, Ph.D. Center for Tropical Research Institute of the Environment University of California, Los Angeles La Kretz Hall, Suite 300 Box 951496 Los Angeles, CA 90095-1496 203-804-9505 ilu...@ucla.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] latex subscripts in title of a plot
Hi Dajiang, try plot(1, main=expression(beta[1])) and, more generally, see ?plotmath or demo(plotmath) Kingsford Jones On Sun, Jun 7, 2009 at 4:43 PM, Dajiang Jeff Liudajiang@gmail.com wrote: Dear All, I want to ask how to make latex symbol \beta_1 into the title of the page. The usual bquote does not seem to work. Any ideas? Thanks a lot. Regards, Dajiang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting two regression lines on one graph
Hi!
I have fitted two glms assuming a poisson distribution which are:
fit1 - glm(Aids ~ Year, data=aids, family=poisson())
fit2 - glm(Aids ~ Year+I(Year^2), data=aids, family=poisson())
I am trying to work out how to represent the fitted regression curves of fit1
and fit2 on the one graph. I have tried:
graphics.off()
plot(Aids ~ Year, data = aids)
line(glm(Aids ~ Year, data=aids, family=poisson()))
line(glm(Aids ~ Year+I(Year^2), data=aids, family=poisson()))
but this does not work.
Can anyone help me?
Thanks
Jo
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This email and any files transmitted with it are confide...{{dropped:15}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting two regression lines on one graph
One approach to this is generating a representative sequence of your
x-variable(s) with seq() or expand.grid(). Next use the predict()
function to make predictions from your glm object along the sequence.
Finally, plot the predictions vs. the new sequence. Putting everything
into a dataframe helps.
# generate some data:
x - rnorm(10)
y - x * 2 + rnorm(10, sd=0.5)
# plot
plot(y ~ x)
# generate linear model:
l - lm(y ~ x)
# generate sequence along x-var
# and predictions
d - data.frame(x.new=seq(from=-1.5, to=1.2, by=0.1))
d$y.new - predict(l, data.frame(x=d$x.new))
# add to plot:
lines(y.new ~ x.new, data=d, lwd=2)
Cheers,
Dylan
On Sun, Jun 7, 2009 at 8:36 PM, Jo Stringerjstrin...@bses.org.au wrote:
Hi!
I have fitted two glms assuming a poisson distribution which are:
fit1 - glm(Aids ~ Year, data=aids, family=poisson())
fit2 - glm(Aids ~ Year+I(Year^2), data=aids, family=poisson())
I am trying to work out how to represent the fitted regression curves of fit1
and fit2 on the one graph. I have tried:
graphics.off()
plot(Aids ~ Year, data = aids)
line(glm(Aids ~ Year, data=aids, family=poisson()))
line(glm(Aids ~ Year+I(Year^2), data=aids, family=poisson()))
but this does not work.
Can anyone help me?
Thanks
Jo
BSES Limited Disclaimer
This email and any files transmitted with it are confide...{{dropped:15}}
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting two regression lines on one graph
Hi Jo,
Next time try prepare a reproducible code.
You have several ways of do that (see Dylan Beaudette) and give a look
below.
x-1:100
y-7+x*(sqrt(x*runif(100)))
plot(y~x)
mod1-glm(y~x)
mod2-glm(y~x+I(x*x))
curve(mod1$coef[1]+mod1$coef[2]*x, col=red, add=T, lwd=3)
curve(mod2$coef[1]+mod2$coef[2]*x+mod2$coef[3]*x*x, col=green, add=T,
lwd=3)
cheers
milton
On Sun, Jun 7, 2009 at 11:36 PM, Jo Stringer jstrin...@bses.org.au wrote:
Hi!
I have fitted two glms assuming a poisson distribution which are:
fit1 - glm(Aids ~ Year, data=aids, family=poisson())
fit2 - glm(Aids ~ Year+I(Year^2), data=aids, family=poisson())
I am trying to work out how to represent the fitted regression curves of
fit1 and fit2 on the one graph. I have tried:
graphics.off()
plot(Aids ~ Year, data = aids)
line(glm(Aids ~ Year, data=aids, family=poisson()))
line(glm(Aids ~ Year+I(Year^2), data=aids, family=poisson()))
but this does not work.
Can anyone help me?
