Re: [R] NAs - NAs are not allowed in subscripted assignments
On Thu, Jul 24, 2008 at 04:45:14PM +0200, Kunzler, Andreas wrote: Hy Richie, thank you for the quick response. Unfortunately my problems hold on. Once again: 2 vectors (numeric) including NAs My intention: I want to replace the values of vector a that are smaller than 2 and larger than 3 into NAs only in case vector b equals 1 a - c(rep(seq(1,4),4),NA,NA) b - c(rep(seq(1,2),7),NA,NA,1,2) Andreas, what is wrong with a[ (a 2 | a 3) b==1 ] - NA ? Isn't this what you want? Btw. I assume you mean replacing values that are either smaller than 2 _OR_ larger than 3, no number is smaller than 2 _AND_ larger than 3, at least if we consider the usual ordering on numbers. Best, Gabor [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] NAs - NAs are not allowed in subscripted assignments
On Thu, Jul 24, 2008 at 09:30:54AM -0700, Nordlund, Dan (DSHS/RDA) wrote: [...] a - c(rep(seq(1,4),4),NA,NA) b - c(rep(seq(1,2),7),NA,NA,1,2) Andreas, what is wrong with a[ (a 2 | a 3) b==1 ] - NA ? Isn't this what you want? [...] As I mentioned in my response to this thread, there are some things I don't quite understand with logical indexing. Using the above example, a[ (a 2 | a 3) b==1 ] returns [1] 1 1 1 1 NA NA Where do the NA values come from? This is not really about logical indexing, just operations on numeric and logical vectors, and how they handle NA values. Just keep in mind that NA means that we don't know the actual value. All operations were desinged (I believe) with this in mind. Here is some help: NA == 1 [1] NA class(NA == 1) [1] logical This is NA, obviously, as _we don't know_ whether NA is equal to 1 or not. TRUE NA [1] NA FALSE | NA [1] NA The same applies here, for the result we would need to know whether NA is TRUE or FALSE. However, we have FALSE NA [1] FALSE TRUE | NA [1] TRUE In these cases the result can be calculated without knowing what actually NA is. Logical indexing is simple, for every TRUE value in the logical vector we choose the corresponding element from the indexed vector. If we index with NA, then the chosen element is NA as well. (1:5)[ c(T,T,T,T,T) ] [1] 1 2 3 4 5 (1:5)[ c(T,T,T,F,T) ] [1] 1 2 3 5 (1:5)[ c(T,T,T,F,NA) ] [1] 1 2 3 NA (1:5)[ c(NA,T,T,F,NA) ] [1] NA 2 3 NA Does this help? Best, Gabor Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] NAs - NAs are not allowed in subscripted assignments
On Thu, Jul 24, 2008 at 10:39:34AM -0700, Nordlund, Dan (DSHS/RDA) wrote: [...] Yes, it does help. I was misunderstanding how logical values are used for indexing. I assumed incorrectly that a value would be returned only if the index expression evaluated as TRUE. It would seem that the philosophy is that not returning a value would imply that the expression evaluated to FALSE. So, indexing with NA must return something, and NA is the appropriate value to return since one doesn't know what it is. Is that a reasonable summary? Yes, I think so. (But I have to say that I'm not completely aware of the ideology behind this choice.) Gabor Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Calculating Betweenness - Efficiency problem
Senthil, sending a 12Mb file to the list is not a good idea. I've run the code in my previous email without any problem, so you need to be a bit more specific about what went wrong for you. This is what I get: library(igraph) tab - read.csv(/tmp/Test.csv) dim(tab) [1] 304711 2 length(unique(tab)) [1] 2 g - graph.data.frame(tab) summary(g) Vertices: 48072 Edges: 304711 Directed: TRUE No graph attributes. Vertex attributes: name. No edge attributes. system.time(bet - betweenness(g)) user system elapsed 661.180 0.098 661.716 length(bet) [1] 48072 bet - data.frame(city=V(g)$name, betweenness=bet) dim(bet) [1] 48072 2 Best, Gabor On Tue, Jul 22, 2008 at 11:58:37AM -0700, Senthil Purushothaman wrote: Dear Gabor, Thank you very much for the insights. I have been using the igraph package for my computations. But I did not know about graph.data.frame(). Thanks again for that. So I did run my data using the steps you had provided. Weirdly, even though the .csv file has approximately 300,000 records (remember that the file gets truncated to 65536 rows when opened in Excel 2003), not all of them are pulled in during the operation and the final betweenness list contains only ~1000+ records but it should be tens of thousands. I know that you are a busy person. This problem seems to be a very different challenge. I am attaching the Test.csv file for your experiments. Thank you very much again. Best regards, Senthil (909) 267-0799 -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: Monday, July 21, 2008 1:57 AM To: Senthil Purushothaman Cc: jim holtman; r-help@r-project.org Subject: Re: [R] Calculating Betweenness - Efficiency problem Senthil, you can try the 'igraph' package. Export your two-column Excel file as a .csv, use 'read.csv' to read that into R, then 'graph.data.frame' to create an igraph graph from it. Finally, call 'betweenness' on the graph. It is really just three/four lines, something like this: tab - read.csv(...) g - graph.data.frame(tab) bet - betweenness(g) bet - data.frame(city=V(g)$name, betweenness=bet) The last line creates a two column data frame with the betweenness score of each city. Best, Gabor [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Calculating Betweenness - Efficiency problem
Senthil, you can try the 'igraph' package. Export your two-column Excel file as a .csv, use 'read.csv' to read that into R, then 'graph.data.frame' to create an igraph graph from it. Finally, call 'betweenness' on the graph. It is really just three/four lines, something like this: tab - read.csv(...) g - graph.data.frame(tab) bet - betweenness(g) bet - data.frame(city=V(g)$name, betweenness=bet) The last line creates a two column data frame with the betweenness score of each city. Best, Gabor On Sat, Jul 19, 2008 at 02:59:07PM -0700, Senthil Purushothaman wrote: Hi Jim, Thank you for the response. Your suggestion will help me avoid the whole text to number conversion process that I perform using LookUp in excel. I will definitely give it a shot. But it still doesn't address the vector conversion since a graph file is drawn only using the vectors. Assuming that I use 'factor' to convert the characters to numbers, how do I convert these numbers into vectors? Thanks, Senthil -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Sat 7/19/2008 4:49 AM To: Senthil Purushothaman Cc: r-help@r-project.org Subject: Re: [R] Calculating Betweenness - Efficiency problem It would seem that you can output the initial file from EXCEL, read it into R with 'read.csv' and then use 'factor' to convert the characters for City1 and City2 to the numbers that you want to use. Have you tried this approach? On Fri, Jul 18, 2008 at 3:51 PM, Senthil Purushothaman [EMAIL PROTECTED] wrote: Hello, I am calculating 'Betweenness' of a large network using R. Currently, I have the node-node information (City1-City2) in an excel file, present in two columns where column A has City1 and column B has City2 that city1 is connected to. These are the steps that I go through to calculate betweenness of my network. a) Convert the City1-City2 (text) into Number1-Number2 in the excel file where every unique city has a unique number. b) Paste all the city-city information separated by comma into c(...) in the R GUI to obtain the corresponding vectors. As you can imagine this copy-paste operation takes a long time. Example: c(1,3,1,5,2,4,2,5). Just fyi, I have a text file that contains all nodes separated by comma based on the appropriate link information. c) Then, I create a graph file with the above vector. d) I use the graph file to calculate betweenness of my network. I am sure there must be a better, more efficient way to calculate betweenness. Ideally, I would like to just have the City1 - City2 (link) information in two columns in an excel file and calculate the betweenness from that file directly. Please provide an optimal solution for this problem. I appreciate your time and help. Thanks, Senthil [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Font quality in base graphics
Hmmm, I did not follow this thread closely, sorry for that, just want to share my 2c. If it is about quality, then I create EPS files and use the psfrag latex package to replace the PS fonts with TeX's fonts. This has the following advantages: 1) The figures have the same font as the text itself. The same size as well. If you resize the figure the fonts stay the same! 2) You can write fancy TeX formulae in the figures. 3) You can have any font TeX supports. Disadvantages: 1) The same as before, if you resize the figure the fonts stay the same! This is quite far from WYSIWYG. 2) You cannot use pdfLaTeX. I have a little script that automates this for .fig files (this is based on figtex, another script that I found somewhere online and can't find it any more), and another one for SVG files. So you save the file with xfig() or svg() and then the script does everything, all you have to do is to include it into the .tex file with a small custom macro. Gabor On Wed, Jul 16, 2008 at 02:25:52AM -0700, Mark Difford wrote: Hi willemf, Glad to hear that it helped. Years ago (late-90s) I Linuxed, but have since been forced into the Windows environment (where, however, I have the great pleasure of being able to use MiKTeX and LyX, i.e. TeX/LaTeX). I therefore can't help you further, except to say that I have never had a problem controlling font sizes c to my admittedly very demanding --- some people say excessively demanding --- standards (and that's on Windows!). And I have never had a problem with labels c not being where they should be, or of the size I want them to be, when I have built the graphic from scratch. And only very rarely have I encountered such problems when using canned graph types. In brief, what I am saying is that the problem almost certainly lies with the way fonts c are set up on your Linux box. Were this not the case, then I can assure you that there would have many and varied sharply worded statements on this list relating to the poor quality of R's graphs. And there would have been just as many pointed, well-written rebukes, pointing that Yet there aren't. If you search the archives you will find that a good many users migrated to R from other systems because of R's excellent graphical subsystems. Look at the graphics in any of the many books now published on using R, or that use R to elucidate problems Set your mind at rest: look at your system setup, and the tools outside R that you are using. Hope it all works out. OpenOffice is now a very good suite of programs, but if you want true quality of output then you really should be TeXing. Check it out. Bye, Mark. willemf wrote: Mark, your suggestion results in about 75% control over the plot. This is the best that I have managed to get it at, so thank you very much. In Linux you create a X11() device for screen output. Specifying identical device characteristics results in a fair degree of similarity between screen version and EPS version. However in this case, for instance, some labels along the X axis are omitted in the screen version and (thankfullly!) included in the Postscript version. Also, the relative sizes of caption font size and label font size are not identical in the two versions. I have learnt a few things in this exercise, so thanks you very much for the advice. -- View this message in context: http://www.nabble.com/Font-quality-in-base-graphics-tp18465608p18483719.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Font quality in base graphics
On Wed, Jul 16, 2008 at 04:48:28AM -0500, Gabor Csardi wrote: [...] I have a little script that automates this for .fig files (this is based on figtex, another script that I found somewhere online and can't find it any more) [...] Ok, it is called figfrag, and it is on CTAN. [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] rm(l*)
Maybe there is a simpler way, but this works fine: l1 - 1 l2 -2 m -10 ls() [1] l1 l2 m rm(list=grep(^l.*, ls(), value=TRUE)) ls() [1] m You can supply a regular expression to grep. Gabor On Mon, Jul 14, 2008 at 10:45:13AM +0200, Oehler, Friderike (AGPP) wrote: Dear Rusers, how can I designate various objects the names of which start (or end) with the same letter to remove them all together? For instance: ls() a,b,c,l1,l2,x rm(list=ls(l*)) ls() a,b,c,x Is there some parallel to the MySQL query: where col1 like l% Thanks a lot in advance, Friderike [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] network
I'm sure this is possible with 'network', but i'm not very familiar with that package. In case you don't get an answer on how to do it with network, here is how to do it with the 'igraph' package: library(igraph) M - matrix(runif(100)*2-1, 10, 10) M[ lower.tri(M, diag=TRUE) ] - 0 M[ abs(M) 0.5] - 0 g - graph.adjacency(M, weighted=TRUE, mode=upper) E(g)$color - green E(g)[ weight0 ]$color - red g$layout - layout.fruchterman.reingold plot(g) Please tell me if something is not clear, Gabor On Fri, Jul 11, 2008 at 02:04:54PM +0100, Dry, Jonathan R wrote: Hello I am a relatively new user of R and am struggling to use the 'network' package. I have a correlation matrix (produced using 'cor'), and want to draw a network where each item showing correlation above a threshold (say 0.5) is joined by a green line, and each item showing correlation below a threshold (say -0.5) is joined by a red line. Does anyone have any hints of how to correctly use functions within the 'network' package to achieve this? __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] network
Jonathan, please stay on the list. The first query i don't understand, can you send a pdf or explain a bit what exactly happens. As for the names, use them as row or column names in the matrix (see ?colnames), and then do V(g)$label - V(g)$name before the plotting. G. On Fri, Jul 11, 2008 at 02:47:55PM +0100, Dry, Jonathan R wrote: Superb - thanks Gabor Two minor queries - firstly the network plot does not seem to fit in the window and so only part of it is plotted. Secondly, the first row and column of my matrix comprise the sample names - is it possible to show the names in the nodes of the graph (currently it just shows the row number)? Your help is much appreciated Kind regards Jonathan -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: 11 July 2008 14:33 To: Dry, Jonathan R Cc: r-help@r-project.org Subject: Re: [R] network I'm sure this is possible with 'network', but i'm not very familiar with that package. In case you don't get an answer on how to do it with network, here is how to do it with the 'igraph' package: library(igraph) M - matrix(runif(100)*2-1, 10, 10) M[ lower.tri(M, diag=TRUE) ] - 0 M[ abs(M) 0.5] - 0 g - graph.adjacency(M, weighted=TRUE, mode=upper) E(g)$color - green E(g)[ weight0 ]$color - red g$layout - layout.fruchterman.reingold plot(g) Please tell me if something is not clear, Gabor On Fri, Jul 11, 2008 at 02:04:54PM +0100, Dry, Jonathan R wrote: Hello I am a relatively new user of R and am struggling to use the 'network' package. I have a correlation matrix (produced using 'cor'), and want to draw a network where each item showing correlation above a threshold (say 0.5) is joined by a green line, and each item showing correlation below a threshold (say -0.5) is joined by a red line. Does anyone have any hints of how to correctly use functions within the 'network' package to achieve this? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] network
Hmmm, it seems that the colum/row names are not added properly, maybe this works only in the not-yet-released version. You can do V(gdata2)$label - colnames(data2) as a workaround. G. On Fri, Jul 11, 2008 at 03:32:15PM +0100, Dry, Jonathan R wrote: Thnaks Ignore the forst problem - seems to solve itself! Trying 'V(g)$label - V(g)$name' I recieve the following error: Error in `V-`(`*tmp*`, value = 0:9) : invalid indexing The full code used (with matrix shown) is below - any help appreciated: data2 G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G1000000.000 0.000 0.0000 0 G200000 -0.356 0.000 0.0000 0 G3000000.000 0.319 0.0000 0 G4000000.000 0.000 0.4290 0 G5000000.000 0.000 -0.4190 0 G6000000.000 0.000 0.0000 0 G7000000.000 0.000 0.0000 0 G8000000.000 0.000 0.0000 0 G9000000.000 0.000 0.0000 0 G10 000000.000 0.000 0.0000 0 gdata2 - graph.adjacency(data2, weighted=TRUE, mode=upper) E(gdata2)$color - green E(gdata2)[ weight0 ]$color - red gdata2$layout - layout.fruchterman.reingold V(gdata2)$label - V(data2)$name Error in V(data2) : Not a graph object V(gdata2)$label - V(gdata2)$name Error in `V-`(`*tmp*`, value = 0:9) : invalid indexing gdata2 Vertices: 10 Edges: 4 Directed: FALSE Edges: [0] 1 -- 5 [1] 2 -- 6 [2] 3 -- 7 [3] 4 -- 7 -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: 11 July 2008 14:54 To: Dry, Jonathan R Cc: R Help list Subject: Re: [R] network Jonathan, please stay on the list. The first query i don't understand, can you send a pdf or explain a bit what exactly happens. As for the names, use them as row or column names in the matrix (see ?colnames), and then do V(g)$label - V(g)$name before the plotting. G. On Fri, Jul 11, 2008 at 02:47:55PM +0100, Dry, Jonathan R wrote: Superb - thanks Gabor Two minor queries - firstly the network plot does not seem to fit in the window and so only part of it is plotted. Secondly, the first row and column of my matrix comprise the sample names - is it possible to show the names in the nodes of the graph (currently it just shows the row number)? Your help is much appreciated Kind regards Jonathan -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: 11 July 2008 14:33 To: Dry, Jonathan R Cc: r-help@r-project.org Subject: Re: [R] network I'm sure this is possible with 'network', but i'm not very familiar with that package. In case you don't get an answer on how to do it with network, here is how to do it with the 'igraph' package: library(igraph) M - matrix(runif(100)*2-1, 10, 10) M[ lower.tri(M, diag=TRUE) ] - 0 M[ abs(M) 0.5] - 0 g - graph.adjacency(M, weighted=TRUE, mode=upper) E(g)$color - green E(g)[ weight0 ]$color - red g$layout - layout.fruchterman.reingold plot(g) Please tell me if something is not clear, Gabor On Fri, Jul 11, 2008 at 02:04:54PM +0100, Dry, Jonathan R wrote: Hello I am a relatively new user of R and am struggling to use the 'network' package. I have a correlation matrix (produced using 'cor'), and want to draw a network where each item showing correlation above a threshold (say 0.5) is joined by a green line, and each item showing correlation below a threshold (say -0.5) is joined by a red line. Does anyone have any hints of how to correctly use functions within the 'network' package to achieve this? __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Turn any vector
It is called 'rev', see ?rev. rev(1:10) [1] 10 9 8 7 6 5 4 3 2 1 G. On Thu, Jul 10, 2008 at 01:56:58PM +0200, Zroutik Zroutik wrote: Dear R-users, I'd like to turn a vector so it starts with it's end. For better understanding, this set of commands will do what I need: i - seq(1:10) i_turned - i for (j in 1:length(i)) i_turned[j] - i[length(i)-j+1] now, i_turned is what I call turned. Is there a function which would make a script lighter? Thank you upfront for any hint. Best regards, Zroutik [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Expression in axis
E.g. plot(1:10,1:10,xlab=NA) title(xlab=expression(mu*mol/10^6* cells)) Gabor On Wed, Jul 09, 2008 at 11:21:46AM +0200, Dani Valverde wrote: Hello, I am creating a plot and I would like to know how to put this expression to the y axis µmol/10^6 cells I've tried some combinations using the expression() function, but none of them worked. Any idea? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Summary Stats (not summary(x))
Why don't you write it for yourself, it takes less time than writing
an email:
mysummary - function(x) {
require(plotrix)
require(e1071)
c(Mean=mean(x), Std.Error=std.error(x), Std.Deviation=sd(x),
Kurtosis=kurtosis(x))
}
Gabor
On Wed, Jul 09, 2008 at 08:15:00AM -0700, nmarti wrote:
I'm looking for a function that lists a few summary stats for a column (or
row) of data. I'm aware of summary(x), but that does not give me what I'm
looking for.
I'm actually looking for something that is very similar to the descriptive
statistics tool in excel; i.e. Mean, Std. Error, Std. Deviation, Kurtosis.
I'm positive that I came across a function that did this (possibly in
Rmetrics), but now I can't find it. I lost it in the endless mass of R
functions.
Any help would be appreciated.
--
View this message in context:
http://www.nabble.com/Summary-Stats-%28not-summary%28x%29%29-tp18363275p18363275.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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Re: [R] Can R do this ?
If this is about more than a handful files, then it is really painful
to do it with OpenOffice.org or LyX, I guess.
You can use imagemagick, this is fairly standard on Linux. Then it is
something like this, assuming you have bash:
for f in *.png; do convert $f ${f%png}pdf; done
for f in *.jpg; do convert $f ${f%jpg}pdf; done
Of course this does not vectorise the files
Gabor
On Tue, Jul 08, 2008 at 10:05:59AM +0100, Paul Smith wrote:
On Tue, Jul 8, 2008 at 6:59 AM, Daren Tan [EMAIL PROTECTED] wrote:
I have a folder full of pngs and jpgs, and would like to consolidate them
into a pdf with appropriate title and labels. Can this be done via R ?
I do not know whether R can do that. However, you can accomplish that
easily with LyX or with OpenOffice.
Paul
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Re: [R] Can R do this ?
Ooops, please ignore my previous mail, I did not read the question carefully enough. Gabor On Tue, Jul 08, 2008 at 02:27:51AM -0700, Mark Difford wrote: Hi Daren, Can R (out)do Emacs? I think you just need to ?Sweave a little. Mark. Daren Tan wrote: I have a folder full of pngs and jpgs, and would like to consolidate them into a pdf with appropriate title and labels. Can this be done via R ? _ Easily publish your photos to your Spaces with Photo Gallery. [[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. -- View this message in context: http://www.nabble.com/Can-R-do-this---tp18332407p18335253.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] trivial list question
I think there are many simple solutions, here is one: lapply(1:92, function(x) c(2*x-1, 2*x)) Gabor On Tue, Jul 01, 2008 at 02:46:07PM +0200, Boks, M.P.M. wrote: Dear experts, For the makeGenotype function I need a list as in the example. However, since my list needs to be 184 long there must be an easy way to make it. list(1:2,3:4,5:6,7:8) [[1]] [1] 1 2 [[2]] [1] 3 4 [[3]] [1] 5 6 [[4]] [1] 7 8 I have tried lis-1:184 dim(lis)=c(92,2,1) as.list(lis) and several other options. Any suggestions? many thanks Marco [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Find classes of each column of data.frame()
A data frame is a special list: d - data.frame( A=numeric(), B=logical(), C=character() ) lapply(d, class) $A [1] numeric $B [1] logical $C [1] factor Gabor On Tue, Jul 01, 2008 at 03:50:18PM +0200, Dong-hyun Oh wrote: Dear UseRs, I would like to know the way to find classes of each column of data.frame(). Thank you in advance. = Dong-hyun Oh Center of Excellence for Science and Innovation Studies Royal Institute or Technology, Sweden e-mail: [EMAIL PROTECTED] cel: +46 73 563 45 22 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Graphs in R
paste(sep=, graf, 1:250, .jpg)
See ?paste,
G.
On Mon, Jun 30, 2008 at 11:58:51AM -0300, Leandro Marino wrote:
Hi list,
I want to make a lot of graphics to my end course project. So, i was using
this sintax:
jpeg(filename = graf01.jpg, width = 1024, height = 1024,
units = px, pointsize = 25, quality = 100, bg = grey95,
res = NA, restoreConsole = TRUE)
i=1
par(mfrow=c(4,1),col=grey90,font.lab=2)
hist(sul[,i+2],nclass=75,xlab=Região
Sul,ylab=Freqüência,col=antiquewhite4,main=)
hist(PR[,i+2],nclass=75,xlab=Paraná,ylab=Freqüência,col=antiquewhite4,
main=)
hist(SC[,i+2],nclass=75,xlab=Santa
Catarina,ylab=Freqüência,col=antiquewhite4,main=)
hist(RS[,i+2],nclass=75,xlab=Rio Grande do
Sul,ylab=Freqüência,col=antiquewhite4,main=)
dev.off()
But, I want to know how can I create an for to do that. Like that:
for(i in 1:250){
jpeg(filename = graf01.jpg, width = 1024, height = 1024,
units = px, pointsize = 25, quality = 100, bg = grey95,
res = NA, restoreConsole = TRUE)
par(mfrow=c(4,1),col=grey90,font.lab=2)
hist(sul[,i+2],nclass=75,xlab=Região
Sul,ylab=Freqüência,col=antiquewhite4,main=)
hist(PR[,i+2],nclass=75,xlab=Paraná,ylab=Freqüência,col=antiquewhite4,
main=)
hist(SC[,i+2],nclass=75,xlab=Santa
Catarina,ylab=Freqüência,col=antiquewhite4,main=)
hist(RS[,i+2],nclass=75,xlab=Rio Grande do
Sul,ylab=Freqüência,col=antiquewhite4,main=)
dev.off()
}
The problem is the name of the file, I want to do something like grafi.jpg
where i goes from 1 to 250.
Thanks a lot for the help.