Thanks
Jo
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Re: [R] Convert a lis to matrix
Thank you, it worked. -Original Message- From: Bernardo Rangel Tura [mailto:t...@centroin.com.br] Sent: Sunday, June 07, 2009 6:14 AM To: Manisha Brahmachary Cc: r-help@r-project.org Subject: Re: [R] Convert a lis to matrix On Sun, 2009-06-07 at 00:14 -0400, Manisha Brahmachary wrote: Hello, This is an urgent request. I want to convert a list of 3 elements into a matrix and I am not sure how to do it. The list looks like this: List of 3 $ : num [1:15364, 1] 0.133 0.622 0.588 1.024 0.583 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL $ : num [1:15364, 1] 3.159 0.265 0.522 1.912 3.380 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL $ : num [1:15364, 1] 3.214 0.277 1.447 1.827 2.054 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:15364] 6420681 3610072 2260458 60689 ... .. ..$ : NULL I'm not sure if understood your question, but look this code a-list(B=1:3,C=2:4,D=3:5) matrix(unlist(a),ncol=3) -- Bernardo Rangel Tura, M.D,MPH,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extract rows having negative values
Thank you Bill, your suggestion works just fine!!! -Original Message- From: bill.venab...@csiro.au [mailto:bill.venab...@csiro.au] Sent: Sunday, June 07, 2009 3:23 AM To: Manisha Brahmachary; r-help@r-project.org Subject: RE: extract rows having negative values rownames(X)[apply(X, 1, function(r) any(r 0))] ... if I understand you correctly. From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Manisha Brahmachary [mb3...@c2b2.columbia.edu] Sent: 07 June 2009 08:54 To: r-help@r-project.org Subject: [R] extract rows having negative values Hello, I have a matrix with 6 columns and 12 rows. I want to extract out those IDs (rownames) from my matrix which have a negative values. For each ID(row) if the negative value is even under 1 column it needs to be extracted out. I will be grateful for any correct suggestion. Thanks Manisha Here is the matrix that I am working on: ID A B C D E F 1 -4.18972 -3.8946 -1.14888 -1.88406 -8.34124 10.97497 2 11.81028 11.1054 0.85112 0.115942 -4.34124 24.97497 3 -0.18972 -1.8946 1.85112 -4.88406 -17.3412 -13.025 4 -1.18972 3.105402 -0.14888 -12.8841 -15.3412 4.974967 6 -3.18972 4.105402 24.85112 0.115942 1.658762 -11.025 7 -2.18972 -10.8946 -20.1489 -1.88406 3.658762 -11.025 8 -0.18972 -7.8946 -7.14888 -9.88406 3.658762 -9.02503 9 -5.18972 -4.8946 -12.1489 0.115942 -12.3412 10.97497 10 17.81028 9.105402 -15.1489 10.11594 19.65876 9.974967 11 538.8103 335.1054 863.8511 229.1159 520.6588 143.975 12 30.81028 18.1054 30.85112 16.11594 9.658762 13.97497 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ridiculous behaviour printing to eps: labels all messed up!
OK, this is really weird! here's an example code: t1-c(1,2,3,4) t2-c(4,2,4,2) plot(t1~t2, xlab=exp1, ylab=exp2) dev.copy2eps(file=test.eps) that all seems fine... until you look at the eps file created, where for some weird reason, if you scroll down to the end, the code reads: /Font1 findfont 12 s 0 setgray 214.02 18.72 (e) 0 ta -0.360 (xp1) tb gr 12.96 206.44 (e) 90 ta -0.360 (xp2) tb gr Which means, that the labels exp1 and exp2 get split up!?!? Now visually that doesn't matter, but I use the labels to refer to them in LaTeX using psfrag, so I have to know exactly what they are called in the .eps file in order to reference them correctly. I've tried other labels and the splitting up seems completely random i.e doesn't have anything to do with the length of the label etc. I am completely lost here, can someone help me figure out what is going on here? Maja -- View this message in context: http://www.nabble.com/ridiculous-behaviour-printing-to-eps%3A-labels-all-messed-up%21-tp23916638p23916638.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Interpreting R -results for Bivariate Normal
HI Guys, I know that this forum is not for homework but I am trying to interpret R output code. I was just wondering if someone might be able to help. I have been given the following. For (X1,X2) distributed bivariate normal with parameters mu1 = 5.8 mu2 = 5.3 sd1 = sd2 = 0.2 and p = 0.6 The r-code and inpit/output are as follows input m - 5.3 + 0.6*(6.3 - 5.8) s - sqrt(0.2^2*(1-0.6^2)) q - seq(5.12,6.08,0.16) print(rbind(q,pnorm(mean=m,sd=sd=s,q=q))) output q 5.1200 5.280 5.44 5.6 5.76 5.926.1 0.0013 0.023 0.16 0.5 0.84 0.981 I have been asked to interpret E[X2|X1 = 6.3] and varE[X2|X1 = 6.3] I take it that s- = 0.16 is the standard variation So I am assuming that varE[X2|X1 = 6.3] = 0.16^2 = .0256 m - 5.3 + 0.6*(6.3 - 5.8) = 5.6this the Expected value of E[X+Y] I see from the output that this would be correct because the probability of 5.6 = 0.5 to interpret E[X2|X1 = 6.3] I can't see it in the output. And I'm not sure how to find the conditional probabilty from the output. Any help would be greatly appreciated -- View this message in context: http://www.nabble.com/Interpreting-R--results-for-Bivariate-Normal-tp23916967p23916967.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting two regression lines on one graph
Since you have provided no executable data and not even a clear enough description of the data to offer advice regarding approaches or pitfalls, I will use the example in glm's help page: counts - c(18,17,15,20,10,20,25,13,12) outcome - gl(3,1,9) treatment - gl(3,3) glm.D93r - glm(counts ~ outcome, family=poisson()) plot(x=as.numeric(as.character(outcome)), y=counts, type=p) #need to convert from factor to ge points lines(1:3, c(exp(3.045), exp(3.0445 -0.4543), exp(3.0445 -0.2930) ) ) #the default link for poisson is log, so you need to transform back to the original scale to predict counts. On Jun 7, 2009, at 11:36 PM, Jo Stringer wrote: I have fitted two glms assuming a poisson distribution which are: fit1 - glm(Aids ~ Year, data=aids, family=poisson()) fit2 - glm(Aids ~ Year+I(Year^2), data=aids, family=poisson()) I am trying to work out how to represent the fitted regression curves of fit1 and fit2 on the one graph. I have tried: graphics.off() plot(Aids ~ Year, data = aids) line(glm(Aids ~ Year, data=aids, family=poisson())) line(glm(Aids ~ Year+I(Year^2), data=aids, family=poisson())) but this does not work. Can anyone help me? David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