Best Regards,
Leandro Marino
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Re: [R] igraph (was Compilation error during package installation)
Wanding, I'm the maintainer of igraph, but missed your previous email. Yes, currently the released version of igraph fails to compile with gcc 4.3.x. I made the required modifications to fix this, but these are still in the igraph development tree, as there has been no release since that. You can do the one of the following things: 1) You download and install http://cneurocvs.rmki.kfki.hu/igraph/download/igraph_0.5.1.tar.gz This is an almost final 0.5.1 version, there will be some more minor updates. 2) You just wait a week for igraph 0.5.1. 3) You download our development tree and build an R package for yourself. Probably 1) is easiest. Best, Gabor Btw. there is also an igraph mailing list, see igraph.sf.net - community - igraph-help On Fri, Jun 27, 2008 at 11:49:29AM +0100, Prof Brian Ripley wrote: Please discuss this with the package maintainer (see the posting guide). He will need lots of details you have omitted, including the precise OS and the C++ compiler used. BTW, this illustrates a common problem with packages using C++, which people often test only under one compiler, and until recently (4.3.x) g++ has been notoriously lax in reporting non-conformance to ISO C++. There are about 30 CRAN packages that fail to install under the Sun C++ compiler, but igraph did at one point recently (there is now a problem with the use of C headers in C++ code). On Thu, 26 Jun 2008, wanding ZHOU wrote: Hi, I am a Newbie for R. I just installed R-base on my notebook with openSuSE 11. However, I always got compilation errors in installing add-on packages. For example, when installing igraph I got the following error: ___ * Installing *source* package 'igraph' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for fmemopen... yes checking for open_memstream... yes checking for rintf... yes checking for finite... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking for xml2-config... none checking for __gmpz_add in -lgmp... no configure: creating ./config.status config.status: creating src/config.h config.status: creating R/config.R config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R -I. -g -O2 -DPACKAGE_VERSION=\0.5\ -DINTERNAL_ARPACK -DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c adjlist.c -o adjlist.o igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R -I. -g -O2 -DPACKAGE_VERSION=\0.5\ -DINTERNAL_ARPACK -DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c arpack.c -o arpack.o igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R -I. -g -O2 -DPACKAGE_VERSION=\0.5\ -DINTERNAL_ARPACK -DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c array.c -o array.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -DUSING_R -I. -g -O2 -DPACKAGE_VERSION=\0.5\ -DINTERNAL_ARPACK -DINTERNAL_LAPACK -DINTERNAL_BLAS -fpic -g -O2 -c atlas.c -o atlas.o igraph.h:435: warning: inline function ‘igraph_es_type’ declared but never defined igraph.h:233: warning: inline function ‘igraph_vs_type’ declared but never defined igraph.h:435: warning: inline function ‘igraph_es_type’ declared but
Re: [R] running R-code outside of R
Some clarifications. R's license (GPL v2) is not about money, you can charge anyone as much as you wish. If you create an R program (and don't modify R itself), then you can distribute that program according to any license you wish. If you modify R itself _and_ distribute the modified version, then you have to give the source code of the modified version, along with the distributed binaries. Again, this is not about money, you _must_ publish the sources, even if your new version is for free. If you create a website and the user uses R and your code through that site only, then you don't have to give the source code to anyone. Basically, you have no obligations in this case. Spencer is right that this might be against the principles of the license, but legally it is fine. It might change if R will ever use GPL version 3. Gabor On Wed, Jun 25, 2008 at 10:28:09AM -0500, Michael Conklin wrote: Spencer Graves wrote: If you want to hide the fact that you are using R -- especially if you charge people for your software that uses R clandestinely -- that's a violation of the license (GPL). I doubt if anyone associated with R would bother with a lawsuit, but a competitor who offers related software might. Best Wishes, Spencer Do I understand the implication of the license correctly (forgive my ignorance here). If I analyze a client's data using an R script I created then I can charge the client a $20,000 consulting fee, but, if I let the client push the button to execute the R script and charge him 10 cents for the privilege then I can be sued for violating the GPL? Or are my assumptions on the first part also incorrect and R can only be used for the free betterment of mankind? Mike __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] selecting values that are unique, instead of selecting unique values
Hmmm, this is not very good: Vec - c(10:1,1) Vec[ table(Vec) == 1 ] [1] 9 8 7 6 5 4 3 2 1 and these are obviously not the unique values. This one is better: Vec [ ! duplicated(Vec) ! duplicated(Vec, fromLast=TRUE) ] Gabor On Wed, Jun 25, 2008 at 11:29:31AM -0500, Marc Schwartz wrote: on 06/25/2008 11:19 AM Daren Tan wrote: unique(c(1:10,1)) gives 1:10 (i.e. unique values), is there any method to get only 2:10 (i.e. values that are unique) ? The easiest might be: Vec [1] 1 2 3 4 5 6 7 8 9 10 1 Vec[table(Vec) == 1] [1] 2 3 4 5 6 7 8 9 10 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] selecting values that are unique, instead of selecting unique values
I'm sorry to say, but this one is wrong, too. Maybe coffee really helps, I just had one. :) Vec - c(20:30,20) which(table(Vec) == 1) 21 22 23 24 25 26 27 28 29 30 2 3 4 5 6 7 8 9 10 11 You would actually need the names, but that would involve some numberic - character - numeric conversion. My previous solution is better in this respect. Btw. to get rid of names 'unname' is better, the code is more readable. Best, Gabor On Wed, Jun 25, 2008 at 11:37:12AM -0500, Marc Schwartz wrote: on 06/25/2008 11:29 AM Marc Schwartz wrote: on 06/25/2008 11:19 AM Daren Tan wrote: unique(c(1:10,1)) gives 1:10 (i.e. unique values), is there any method to get only 2:10 (i.e. values that are unique) ? The easiest might be: Vec [1] 1 2 3 4 5 6 7 8 9 10 1 Vec[table(Vec) == 1] [1] 2 3 4 5 6 7 8 9 10 Correction! That should be: which(table(Vec) == 1) 2 3 4 5 6 7 8 9 10 2 3 4 5 6 7 8 9 10 or if you don't want a named vector: as.vector(which(table(Vec) == 1)) [1] 2 3 4 5 6 7 8 9 10 My initial solution was incorrect and only worked because of the ordering of the example vector. Time for another cup of cawfee...Oy Marc __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] selecting values that are unique, instead of selecting unique values
Wow, that is smart, although is seems to be overkill. I guess 'duplicated' is better than O(n^2), is it really? Gabor On Wed, Jun 25, 2008 at 05:43:30PM +0100, Prof Brian Ripley wrote: On Wed, 25 Jun 2008, Marc Schwartz wrote: on 06/25/2008 11:19 AM Daren Tan wrote: unique(c(1:10,1)) gives 1:10 (i.e. unique values), is there any method to get only 2:10 (i.e. values that are unique) ? The easiest might be: Vec [1] 1 2 3 4 5 6 7 8 9 10 1 Vec[table(Vec) == 1] [1] 2 3 4 5 6 7 8 9 10 I don't think that is right: you are relying on recycling indices. Try Vec - c(1,1:10) Vec[table(Vec) == 1] which should be the same. I was about to write tab - table(Vec) names(tab)[tab==1] but that gives a character vector. Here's a different way: Vec[rowSums(outer(Vec, Vec, ==))==1] -- 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@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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] reset row numbers when extracting a subset of a table
Nina, these are not row NUMBERS, but row NAMES. Numbers are actually reset, they always start with 1 and they are continuous. Just try doing T[1,] on your table. If you want to reset row names, you can do this: rownames(T) - seq(length=nrow(T)) or you can even remove them: rownames(T) - NULL Best, Gabor On Tue, Jun 24, 2008 at 11:23:56AM -0400, [EMAIL PROTECTED] wrote: Hi I created a new table by extracting only certain rows of table, but the row numbers in my new table correspond to those from the original table. Is there a way to reset the row numbers in my new table so that they start from one? like below: my table: COL1 COL2 17 v 45 18 b 14 25 x 98 desired: COL1 COL2 1 v 45 2 b 14 3 x 98 Thank you! -Nina __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] 3D histogram
Maybe I'm missing something, but where is the 3D here?
My tip is hist3d in package rgl. But there might be others,
it might worth to search the archive, I remember seeing this
question once.
Gabor
On Fri, Jun 20, 2008 at 08:55:36AM -0400, Richardson, Patrick wrote:
Try
?hist
-and-
?plot.histogram
You should find what you need there.
Cheers,
Patrick
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sumit gupta
Sent: Friday, June 20, 2008 8:46 AM
To: r-help@r-project.org
Subject: [R] 3D histogram
Hii..
Could anyone please tell me how to draw 3D histogram in R
I have a 20X3 matirx. Now I want 2 of the variable on X and Y axis .And
Height of the bar should denote the value of third variable.
Thanx
Sumit
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Re: [R] highest eigenvalues of a matrix
Baptiste, the igraph ARPACK interface is quite experimental, and igraph includes only the ARPACK files (converted to C) that it needs to calculate some graph measures on sparse graphs. Btw. the development version of igraph is a bit better in this respect, I can send you a link to the development version if you think that can help... Btw. what options would you need? (Sorry, it might have been in your previous mails that i haven't read) Best, Gabor On Thu, Jun 19, 2008 at 03:12:50PM +0100, baptiste Auguié wrote: Dear all, Thank you for the suggestions and pointers. It looks like I'll need to do some interface with Fortran/C code. The igraph package seems to provide an interface with ARPACK, albeit not with the options I need, so it could be a good starting point. Best regards, baptiste -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Hyper-elegant code to get a text file, transpose it, and write it
On Thu, Jun 05, 2008 at 10:26:08AM -0200, Alberto Monteiro wrote: Uwe Ligges wrote: You probably want write.table(t(read.table(file.in)), file = file.out, row.names = FALSE, col.names = FALSE) Ok, almost there. I forgot to tell (because I didn't know) that the strings were separated by tabs (I just thought of splitting by _any_ space), and that the output would also be tab-separated. But there's still a minor feature: write.table(t(read.table(file.in, sep =\t)), file = file.out, row.names = FALSE, col.names = FALSE, sep = \t) writes each output enclosed with quotation marks, like: 1/2/20030.56380.62330.45590.8746 I didn't find in the documentation of write.table a way to remove those quotes, because qmethod is either escape or double :-( What about 'quote=FALSE'? Is it not good enough? G. Alberto Monteiro __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] For Social Network Analysis-Graph Analysis - How to convert 2 mode data to 1 mode data?
Solomon, sorry for the delay. In igraph vertices are numbered from 0, so you
need
keep - 0:3
and then the function i've sent seems to work. But i can see that you also have
a solution
now.
Gabor
On Sat, May 17, 2008 at 09:32:27AM -0400, Messing, Solomon O. wrote:
Consider the following two mode-data:
edgelist:
actor event
1 Sam a
2 Sam b
3 Sam c
4 Greg a
5 Tom b
6 Tom c
7 Tom d
8 Mary b
9 Mary d
Two-Mode Adjacency Matrix:
a b c d
Sam 1 1 1 0
Greg 1 0 0 0
Tom 0 1 1 1
Mary 0 1 0 1
To transform two mode to one mode data, we need a function that transforms the
data like so:
Sam is connected to Greg (via event a)
Sam is connected to Tom (via event b and c)
Sam is connected to Mary (via event b)
Tom is connected to Mary (via event b and d)
OK, now I load my data by executing the following:
###
require(igraph)
df - data.frame(actor = c
('Sam','Sam','Sam','Greg','Tom','Tom','Tom','Mary','Mary'),
event =c('a','b','c','a','b','c','d','b','d') )
g = graph.data.frame(df, directed=F) #Coerce data to igraph object 'g'
#Loading Function two.to.one:
##two.to.one() transforms 2-mode data to 1-mode
two.to.one - function(g, keep) {
neis - neighborhood(g, order=2)
neis - lapply(seq(neis), function(x) neis[[x]][ neis[[x]] != x-1]) ## drop
self-loops
neis - lapply(neis, function(x) x[ x %in% keep ]) ## keep
only these
neis - lapply(seq(neis), function(x) t(cbind(x-1, neis[[x]]))) ## create
edge lists
neis[-keep-1] - NULL ## these
are not needed
neis - matrix(unlist(neis), byrow=TRUE, nc=2) ## a
single edge list
neis - neis[ neis[,1] neis[,2], ]## count
an edge once only
mode(neis) - character
g2 - graph.edgelist(neis, dir=FALSE)
V(g2)$id - V(g2)$name ## 'id' is used in Pajek
g2
}
#Actors are the first 4 verticies, set them to be kept:
keep = V(g)[1:4]
#Convert matrix with two.to.one:
g2 = two.to.one(g, keep)
g2
###
This yields the following output:
g2
Vertices: 4
Edges: 2
Directed: FALSE
Edges:
[0] 3 -- 2
[1] 4 -- 1
But, this can't be right. Here there are only two edges where there should be
four, and if I am inturpreting correctly, the output it is reporting that Tom
is connected to Greg (he is not) and Sam is connected to Mary (which is true).
When I load my function, which is designed to transform a two mode edgelist
(e.g. two columns of data) into a one-mode adjacency matrix it seems to work:
###
#load my function
df.to.nxn - function( x, y )
{ # x values will be the N
x N values
M - matrix( nrow = length( unique( x ) ), ncol = length( unique( x ) ),
dimnames = list( unique( x ), unique( x ) ) )
M[ 1:length( unique( x ) ), 1:length( unique( x ) ) ] -
0#initialize the values to 0 - this possibly could be
removed for illustrative purposes
for( i in 1:length( x ) )
{ # iterate through rows of
data
index = which( y == y[i] )
M[ as.character( x[ index ] ), as.character( x[ index ] ) ] =
1
}
M
# return M, an N x N matrix
}
#Convert matrix
g3 = df.to.nxn(df$actor, df$event)
g4 = graph.adjacency(g3, mode = undirected, diag = F)
V(g4)$name = row.names(g3)
g4
###
This yields:
g4
Vertices: 4
Edges: 4
Directed: FALSE
Edges:
[0] Sam -- Greg
[1] Sam -- Tom
[2] Sam -- Mary
[3] Tom -- Mary
Which is what we wanted. I have not figured out how to weight edges yet (the
Sam and Tom edge and the Tom and Mary edge should perhaps be weighted at 2
because 'connected twice' -- connected by two events).
-Solomon
━━━
From: Gabor Csardi [mailto:[EMAIL PROTECTED]
Sent: Wed 5/14/2008 4:01 AM
To: Messing, Solomon O.
Cc: R Help list
Subject: Re: [R] For Social Network Analysis-Graph Analysis - How to convert 2
mode data to 1 mode data?
Please stay on the list.
On Tue, May 13, 2008 at 06:05:15PM -0400, Messing, Solomon O. wrote:
Gabor,
By the way, this seems to work:
I'm a bit lost. So now you're converting your data frame
to a matrix? Why? Or you're doing the two-mode to one-mode
conversion here? It does not seem so to me.
Btw
Re: [R] For Social Network Analysis-Graph Analysis - How to convert 2 mode data to 1 mode data?
Hi Solomon,
On Tue, May 13, 2008 at 05:53:44PM -0400, Messing, Solomon O. wrote:
Hi Gabor,
Thank you for your help, and thanks for making the excellent igraph
package. The function below seems not generate an edge list that works
for my data. I coerced a my data from a data frame using
graph.data.frame.
You asked in your previous post if 2-mode networks are bipartite. I
believe the answer is yes. However, in
Hanneman, Robert A. and Mark Riddle. 2005. Introduction to social
network methods. Riverside, CA: University of California, Riverside (
published in digital form at http://faculty.ucr.edu/~hanneman/ )
I found the following:
Two-mode data are sometimes stored in a second way, called the
bipartite matrix. A bipartite matrix is formed by adding the rows as
additional columns, and columns as additional rows.
Did I need to convert my data frame to a bipartite matrix before
applying the two.to.one function?
No. The function i've sent assumes that your network is bipartite, i.e.
if A and B are connected by an edge, then they're assumed to be
different types of nodes. Just create the graph, calculate the 'keep'
parameter, I assume that you know this from external information, and
then call the function.
G.
Solomon
-Original Message-
From: Gabor Csardi [mailto:[EMAIL PROTECTED]
Sent: Saturday, May 10, 2008 1:09 PM
To: Messing, Solomon O.
Cc: r-help@r-project.org
Subject: Re: [R] For Social Network Analysis-Graph Analysis - How to
convert 2
mode data to 1 mode data?
Solomon, if i understand two-mode networks properly (they're bipartite,
right?),
then this is not hard to do with igraph. Basically, for each vertex
create an
order=2 neighborhood, and then create a graph from the adjacency list,
it is something like this:
two.to.one - function(g, keep) {
neis - neighborhood(g, order=2)
neis - lapply(seq(neis), function(x) neis[[x]][ neis[[x]] != x-1])
## drop
self-loops
neis - lapply(neis, function(x) x[ x %in% keep ])
## keep
only these
neis - lapply(seq(neis), function(x) t(cbind(x-1, neis[[x]])))
## create
edge lists
neis[-keep-1] - NULL
## these
are not needed
neis - matrix(unlist(neis), byrow=TRUE, nc=2)
## a
single edge list
neis - neis[ neis[,1] neis[,2], ]
## count
an edge once only
mode(neis) - character
g2 - graph.edgelist(neis, dir=FALSE)
V(g2)$id - V(g2)$name
## 'id'
is used in Pajek
g2
}
It does not check that the graph is indeed two-mode, and it keeps the
vertices given in the 'keep' argument. 'keep' is made of igraph vertex
ids.
You can use it like this:
g - graph.ring(10)
keep - seq(0,8,by=2) ## we keep the 'even' vertices
g2 - two.to.one(g, keep)
write.graph(two.to.one(g, keep), format=pajek, file=/tmp/a.net)
I haven't tested it much. We'll have a better function in the next
igraph
version.
Gabor
On Fri, May 09, 2008 at 03:37:05PM -0400, Messing, Solomon O. wrote:
Hi,
Does anyone know of a package in R that has a function to convert
network data (e.g. an adjacency matrix or ) from 2-mode to 1-mode? I
am
conducting social network analysis. I know that Pajek has this
function
under Net -- Transform -- 2-mode to 1-mode -- Rows. I have
searched
the documentation under packages 'sna', 'network', 'igraph', and
'dynamicgraph' but I was not able to identify a comparable function.
I would just export my data to Pajek and import it to R, but I'm
going
to have to generate hundreds of these graphs, so it would take quite
a
bit of time to do it this way.
Thanks,
Solomon
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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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] For Social Network Analysis-Graph Analysis - How to convert 2 mode data to 1 mode data?
Please stay on the list.
On Tue, May 13, 2008 at 06:05:15PM -0400, Messing, Solomon O. wrote:
Gabor,
By the way, this seems to work:
I'm a bit lost. So now you're converting your data frame
to a matrix? Why? Or you're doing the two-mode to one-mode
conversion here? It does not seem so to me.
Btw. there is a get.adjacency function in igraph to convert
a graph to an adjacency matrix.
G.
df.to.nxn - function( x, y ){
# x values will be the N x N values
M - matrix( nrow = length( unique( x ) ), ncol = length( unique( x
) ),
dimnames = list( unique( x ), unique( x ) ) )
M[ 1:length( unique( x ) ), 1:length( unique( x ) ) ] - 0
# initialize the values to 0
for( i in 1:length( x ) ) {
# iterate through rows of data
index = which( y == y[i] )
M[ as.character( x[ index ] ), as.character( x[ index ]
) ] = 1
}
M
# return M, an N x N matrix
}
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
__
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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] Remove an object by the reference
a - 1
x - a
rm(list=x)
a
Error: object a not found
See ?rm for details.
Gabor
On Tue, May 13, 2008 at 05:13:41PM +0530, Shubha Vishwanath Karanth wrote:
Hi R,
A simple question, but don't know the answer...
x=a
a=5
I need to remove the object a by using only x. something like
rm(somefunction(x))...Is this possible?
Shubha Karanth | Amba Research
Ph +91 80 3980 8031 | Mob +91 94 4886 4510
Bangalore * Colombo * London * New York * San Jos? * Singapore *
www.ambaresearch.com
This e-mail may contain confidential and/or privileged i...{{dropped:13}}
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--
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Re: [R] Creating Matrix
See ?cbind and ?matrix. Gabor On Sat, May 10, 2008 at 03:21:26PM -0700, Claire_6700 wrote: Hello, I have two data. x-c(1, 2, 1, 3, 2) y-c(3, 1, 2, 3, 5) How do i create matrix from this two. what i want is this x y 1 1 3 2 2 1 3 1 2 4 3 3 5 2 5 thanks Claire -- View this message in context: http://www.nabble.com/Creating-Matrix-tp17168173p17168173.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] For Social Network Analysis-Graph Analysis - How to convert 2 mode data to 1 mode data?
Solomon, if i understand two-mode networks properly (they're bipartite, right?),
then this is not hard to do with igraph. Basically, for each vertex create an
order=2 neighborhood, and then create a graph from the adjacency list,
it is something like this:
two.to.one - function(g, keep) {
neis - neighborhood(g, order=2)
neis - lapply(seq(neis), function(x) neis[[x]][ neis[[x]] != x-1]) ## drop
self-loops
neis - lapply(neis, function(x) x[ x %in% keep ]) ## keep
only these
neis - lapply(seq(neis), function(x) t(cbind(x-1, neis[[x]]))) ## create
edge lists
neis[-keep-1] - NULL ## these
are not needed
neis - matrix(unlist(neis), byrow=TRUE, nc=2) ## a
single edge list
neis - neis[ neis[,1] neis[,2], ]## count
an edge once only
mode(neis) - character
g2 - graph.edgelist(neis, dir=FALSE)
V(g2)$id - V(g2)$name ## 'id'
is used in Pajek
g2
}
It does not check that the graph is indeed two-mode, and it keeps the
vertices given in the 'keep' argument. 'keep' is made of igraph vertex ids.
You can use it like this:
g - graph.ring(10)
keep - seq(0,8,by=2) ## we keep the 'even' vertices
g2 - two.to.one(g, keep)
write.graph(two.to.one(g, keep), format=pajek, file=/tmp/a.net)
I haven't tested it much. We'll have a better function in the next igraph
version.
Gabor
On Fri, May 09, 2008 at 03:37:05PM -0400, Messing, Solomon O. wrote:
Hi,
Does anyone know of a package in R that has a function to convert
network data (e.g. an adjacency matrix or ) from 2-mode to 1-mode? I am
conducting social network analysis. I know that Pajek has this function
under Net -- Transform -- 2-mode to 1-mode -- Rows. I have searched
the documentation under packages 'sna', 'network', 'igraph', and
'dynamicgraph' but I was not able to identify a comparable function.
I would just export my data to Pajek and import it to R, but I'm going
to have to generate hundreds of these graphs, so it would take quite a
bit of time to do it this way.
Thanks,
Solomon
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
I would rather not comment on matlab (where is
your matlab code by the way?), but your function
could be simplified a bit:
grw.permute - function(v) {
cbind( rep(v, each=length(v)), rep(v, length(v)) )
}
system.time(tmp - f( 1:300))
user system elapsed
0.020 0.000 0.019
This is on my quite busy 4 years old laptop
Best,
Gabor
On Wed, Apr 30, 2008 at 04:15:46PM -0400, Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
[...]
--
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
But please consider that this benchmark is five years old, and i believe that R has changed quite a lot since version 1.9. Gabor On Wed, Apr 30, 2008 at 04:21:51PM -0400, Wensui Liu wrote: Hi, ZD, Your comment about speed is too general. Here is a benchmark comparison among several languages and HTH. http://www.sciviews.org/benchmark/index.html [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] efficiency profiling? (was: Why R is 200 times slower than Matlab ?)
On Wed, Apr 30, 2008 at 06:59:38PM -0400, esmail bonakdarian wrote:
This has been an interesting discussion, and brings up two questions
for me:
Is there a good collection of hints/suggestions for R language idoms in terms
of efficiency? For instance I read not to use for-loops, so I used apply only
to
later read that apply is internally implemented as a for so nothing gained
here. Warnings about pitfalls (such as nested loops), hints, suggestions would
be great.
Personally i like {l,t,}apply better, 1) it is more readable,
2) it takes two minutes to change it to par{L,S,}apply and then
it runs in parallel.
The second question - is there some sort of profiling tool available that
would
make it easy to recognize where the script is spending most of its time? Might
be especially useful for newbies like me.
See ?Rprof
G.
[...]
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Re: [R] removing zero rows from matrix/table
See ?apply M2 - M[ apply(M!=0, 1, any), , drop=FALSE] Gabor On Tue, Apr 22, 2008 at 11:52:08AM +0200, Patrick Zimmermann wrote: Dear R-community, I have matrices/tables of different sizes which may contain rows with only zeros. Now I would like to delete these zero lines or create new matrices composed only of the non-zero lines. Columns only containing zeros I want to preserve. Here an example: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 1 0 1 1 0 0 0 [2,] 0 0 0 0 0 0 0 [3,] 1 0 0 0 0 0 0 [4,] 1 0 1 1 1 1 1 [5,] 1 0 1 0 1 0 1 [6,] 0 0 1 1 1 1 1 [7,] 0 0 0 0 0 0 0 Rows 2 and 7 shall be deleted, but column 2 shall be maintained. I believe this should be a simple operation with basic commands, but have no idea how to manage it. Looking forward do any help, Patrick __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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 to insert a vector or matrix into an existing matrix
On Sun, Apr 20, 2008 at 08:16:11PM +, David Winsemius wrote: Gabor Csardi [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Hmm, my understanding is different, m - matrix(sample(10*10), ncol=10) m2 - rbind( m[1:5,], 1:10, m[6:10,] ) m3 - cbind( m[,1:8], 1:10, m[,9:10] ) I read the question the same way and, in response to the part of the question asking for no temporary matrix, offer this refinement on your suggestion: m - rbind( m[1:5,], 1:10, m[6:10,] ) # row insertion or ... # not to be followed by, but rather instead column insertion .. m - cbind( m[,1:8], 1:10, m[,9:10] ) There might be something wrong with my eyes, but where is the refinement here? Your lines are literally the same as mines. There is no temporary matrix here, m2 and m3 are the results, he wanted either between row 5 and 6 _OR_ column 8 and 9. Oh, if you mean that we immediately put back the result into 'm', then 1) it does not really matter, R will create a temporary matrix internally anyway, 2) i assumed that the user can figure this out him/herself. G. -- David Winsemius G. On Sun, Apr 20, 2008 at 10:21:47AM -0300, Henrique Dallazuanna wrote: If I understand: m - matrix(sample(10*10), ncol=10) m[5:6, 8:9] - 1:4 On 4/18/08, Ng Stanley [EMAIL PROTECTED] wrote: Hi, Is there any functions to insert a vector or matrix into an existing ma trix say between row 5 and 6 or column 8 and 9, without creating a temporary matrix ? Thanks Stanley __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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 to insert a vector or matrix into an existing matrix
On Mon, Apr 21, 2008 at 12:50:08PM +, David Winsemius wrote: [...] Am I correct in assuming that after the creation of m by way of a temporary matrix that the temporary matrix would then be available for garbage collection, whereas if both m and m2 were created, there would be more memory occupied by the two objects? Of course, yes. We just had a different interpretation about without a temporary matrix. G. -- David Winsemius __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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 to insert a vector or matrix into an existing matrix
Hmm, my understanding is different, m - matrix(sample(10*10), ncol=10) m2 - rbind( m[1:5,], 1:10, m[6:10,] ) m3 - cbind( m[,1:8], 1:10, m[,9:10] ) G. On Sun, Apr 20, 2008 at 10:21:47AM -0300, Henrique Dallazuanna wrote: If I understand: m - matrix(sample(10*10), ncol=10) m[5:6, 8:9] - 1:4 On 4/18/08, Ng Stanley [EMAIL PROTECTED] wrote: Hi, Is there any functions to insert a vector or matrix into an existing matrix say between row 5 and 6 or column 8 and 9, without creating a temporary matrix ? Thanks Stanley [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Is there any function to skip a loop in a for loop ?
next break Another 'Introduction to R', or even ?for question G. On Fri, Apr 18, 2008 at 04:55:01PM +0800, Ng Stanley wrote: Hi, Is there any function to skip a loop in a for loop ? Thanks Stanley [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] = vs. ==?
I'm sure you'll get a friendlier answer, but... see ?= ?== Introduction to R G. On Tue, Apr 15, 2008 at 05:28:53AM -0700, Linn wrote: Hi Could anyone please explain to me the difference between the = and the ==? I'm quite new to R and I've tried to find out but didn't get any wiser... Thanks -- View this message in context: http://www.nabble.com/%3D-vs.-%3D%3D--tp16700216p16700216.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Associative array and How to store a set of objects ?
On Mon, Apr 14, 2008 at 08:32:55PM +0800, Ng Stanley wrote:
Hi,
Two questions:
A) Assuming OB is an object, how do I store 20 of OB in a vector or list ?
replicate(20, OB, simplify=FALSE)
B) Does R has something similar associative array to Perl ? For example,
%our_friends = ('best', 'Don', 'good', 'Robert', 'worst', 'Joe');
$our_friends{'cool'} = Karen;
our.friends - list(best=Don, good=Robert, worst=Joe)
our.friends[[cool]] - Karen
G.
PS. Concerning the second question, what about reading 'Introduction to R'?
Thanks
Stanley
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Re: [R] Initialize many variables to NUL, check whether an object exist
On Mon, Apr 14, 2008 at 09:47:49PM +0800, Ng Stanley wrote: Hi, Two questions: A) I need to initialize many variables to NULL. So I created variable_names - c(a1, a2). What can I do to variable_names so that variable a1 is NULL and a2 is NULL ? for (n in variable_names) assign(n, NULL) B) How can I check whether an object exist ? help.search(exists) G. Thanks Stanley [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Initialize many variables to NUL, check whether an object exist
What is RG? I suspect it is not a list but a vector and you operation you wrote does not make sense. Convert it to a list if you want to store c(a,b) is RG[[AB]]. G. On Tue, Apr 15, 2008 at 12:06:14AM +0800, Ng Stanley wrote: Hi, How can I force the assignment ? RG[[ABC]] - c(a, b) Error in RG[[ABC]] - c(a, b) : more elements supplied than there are to replace On Mon, Apr 14, 2008 at 9:53 PM, Gabor Csardi [EMAIL PROTECTED] wrote: On Mon, Apr 14, 2008 at 09:47:49PM +0800, Ng Stanley wrote: Hi, Two questions: A) I need to initialize many variables to NULL. So I created variable_names - c(a1, a2). What can I do to variable_names so that variable a1 is NULL and a2 is NULL ? for (n in variable_names) assign(n, NULL) B) How can I check whether an object exist ? help.search(exists) G. Thanks Stanley [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] R beginner - how to apply function to more than one matrix / data.array / ...
Yes, it is exactly 'apply', and its friends. E.g. you can collect the objects into a list and then do sapply(mylist, is.matrix) G. On Wed, Apr 09, 2008 at 11:52:08AM -0400, Mon Mag wrote: I would like to apply a simple function, like is.matrix to more than one data.frame How can I call on more than one data.frame? (are there any wildcards, etc?) I am a true beginner and have tried to look this up in help files, but cannot figure it out. Thank you. [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Draw Circles
May i ask what was the problem with symbols()? G. On Sun, Mar 23, 2008 at 04:10:38AM -0700, ermimi wrote: Thank you very much for the help!!! Felix Andrews wrote: help.search(circle) should point you to grid.circle in the grid package, at least in my R version 2.6.1 (grid package version 2.6.1). On Sun, Mar 23, 2008 at 8:44 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Look at draw.circle and draw.arc in the plotrix package. On Sat, Mar 22, 2008 at 5:40 PM, ermimi [EMAIL PROTECTED] wrote: Hello!!! I would want to draw a circle but I don´t want use the function symbol(..). Do anybody know other function that allow me draw a circle? Thank you very much, Greetings Luismi __ 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. -- Felix Andrews / 安福立 PhD candidate Integrated Catchment Assessment and Management Centre The Fenner School of Environment and Society The Australian National University (Building 48A), ACT 0200 Beijing Bag, Locked Bag 40, Kingston ACT 2604 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 __ 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. -- View this message in context: http://www.nabble.com/Draw-Circles-tp16227640p16234383.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] mapply
On Sun, Mar 23, 2008 at 11:06:05AM -0400, Mark Leeds wrote: In an earlier post, a person wanted to divide each of the rows of rawdata by the row vector sens so he did below but didn't like it and asked if there was a better solution. rawdata - data.frame(rbind(c(1,2,2), c(4,5,6))) sens - c(2,4,6) temp - t(rawdata)/sens temp - t(temp) print(temp) Gabor sent three other solutions and I understood 2 of them but not the one below. I think I understand mapply a little but what I don't understand how it knows to take the rows of rawdata and then I guess recycle sens ? how did the mapply know not to take the columns of rawdata and do something to them ? or maybe mapply does things element by element and it is doing more complex recycling ? I guess I don't really understand mapply that well but I did read the help of it. Thanks so much for any enlightenment from anyone besides Gabor. I bother him enough already and he does more than enough. tempc - data.frame(mapply(/, rawdata, sens)) print(tempc) Mark, there is no recycling here. rawdata[1] is the first column of the data frame, rawdata[2] is the second, etc. and the mapply construct is just calculating rawdata[1] / sens[1] rawdata[2] / sens[2] rawdata[3] / sens[3] data.frame() is only needed because the result of mapply would be a matrix otherwise. (the other (?)) Gabor Mark [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] rounding in calculation
Read R FAQ 7.31 ? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Gabor On Fri, Mar 21, 2008 at 04:17:28PM +0100, John Lande wrote: dear all, I report a problem very simple, that I does non know how to handle. look at the following code: a = rep(16.256, 5) sum(a[1:5]^2) - (sum(a[1:5])^2/5) [1] 2.273737e-13 as you can see i retrieve a non 0 value, when i am expected to. what can I do? sessionInfo() R version 2.6.2 (2008-02-08) i386-pc-mingw32 locale: LC_COLLATE=Italian_Italy.1252;LC_CTYPE=Italian_Italy.1252;LC_MONETARY=Italian_Italy.1252;LC_NUMERIC=C;LC_TIME=Italian_Italy.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] download webpage in R
If you do help.search(download) you find ?download.file G. On Thu, Mar 20, 2008 at 04:51:22PM -0500, gilbert feng wrote: Hi, everyone I want to download a XML webpage and save it as a file in my local machine. Is there any way to do it in R? Thanks a lot Gilbert [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] unsubscribe
What about reading the very last four lines of any email you get from the list? Like this one. G. On Wed, Mar 19, 2008 at 12:09:29PM -0400, ablukacz wrote: Dear All, Can someone please give me instruction on how to unsubscribe from this list. I do not have the original emial that arrived with the subscription. Thank you, Agnes On Wed, 19 Mar 2008, Matthias Ganninger wrote: Has anyone yet implemented or seen an implementation of a Cox (1987) controlled rounding algorithm in R? The controlled rounding procedure is described in: Cox, L.H. (1987): A Constructive Procedure for Unbiased Controlled Rounding. JASA, Vol. 82, No. 398, pp. 520-524. Kind regards Matthias Ganninger __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] R GUI question
On Wed, Mar 19, 2008 at 12:56:13PM -0700, jeffreya wrote: Hi. I'm looking to create a user-friendly program built around some R methods I've written. The program should be as easy to install and use as possible and will be built around a GUI. This program will be cross-platform; that's crucial. I'm familiar with Java and its GUI packages, I've been looking at the JRI package (interfaces R with Java) but I'm a little uneasy about asking my users to go through its installation (necessitates mingw, among other things, in Windows). Though, once installed, it could work very well. I have a little exposure to Tcl/TK. Though I'm not as big of a fan of this as I am of Java, I could suck it up and use it, but I'm not sure that its installation is a whole lot simpler? Should be. It comes with R. I believe that it is still the only cross-platform solution that requires nothing, but the base R installation. What, in your experience, is the easiest way to accomplish something like this? To recapitulate, my criteria are: 1.) Easy installation Tcl/Tk wins here, IMHO. 2.) Ease of use (GUI) Tcl/Tk is not the most modern GUI, so it might be a little clumsy. 3.) Interface with functions written in R That's no problem for any of the R GUI options, i believe. 4.) Cross-platform Tcl/Tk is. Furthermore, Tcl/Tk is quite poorly documented, even if you can usually use its normal (not R) documentation. Sometimes it is hard to find the right way of doing things. Gabor I'm willing to learn a new language (scripting or otherwise) if necessary. Thanks so much. -- View this message in context: http://www.nabble.com/R-GUI-question-tp16149624p16149624.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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 does one do simple string concatenation?
First 'c' and then 'paste' with 'collapse': paste(collapse=, c(c(a, b, c), d)) See ?paste G. On Mon, Mar 17, 2008 at 04:26:17PM +0530, Ajay Shah wrote: How does one convert objects c(a,b,c) and d into abcd? paste(c(a,b,c), d) of course yields [1] a d b d c d -- Ajay Shah http://www.mayin.org/ajayshah [EMAIL PROTECTED] http://ajayshahblog.blogspot.com *(:-? - wizard who doesn't know the answer. __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] empty array
On Sat, Mar 15, 2008 at 04:33:32PM +0100, Christophe Genolini wrote: Hi the list Is it possible to create an empty matrix ? I do not mean an matrix with a single value that is NA (which is not empty) but a real empty one, with length=0. Sure: matrix(nrow=0, ncol=5) [,1] [,2] [,3] [,4] [,5] a - array( dim=c(5,4,0) ) dim(a) [1] 5 4 0 length(a) [1] 0 I do not understand why we have length(numeric()), length(factor()) and length(character()) to zero, and length(array()) to one... Any rason for that ? That i don't know, maybe someone else does. G. Thanks Christophe __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Selecting elements in vector
Use %in%: x [ x %in% y ] G. On Fri, Mar 14, 2008 at 12:37:45PM +0200, Rainer M Krug wrote: Hi Consider the following code x - rep(1:13, 13) y - 1:3 I want to select all elements in x which are equal to 1, 2 or 3. I know that I could use sel - x==y[1] | x==y[2] | x==y[3] x[sel] to obtain the values, but in my analysis, the y-vector is thousands of elements long. Is there any way, that I can do that easily? Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Plant Conservation Unit Department of Botany University of Cape Town Rondebosch 7701 South Africa __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] test individual values in rows
keep - apply( DATA, 1, min ) = 100 DATA - DATA[ keep, ] See ?apply for more. Gabor On Fri, Mar 14, 2008 at 01:26:49PM +, IAIN GALLAGHER wrote: Hi list. I have a numerical dataset 22,000 rows deep and 43 columns wide. I would like to remove those rows which contain only values less than 100 (ie if any value in the row is greater than 100 the row stays in the dataset). I am unsure how to test each individual value across the rows and then identify the rows which meet my criteria. Can anyone help? Thank you. Iain [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] using nrow to identify one row
Try temp[1,,drop=FALSE] See ?[ for the explanation. Gabor On Fri, Mar 14, 2008 at 04:46:10PM -0400, Gregory Gentlemen wrote: Hi fellow R-users, I have run into a problem when trying to identify the number of rows in a matrix. Say we have an arbitrary 5 by 5 matrix called temp: temp - matrix(norm(25), nrow=5) The problem is that nrow(temp[1,]) returns NULL. I would like it to return 1 because in my larger program I am indexing the rows of large matrices according to another variable and I need to test when the resulting matrices have 0, 1 or more rows. Thanks in advance for any assistance. Best regards, Gregory Gentlemen - [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] cumsum list..
cumsum( mapply(function(i,j) sum(a$data[i:j]), x, y) ) Is this what you want? Gabor On Thu, Mar 13, 2008 at 06:02:13AM -0700, yoo wrote: Hi all, i have the following.. a - data.frame(data = seq(1,10)) i have indices: x - c(1, 5, 3, 9) y - c(2, 7, 4, 10) I want the cumsum of a[1:2], a[5:7], a[3:4]... is there an elegant way to do it without any loop? Thanks! -- View this message in context: http://www.nabble.com/cumsum-list..-tp16025202p16025202.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] joining matrices, vectors, scalars in one object
You want to do
thing - list()# empty thing
for ( i in 1:100 ) {
thing[[i]] - ?
}
But where is ? coming from? If you can index it with an integer
then it is exactly coming from the kind of object you want to create.
Chicken-egg problem. No?
G.
On Thu, Mar 13, 2008 at 09:04:11AM -0400, Gonçalo Ferraz wrote:
Hi,
I have:
a - matrix(c(0,1,0,1),nrow=2)
b - matrix(c(1,1,1,0,0,0),nrow=3)
c - 1
d - c(1,0,1)
And I would like to join them in an object 'thing' so that I can
access a, b, c, or d through an index in a for loop.
For example:
thing[4]
would return
[1] 1 0 1
Note however, that I have many of these 'thing' components. So many
that a command like
thing - list(a = matrix(c(0,1,0,1),nrow=2), b = matrix(c
(1,1,1,0,0,0),nrow=3), c = 1, d = c(1,0,1))
would become long and awkward.
Is there a way of declaring an empty 'thing' of a given length and
then assigning its elements from a for loop? I need to allow elements
a, b, c... that can be scalars, vectors or matrices with varying
dimensions.
Thanks!
Gon?alo
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Re: [R] R-Logo in \LaTeX
On Thu, Mar 06, 2008 at 06:54:41PM -0500, Charilaos Skiadas wrote: On Mar 6, 2008, at 1:49 PM, Mag. Ferri Leberl wrote: Dear everybody! Is there a command in \LaTeX to display the R-Logo or has anybody made it up? Thank you in advance. Isn't it just an image? Hence you would include it like one usually includes images. Or do you mean something else? Yes, it is an image, but it would be nice to have it in a vector-based format like EPS or SVG. Anyway, here are some versions (=different sizes): http://developer.r-project.org/Logo/ Gabor Yours, sincerely Mag. Ferri Leberl Haris Skiadas Department of Mathematics and Computer Science Hanover College __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] R-Logo in \LaTeX (Mag. Ferri Leberl)
Jean,
this is nice, but 1) the logo is a bitmap, it is ugly if you
resize it, 2) you don't need a pdf version for pdflatex, it
handles jpg (and maybe also png as well), so you can
just use the logos at the R developer site.
It would be really nice to have a non-bitmap version, though.
If it exists.
Gabor
On Fri, Mar 07, 2008 at 04:08:21PM +0100, Jean lobry wrote:
Dear Mag. Ferri Leberl,
I'm using something like:
--- tex.tex ---
\documentclass{article}
\usepackage{graphicx}
\usepackage{fancyvrb}
\newcommand{\Rlogo}{\protect\includegraphics[height=1.8ex,keepaspectratio]{Rlogo.pdf}}
\newcommand{\myinput}[1] {\begin{scriptsize}
\VerbatimInput[frame=single,label=#1]{#1}
\end{scriptsize}}
\title{The R logo, \Rlogo, in \LaTeX}
\author{J.R. Lobry}
\begin{document}
\maketitle
\section{Introduction to \Rlogo:}
This is about the \Rlogo~sofware suite\footnote{
\Rlogo~is available at...}.
% include source in final document
\myinput{tex.tex}
\end{document}
--
with:
unix$ pdflatex tex.tex
this is what I get:
http://pbil.univ-lyon1.fr/members/lobry/tmp/tex.pdf
The PDF version of the R-Logo I'm using is here:
http://pbil.univ-lyon1.fr/members/lobry/tmp/Rlogo.pdf
HTH,
Jean
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Re: [R] R-Logo in \LaTeX
Jean,
On Fri, Mar 07, 2008 at 06:09:35PM +0100, Jean lobry wrote:
Gabor,
this is nice, but
1) the logo is a bitmap, it is ugly if you resize it
Sure, it's a bitmap, but the naked eye resolution is only
100 $\mu$m so that a vectorized solution is overkilling
in most common situations IMHO.
a vectorized solution can be rendered smoothly at any
desired size. Furthermore, it can be easily edited and the
size of the file is (usually) much smaller than the bitmap
version. No overkill at all, as it is SIMPLER to use the
vector version.
I have to zoom by a factor
1200% to see some pixellization problems on my screen,
but my eyes are admitedly getting older and older, one more
instance of fortune(75) issue I guess :-(
Hmmm, i've downloaded your pdf, and it is clearly ugly at 400%.
I'm talking about the Rlogo.pdf file. E.g. i'm not sure that
it would look good on an A0 poster.
2) you don't need a pdf version for pdflatex, it
handles jpg (and maybe also png as well), so you can
just use the logos at the R developer site.
Not so sure, I had to convert it a long time ago into a PDF
format for a reason I don't remember. I'm sharing my *.rnw
on a CVS with colleages working under Linux, Unix, Mac and
Windows, so the reason could be that there was a problem
in a given platform. The PDF choice is defensive in the sense
that we are Sweaving with \SweaveOpts{pdf = T, eps = F},
so that including PDF is a pre-condition.
Maybe this is different if you use Sweave. pdflatex itself
handles jpg without problems.
It would be really nice to have a non-bitmap version, though.
If it exists.
There was a not so-old thread about this on R-devel:
http://finzi.psych.upenn.edu/R/R-devel/archive/19448.html
Of which the conclusion is that there is no vector version.
Best,
Gabor
Best,
Jean
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Re: [R] vertex labels in igraph from adjacency matrix
On Wed, Mar 05, 2008 at 02:27:21AM -0500, Charilaos Skiadas wrote: [...] Btw, you will likely want to take the betweenness call out, and call it once and store the result, instead of calling it twice (well, assuming the graph is largish). Or even better, use which.max: which.max(betweenness(graph = my.graph, v=V(my.graph), directed = FALSE)) This is almost good, but there is a catch, in igraph vertices are numbered from zero. So if you want an igraph vertex id, then you need to subtract one from this, i.e.: maxb - which.max(betweennness(my.graph, directed=FALSE))-1 You can double check it: betweenness(my.graph, maxb, directed=FALSE) Gabor PS. there is also an igraph mailing list, see the igraph homepage at igraph.sf.net Haris Skiadas Department of Mathematics and Computer Science Hanover College [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] vertex labels in igraph from adjacency matrix
Mark, graph.adjacency always preserves the order of the vertices, so the vertex at row/column 1 will be vertex #0 in the igraph graph, etc. I'll document this in a minute. This means that you can always do g - graph.adjacency(A) V(g)$name - colnames(A) But i completely agree that this should be done by default, i'll do that in the near future. Btw, weighted shortest path calculation (= where the edges have weights or capacities) is only implemented in the development version of igraph. Just in case you're looking for that. Best, Gabor On Wed, Mar 05, 2008 at 01:39:41AM -0500, Mark W Kimpel wrote: I am getting some unexpected results from some functions of igraph and it is possible that I am misinterpreting the vertex numbers. Eg., the max betweenness measure seems to be from a vertex that is not connected to a single other vertex. Below if my code snippet: require(igraph) my.graph - graph.adjacency(adjmatrix = my.adj.matrix, mode=c(undirected)) most.between.vert - colnames(my.adj.matrix)[which(betweenness(graph = my.graph, v=V(my.graph), directed = FALSE) == max(betweenness(graph = my.graph, v=V(my.graph), directed = FALSE))) + 1] sum(my.adj.matrix[most.between.vertext,]) 0 Is there a way to automatically set the vertex name attributes from the row and colnames of the inputted adjacency matrix to graph.adjacency? This would seem like an intuitive feature, but I can't find it documented. In the absence of this feature, how can I make sure that I am setting the vertex name attributes correctly? -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpelatgmaildotcom ** -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] R-Terminal
options(width=120) See ?options G. On Tue, Mar 04, 2008 at 12:04:54PM +0100, Martin Kaffanke wrote: Hi there! I use an gnome-terminal for using R. When I resize the termial to the maximum size, R uses only the left side of the window. Can I tell R to use the whole window somehow? Thanks, Martin -- Ihr Partner für Webdesign, Webapplikationen und Webspace. http://www.roomandspace.com/ Martin Kaffanke +43 650 4514224 [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] R-Terminal
On Tue, Mar 04, 2008 at 01:18:43PM +0100, Martin Kaffanke wrote: Am Dienstag, den 04.03.2008, 12:34 +0100 schrieb Peter Dalgaard: Martin Kaffanke wrote: Hi there! I use an gnome-terminal for using R. When I resize the termial to the maximum size, R uses only the left side of the window. Can I tell R to use the whole window somehow? This seems to do it: options(width=Sys.getenv(COLUMNS)) Thats great! Is there something like an rc file where I can generally save this? See ?Startup G. lg, Martin -- Ihr Partner für Webdesign, Webapplikationen und Webspace. http://www.roomandspace.com/ Martin Kaffanke +43 650 4514224 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] request if a variable is defined
Bingo!
See ?exists
G.
On Tue, Mar 04, 2008 at 04:38:31PM +0100, Paul Hammer wrote:
hi members,
give it a function for requesting if a object, matrix, vector, variable
or whatever already exists?
e.g. if (*exists*(a) {print(yes) } else { print(no) }
thanks
paul
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Re: [R] help for the first poster- a simple question
R FAQ 7.31. G. On Mon, Mar 03, 2008 at 12:52:43PM -0500, Xuejun Qin wrote: Hi, there, I cannot get accurate value for calculation. for example: ld-sqrt(1*0.05*0.95*0.05*0.95) 0.05*0.95-ld=-6.938894e-18 0.05*0.95-ld==0 is False. I met this problem in my program, how can I handle it. Thanks. xj. __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] [OT] normal (as in Guassian)
I'm not a statistician, but do i remember well that among all distributions with a given mean and variance, the normal distribution has the highest entropy? This is good enough for me to call it normal Gabor On Sun, Mar 02, 2008 at 10:10:21AM -0600, roger koenker wrote: A nice survey of this territory is: http://books.google.com/books?id=TN3_d7ibo30Cpg=PA85lpg=PA85dq=stigler+normal+oxymoronsource=webots=OwGhmnDk3Osig=J7ou_L8-_Mu4L14c3KJAhefrD4Ihl=en I particularly like the phrase: [normal] is in this respect a rare one-word oxymoron. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 On Mar 2, 2008, at 7:33 AM, (Ted Harding) wrote: Hi Folks, Apologies to anyone who'd prefer not to see this query on this list; but I'm asking because it is probably the forum where I'm most likely to get a good answer! I'm interested in the provenance of the name normal distribution (for what I'd really prefer to call the Gaussian distribution). According to Wikipedia, The name normal distribution was coined independently by Charles S. Peirce, Francis Galton and Wilhelm Lexis around 1875. So be it, if that was the case -- but I would like to know why they chose the name normal: what did they intend to convey? As background: I'm reflecting a bit on the usage in statistics of everyday language as techincal terms, as in significantly different. This, for instance, is likely to be misunderstood by the general publidc when they encounter statements in the media. Likewise, normally distributed would probably be interpreted as distributed in the way one would normally expect or, perhaps, there was nothing unusual about the distribution. Comments welcome! With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 02-Mar-08 Time: 13:04:17 -- 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-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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Make plots with GNUplot. Have anyone tried that?
On Sat, Mar 01, 2008 at 12:54:56AM +0100, Louise Hoffman wrote: If you still want to then read ?write.table, that can export your data into a spreadsheet-like ascii format which can be used from GNUplot easily. Very interesting. So if I e.g. write: ts.sim - arima.sim(list(order = c(1,1,0), ar = 0.7), n = 200) ts.plot(ts.sim) How do I know the names of the rows to put in the data.frame() command? ??? Which data.frame() command? (Btw. now you're trying to plot from R?) Btw, comparing the graphics capabilities of GNUplot and R, it is something like a three-wheel bicycle and a spaceship. Guess which is which. =) I know that I will most likely spend a lot of time on just making the plots, but I atleast (for now =) ) think it could be fun to try. For you maybe, not for me. I'm lost, and I apologize, but I'll quit the discussion here. G. ps. i take back half of what i've said about GNUplot. It's a nice tool. Still, IMHO, (in most cases) it makes no sense to export data from R and plot it with GNUplot. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Column sums from a data frame (without the headers)
colSums gives you exactly what you want, but the vector is *named*. You can use it like a not-named numeric vector, without much trouble. If you still want to get rid of the names see ?unname G. On Fri, Feb 29, 2008 at 12:02:46PM -0500, Jason Horn wrote: Does anyone know how to get a vector of column sum from a data frame? You can use colSums(), but this gives you a object of type numeric with the column labels in the first row, and the sums in the second row. I just want a vector of the sums, and I can't figure out a way to index the numeric object. Thanks! __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Make plots with GNUplot. Have anyone tried that?
I believe that R can export all formats that GNUplot can produce, so i don't really see why you want to use GNUplot if you don't know it. If you still want to then read ?write.table, that can export your data into a spreadsheet-like ascii format which can be used from GNUplot easily. Btw, comparing the graphics capabilities of GNUplot and R, it is something like a three-wheel bicycle and a spaceship. Guess which is which. Gabor On Fri, Feb 29, 2008 at 11:12:50PM +0100, Louise Hoffman wrote: [snip] Seriously. Be specific if you have a problem. (read the posting guide). R can also plot. If you don't like R's plots (which I could not understand) you can export data and import them to gnuplot. So what? Okay, my post was not very good. The reason (I think) I need GNUplot, is that I would like to include the plots from R in a Latex report, where I would like to have all the text and equations in the plots with the same font as used in Latex. So when I read about opening and closing dev for making a pdf I figured that the plots that R produces are like the once Matlab makes; shows what they ought to, nothing more, nothing less. So I was wondering if anyone know of an GNUplot friendly format and the code that would produce that text file. I am new to both R and GNUplot, so I am pure ears if someone knows how to make such plots in R. __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] cohesive blocks.. again
Simone, they are currently ignored. Just like edge direction. Gabor On Thu, Feb 28, 2008 at 03:17:24PM +0100, Simone Gabbriellini wrote: hello, I have a last question on cohesive blocks: if there are multiple links between some nodes in the graph, this is taken into account by cohesive blocks? or the multiple links are simply ignored? thank you, Simone __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Newbie: Where is lmFit function?
It's in the 'limma' Bioconductor package. Next time you can try help.search(lmFit) RSiteSearch(lmFit) Gabor On Sun, Feb 24, 2008 at 01:02:41PM -0800, Keizer_71 wrote: Hi Everyone, I am trying to use lmFit function; however, i cannot find it function anywhere. I have been trying to find the function in Bioconductor and elsewhere. I re-install bioconductor source, update package and update R as well. no luck Is there a command in R where i can just type, and it will download it for me? -- View this message in context: http://www.nabble.com/Newbie%3A-Where-is-lmFit-function--tp15669332p15669332.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Hiding a function
It depends what you mean by 'hiding', you can start the function names with a dot and then they are not listed by ls(), so this is kind of hiding. .a - function() TRUE ls() character(0) .a function() TRUE Personally i would not do this though. G. On Sat, Feb 23, 2008 at 11:58:57AM +0100, Christophe Genolini wrote: [...] If I understand, it is possible only in a package, not in a programme (unless the other ways), is that it ? Ok, thanks. [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Viable Approach to Parallel R?
Similar experience, with snow MPI (LAM). Actually, plug and play. G. On Sat, Feb 23, 2008 at 10:57:22AM -0700, Eric W Anderson wrote: Hi Dan, I've had pretty good luck using Snow with with Rpvm. It's definitely not what you'd call plug and play, but it does work. I'm using it on a single computer to just take advantage of multiple processors, and it does a pretty good job of keeping them busy. The main gotchas I've found with Snow are in data dissemination: You may have to clusterCall(cl, require(foo)) or clusterExport(cl,bar) more things than you would have expected. -Eric -- Eric W. Anderson University of Colorado [EMAIL PROTECTED] Dept. of Computer Science phone: +1-720-984-8864 Systems Research Lab - ECCR 1B54 PGP key fingerprints: personal: 1BD4 CFCE 8B59 8D6E EA3E EBD5 4DC9 3E61 656C 462B academic: D3C5 D6FF EDED 9F1F C36D 53A3 74B7 53A6 3C74 5F12 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] [R-pkgs] igraph package, version 0.5
igraph is a package for graphs and networks. It has a C core and uses a simple and fast graph representation allowing millions of vertices and edges. NEW FEATURES: - We use the ARPACK library for graph related eigenvalue problems, like Page Rank calculation, Kleinberg's hub and authority scores, eigenvector centrality, etc. There is also a generic interface if someone wants to use ARPACK for a different (not necessarily graph-related) problem. - We support the BLISS graph isomorphism algorithm, and the implementation of the VF2 algorithm can calculate subgraph isomorphisms now. - We include a collection of famous graphs, these can be created by referring to their name. - We have a new 'graph.formula' function, for creating small graphs using symbolic names, by giving simple R formulae. - Many functions support weighted graphs now: Page Rank, modularity calculation, the fast greedy community finding algorithm, etc. - We have a new graph layout algorithm called 'graphopt'. - A bunch of new functions are added: biconnected components and articulation points, dyad and triad census, functions for vertex similarity, functions for estimating closeness, betweenness and edge betweenness, etc. - igraph can write files in the DOT format now. - Some graphics improvements, e.g. it is possible to draw graphs on top of each other, etc. - Many bugs were fixed, the most important one is probably that now memory is always properly deallocated when CTRL+C (ESC) is used to interrupt a computation. PACKAGE DESCRIPTION: igraph is originally a C library for graphs, but has interfaces to high level languages like R, Python and Ruby. The R package contains BOTH the C library and its R interface. igraph supports: - graph generators, creating both regular structures like trees, lattices, etc. and various random graphs. - a rich set of functions calculating structural properties of graphs, like vertex centrality (degree, betweenness, closeness, page rank, eigenvector centrality, Burt's constraints, etc.), shortest paths, dyad and triad census, network motifs, girth, K-core decomposition, etc. - attributes can be associated with the vertices/edges of the graph, or the graph itself. The attributes can be arbitrary R objects. - graph visualization using regular R devices, interactive visualization using Tcl/Tk, 3D visualization using RGL. - graph layout generators, the standard Kamada-Kawai and Fruchterman-Reingold algorithms are included, plus many more. - Functions for graph and subgraph isomorphism, the BLISS and the VF2 algorithms are included. - Functions for maximal network flows, minimal cuts, vertex and edge connectivity. - igraph can read and write many popular file formats used for storing graph data: GraphML, Pajek, GML and others. - igraph contains implementations of many community structure detection algorithms proposed recently. See more at the igraph homepage: http://cneurocvs.rmki.kfki.hu/igraph/index.html -- Csardi Gabor [EMAIL PROTECTED] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] change NA values
?RSiteSeach is useful. It gives you this: http://tolstoy.newcastle.edu.au/R/e2/help/07/09/25536.html and then keep clicking on Next in thread. Gabor On Tue, Feb 19, 2008 at 12:33:21PM +0100, Alfonso Pérez Rodríguez wrote: Hello, I'm sure that this question is too simple, but, I'm begining with R and I'm not able to change the NA values in a matrix by 0 values, and it's necessary for my work, how can I do It? Thank you. Alfonso P?rez Rodr?guez Instituto de Investigaciones Marinas C/ Eduardo Cabello n? 6 C.P. 36208 Vigo (Espa?a) Tlf.- 986231930 Extensi?n 241 e-mail: [EMAIL PROTECTED] [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Building a package and Depends search
I think you need -l: R CMD check -l your_library your_package Gabor On Tue, Feb 19, 2008 at 02:00:38PM -, john seers (IFR) wrote: [...] I think this is because I install my packages in mylibrary and use R_LIBS=C:/PROGRA~1/R/mylibrary in my Renviron.site file. If I move the package to the R main library it fixes the problem. But rather defeats the intention behind having a separate mylibrary. Can anybody tell me how to solve this? That is keep my installed packages in mylibrary but get the package check/build to work? I guess Depends: has a search path but I cannot find it or how to alter it. Can anybody point me to some documentation? [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] library(convert)
.. (Counting to ten.) The package is called 'convert'. It seems that this package is not on CRAN, however. I think you should ask the person whose code you're running. Gabor On Mon, Feb 18, 2008 at 10:17:41AM +0100, Schmitt, Corinna wrote: Hallo, I am running R-2.6. on Windows. I have a code which uses library(convert). Can anyone tell me which package I need to install to run this code. Everytime I receive the error message library (convert) not found. Thanks, Corinna __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] library(convert)
Update: it is a Bioconductor package, so you need to do: source(http://bioconductor.org/biocLite.R;) biocLite(convert) Gabor On Mon, Feb 18, 2008 at 10:17:41AM +0100, Schmitt, Corinna wrote: Hallo, I am running R-2.6. on Windows. I have a code which uses library(convert). Can anyone tell me which package I need to install to run this code. Everytime I receive the error message library (convert) not found. Thanks, Corinna __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] function similar to str_replace() in php.
I don't know php very well, but perhaps you need ?sub Gabor On Fri, Feb 15, 2008 at 03:54:19PM +0100, Dong-hyun Oh wrote: Dear expeRt, I would like to know whether a function similar to str_replace() in php exists in R. Looking forward to hearing from you. Best, = Center of Excellence for Science and Innovation Studies, Royal Institute of Technology Drottning Kristinas väg 30 100 44 Stockholm, Sweden e-mail: [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED] Office: +46 8 790 67 93 Fax: +46 8 790 95 17 Cell phone: +46 73 563 45 22 = __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Removing columns that are all NA from a matrix
data - data[ , !apply(is.na(data), 2, all)] (or something like that) G. On Thu, Feb 14, 2008 at 12:59:46PM +, Martin Waller wrote: Hi, I guess this might be a FAQ or something, and there's probably a nice simple way to do it, but I can't think of it: Given a matrix, I want to remove columns that are _entirely_ filled with NAs (partial NAs are fine). How please? Thanks, Martin __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] finding source for a function
RSiteSearch is your friend. E.g.: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/63365.html and then click on 'Next in thread a couple of times Gabor On Thu, Feb 14, 2008 at 03:23:30PM -0600, Edna Bell wrote: Dear R Gurus: How do you get source for functions which say UseMethod when you type in their names, please? I've tried getAnywhere and getMethods...I thought that might produce them. Thanks in advance. Sincerely, Edna __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] matching last argument in function
It should be possible i think. You just supply all the arguments via
'...' and then cut off the last one. I don't see why this wouldn't work,
but maybe i'm missing something.
Gabor
On Tue, Feb 12, 2008 at 12:58:25PM -0600, Erik Iverson wrote:
Alistair -
I don't believe this is possible. The only way formal arguments (like
expr) can be matched after a '...' is with *exact* name matching. Why
do you want to avoid explicitly naming the expr argument?
If you always want the expr argument last, you might be able to just use
... as the sole argument to your function, and strip off the last
element inside the function as 'expr', and use all but the last element
as your list of options. This requires that expr always be given last
though. Probably best just to explicitly name the expr argument.
Erik Iverson
Alistair Gee wrote:
I often want to temporarily modify the options() options, e.g.
a - seq(1001, 1001 + 10) # some wide object
with.options - function(..., expr) {
options0 - options(...)
tryCatch(expr, finally=options(options0))
}
Then I can use:
with.options(width=160, expr = print(a))
But I'd like to avoid explicitly naming the expr argument, as in:
with.options(width=160, print(a))
How can I do this with R's argument matching? (I prefer the expr as
the last argument since it could be a long code block. Also, I'd like
with.options to take multiple options.)
TIA
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Re: [R] sort a data frame according to roman characters
I assume that data$Roman is character. data[order(as.numeric(as.roman(data$Roman))),] should do it. Maybe data[order(as.roman(data$Roman)), ] is enough too. Gabor On Tue, Feb 12, 2008 at 10:36:50AM +, Luis Ridao Cruz wrote: R-help, I have a data frame with one column containing roman numbers The data are not sorted as : III III IV VVI VII VIII IX XXI XII XIII XIV XV Using data[order(data$Roman),] does not do the job. How can this be done? Thanks in advance. __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Conditional rows
Because you need test = 0.2 | test 0.3 See ?| Gabor On Mon, Feb 11, 2008 at 09:12:57PM +0800, Stanley Ng wrote: That works beautfully. Why using test=0.2 || test 0.3 gives error ? -Original Message- From: Gabor Csardi [mailto:[EMAIL PROTECTED] Sent: Monday, February 11, 2008 18:27 To: Ng Stanley Cc: r-help Subject: Re: [R] Conditional rows which(apply(test=0.2, 1, all)) See ?which, ?all, and in particular ?apply. Gabor On Mon, Feb 11, 2008 at 06:22:09PM +0800, Ng Stanley wrote: Hi, Given a simple example, test - matrix(c(0.1, 0.2, 0.1, 0.2, 0.1, 0.1, 0.3, 0.1, 0.1), 3, 3) How to generate row indexes for which their corresponding row values are less than or equal to 0.2 ? For this example, row 2 and 3 are the correct ones. Thanks [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Conditional rows
which(apply(test=0.2, 1, all)) See ?which, ?all, and in particular ?apply. Gabor On Mon, Feb 11, 2008 at 06:22:09PM +0800, Ng Stanley wrote: Hi, Given a simple example, test - matrix(c(0.1, 0.2, 0.1, 0.2, 0.1, 0.1, 0.3, 0.1, 0.1), 3, 3) How to generate row indexes for which their corresponding row values are less than or equal to 0.2 ? For this example, row 2 and 3 are the correct ones. Thanks [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] grep etc.
sub(-, --, v, fixed=TRUE)
See ?sub.
Gabor
On Sun, Feb 10, 2008 at 02:14:48PM -0500, Michael Kubovy wrote:
Dear R-helpers,
How do I transform
v - c('insd-otsd', 'sppr-unsp')
into
c('insd--otsd', 'sppr--unsp')
?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
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Re: [R] Loading Data to R
It is a good idea to start with RSiteSearch(Excel) G. On Fri, Feb 08, 2008 at 03:49:29PM -0500, Christine Lynn wrote: This is the most basic question ever...I haven't used R in a couple years since college so I forget and haven't been able to find what I'm looking for in any of the manuals. I just need to figure out how to load a dataset into the program from excel! Thanks! CL [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] revision control software for managing R-code?
This is a religion question in some sense. Personally, i used CVS and a bit Subversion too, but arch and bazaar look much better. Especially if you're not always in online connection with the central repository, or you don't really want a central repository at all. Gabor On Thu, Feb 07, 2008 at 08:18:49AM -0800, Thomas Pujol wrote: Does anyone use revision control software to manage their R-code? Any suggestions? Ideally, I'm looking for a, effective yet easy to implement/maintain package. http://en.wikipedia.org/wiki/Revision_control http://en.wikipedia.org/wiki/Comparison_of_revision_control_software - [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] extracting rows from dataframe that match a vector
You almost got it right. THe solution is df[df$ind %in% subgr,] See ?%in% G. On Tue, Feb 05, 2008 at 04:47:02PM +0100, Karin Lagesen wrote: Hi! I have a large dataframe that I want to extract a subset from. This subset has a certain column value that matches elements in a vector I have defined. So, my question is how do I get the rows that match one of the elements in the vector. Example: a = c(1:5) b = letters[1:10] df = data.frame(ind = a, letrs = b) df ind letrs 11 a 22 b 33 c 44 d 55 e 61 f 72 g 83 h 94 i 10 5 j # Now I want to extract all of the rows where ind == 2, 4 or 5. # This would be rows 2, 4, 5, 7, 9 and 10 subgr = c(2,4,6) My most natural inclination would be to do df[df$ind == subgr,] However, this does not work: df[df$ind == subgr,] ind letrs 7 2 g Warning message: In df$ind == subgr : longer object length is not a multiple of shorter object length So, which part of this is it that I have misunderstood? Thanks for your help btw! Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] http://folk.uio.no/karinlag __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] counts of each column that are not NA, and/or greater than column means
On Mon, Feb 04, 2008 at 03:21:10PM +0800, Ng Stanley wrote: Hi, Given a test matrix, test - matrix(c(1,2,3,NA,2,3,NA,NA,2), 3,3) A) How to compute the counts of each column (excluding the NA) i.e., 3, 2, 1 apply(test, 2, function(x) sum(!is.na(x))) B) How to compute the counts of each column (excluding the NA) that are greater than the column means ? i.e., 1, 1, 0 apply(test, 2, function(x) sum(x mean(x, na.rm=TRUE), na.rm=TRUE)) In general, you need ?apply to calculate something for each row/column of a matrix. Gabor I could write a for loop, but hope to use better alternative. [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Saving a big table or matrix
?save ?load Gabor ps. although i'm not sure what an Rdata-project means, so maybe you need something else On Fri, Feb 01, 2008 at 08:24:32AM +0200, Atte Tenkanen wrote: Dear R-users, How do you save a big table or matrix as an independent object and attach it to your Rdata-project when needed? Atte Tenkanen University of Turku, Finland Department of Musicology +023335278 __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] re placing values in a matrix
Actually, you don't need apply. If there are no NA's then it is very easy: m[] - y[ col(m) ] If you want to keep the NA's then it is a bit more tricky: m[] - 0*m + y[ col(m) ] G. On Thu, Jan 31, 2008 at 07:03:51PM -0800, dxc13 wrote: useR's, Consider: y - c(20, 25, 30) m - matrix(c(0.0,1,NA,0.5,1.25,0.75, 0.5, NA, NA),byrow=TRUE,nrow=3,ncol=3) m [,1] [,2] [,3] [1,] 0.0 1.00 NA [2,] 0.5 1.25 0.75 [3,] 0.5 NA NA For each numeric value, I want to replace them with their corresponding y-value. The result should look like (here, each row represents a variable rather than the columns): [,1] [,2] [,3] [1,] 20 25 NA [2,] 20 25 30 [3,] 20 NA NA Does anyone know how I can do this using apply()? Or is there an easier way? Thanks in advance. Derek -- View this message in context: http://www.nabble.com/replacing-values-in-a-matrix-tp15219764p15219764.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] re placing values in a matrix
Derek, the 0*m part zeros out everything in the matrix, expect for the NA's, 0*NA=NA by definition. If we add this to the y[ col(m) ] matrix, then NA+anything=NA, but 0+anything=anything. G. ps. please answer to the list (as well) On Fri, Feb 01, 2008 at 08:52:50AM -0500, Derek Cyr wrote: Thank you, that works very nicely. I am a little curious as to why you need to do 0*m and add that to y[col(m)] in the second expression. It works perfectly, but I am just not sure how, lol. Thanks D [...] Actually, you don't need apply. If there are no NA's then it is very easy: m[] - y[ col(m) ] If you want to keep the NA's then it is a bit more tricky: m[] - 0*m + y[ col(m) ] G. On Thu, Jan 31, 2008 at 07:03:51PM -0800, dxc13 wrote: useR's, Consider: y - c(20, 25, 30) m - matrix(c(0.0,1,NA,0.5,1.25,0.75, 0.5, NA, NA),byrow=TRUE,nrow=3,ncol=3) m [,1] [,2] [,3] [1,] 0.0 1.00 NA [2,] 0.5 1.25 0.75 [3,] 0.5 NA NA For each numeric value, I want to replace them with their corresponding y-value. The result should look like (here, each row represents a variable rather than the columns): [,1] [,2] [,3] [1,] 20 25 NA [2,] 20 25 30 [3,] 20 NA NA Does anyone know how I can do this using apply()? Or is there an easier way? Thanks in advance. Derek -- View this message in context: http://www.nabble.com/replacing-values-in-a-matrix-tp15219764p15219764.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] permutates and/or samples a matrix
What exactly is the question? Selecting/permuting rows? M[sample(length=nrow(M), count), ] Selecting/permuting columns? M[ , sample(length=ncol(M), count) ] Permuting elements? structure(sample(M), dim=dim(M)) Selecting elements? sample(M, count) Gabor On Thu, Jan 31, 2008 at 09:10:11PM +0800, Ng Stanley wrote: Hi, sample(x) only permutates and/or samples from a vector, which I can't use for a matrix. Please help. Thanks Stanley [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] permutates and/or samples a matrix
I mean On Thu, Jan 31, 2008 at 02:32:20PM +0100, Gabor Csardi wrote: What exactly is the question? Selecting/permuting rows? M[sample(length=nrow(M), count), ] M[sample(seq(length=nrow(M)), count), ] Selecting/permuting columns? M[ , sample(length=ncol(M), count) ] M[ , sample(seq(length=ncol(M)), count) ] G. Permuting elements? structure(sample(M), dim=dim(M)) Selecting elements? sample(M, count) Gabor On Thu, Jan 31, 2008 at 09:10:11PM +0800, Ng Stanley wrote: Hi, sample(x) only permutates and/or samples from a vector, which I can't use for a matrix. Please help. Thanks Stanley [[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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] [OT] emacs / xemacs for unix without compile
You don't need root access to compile a program (in mose cases). Just a compiler and enough space. Gabor On Thu, Jan 31, 2008 at 03:45:51PM -0500, Wensui Liu wrote: I think the unix is SunOS. the secret is I don't have root priviledge. ^_^. So is there a possibility? Thanks. On Jan 31, 2008 3:35 PM, Wittner, Ben, Ph.D. [EMAIL PROTECTED] wrote: I don't know what unix you're using, but if it's fedora 8, the command yum install emacs did the trick for me. You probably need to have root (a.k.a. superuser) privileges to do that. If you like to use ESS with emacs to edit R scripts, yum install emacs-ess My guess is this would work for any Red Hat linux, but I don't know. -Ben [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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.
