[R] Generating valid R code using R
Hi,
I'm trying to generate valid R code using R. Parts of the task is to
read a sequence of characters from file and escape them such that they
can be put in quotation marks to form a valid R code string. Example:
Let the input file be (four rows containing ASCII 0-255 characters):
abcdeftabghijk\nlmno
second row\t\a\\
fourth and so on...
EOF
Now, find escapeString() such that the following piece of code
generates a second file called 'file2.txt' which is identical to
'file1.txt':
inStr - readChar(file1.txt, nchars=999)
esStr - escapeString(inStr)
rCode - sprintf('cat(file=file2.txt, %s)', esStr)
cat(file=foo.R, rCode)
source(foo.R)
For instance, quotation marks has to be escaped in order for 'rCode'
to be valid, same with newlines etc. What's the best way to do this?
Currently I use an ad hoc sequence of gsub() substitutions to do this,
but is there a better way to create the 'rCode' string?
Thanks
Henrik
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[R] CFD Plots in R and Other Things
Dear All, I am getting some data from fluid dynamics simulations (air mixing in a pipe, 2D axial symmetry, geometry described by a radial coordinate r and an axial coordinate z) which I'd like to plot and analyze with R. Think about slicing the cylinder along its axial direction to get a set of cross sections which are orthogonal to the z axis. For each section, I have a set of velocity readings, i.e. the data I would like to plot are in the form: v_11 v_12 v_13 . v_1n v_21 v_22 v_23 . v_2n .. v_m1 v_m2 v_m3 . v_mn where v_ij is the velocity reading on the i-th position along z and the j-th position along r. Tipically, these sets of data are plotted in 2D with r and z as axis and the velocity field represented by using colours explained by a legenda. Can R do anything like this? Second (and much simpler question): I have a list of data which I can plot easily, but I would like to have the time during the day to label the x axis (starting from 19:00 for forty hours). How can I do that? Many thanks Lorenzo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] dataframe computation behaviour
Greetings: I have a simple issue; the (probably cumbersome) code follows: #___ datmod=(dat) datmod$em96gbr=ifelse(datmod$em96gbr 0, log(datmod$em96gbr), datmod$em96gbr) datmod$em96spbr=ifelse(datmod$em96spbr 0, log(datmod$em96spbr), datmod$em96spbr) datmod[,4:8]=log(datmod[,4:8]) datmod[,10:13]=log(datmod[,10:13]) datmod[,15:28]=log(datmod[,15:28]) datmod[,4:23]=datmod[,4:23]-datmod$p97 datmod[,25:26]=datmod[,25:26]-datmod$p97 #__ It works fine with the exception of datmod[,26] where the operation - datmod$p97 is not performed. I thought this might be interesting enough to share with the list :-) mihai [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] break axis using plotrix
Dear all, I am trying to plot some data with differing range in y-values with type=b, adding error bars and break the y-axis into two parts, one lower part from 12 to 20, and one upper part from 34 to 40. I have tried to follow the basic ideas from the script provided here by Jim Lemon: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/56487.html My attempt looks like this: ### # x-values x - 1:4 # small y-values with corresponding standard errors meansarr - c(14.9, 18.2, 14.5, 18.3) searr - c(0.47, 1.27, 1.22, 0.49) # large values meanslay - c(36.4, 39.0, 35.3, 38.6) selay - c(0.51, 0.34, 0.57, 0.40) library(plotrix) # plot small values plot(x, meansarr, ylim=c(12, 30), axes=F, type=b, xlab=, ylab=Day) arrows(x, meansarr-searr, x, meansarr+searr, code = 3, angle = 90, length = 0.03) box() # x-axis axis(1, tck=0.01, las=1, at=1:4, labels=c(1998, 1999, 2002, 2003), mgp=c(3, 0.5, 0)) # y-axis axis(2,at=c(12, 14, 16, 18, 20, 24, 26, 28, 30),labels=c(12,14,16,18,20, 34,36,38,40)) # break axis axis.break(2, 22, style=zigzag) # add large values to same plot par(new=TRUE) plot(x, meanslay, ylim=c(30, 40), type=b, xlab=, ylab=Day, axes=F) arrows(x, meanslay-selay, x, meanslay+selay, code = 3, angle = 90, length = 0.03) As you can see, I have problems adding the larger y-values - they end up in the wrong place in the graph. I suppose Jim's warning 'just be careful that the ylim= and labels= arguments match up' is relevant here, but I don't manage to fix it... Can anyone help me to plot the large y-values on the right placeaccording to the y-axis labeling? I am using R 2.3.1 and WinXp. Thanks a lot in advance! Henrik -- Henrik Pärn Department of Biology NTNU 7491 Trondheim Norway +47 735 96282 (office) +47 909 89 255 (mobile) +47 735 96100 (fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] CFD Plots in R and Other Things
Look at ?image, ?contour and in the lattice package ?contourplot, ?levelplot, ?wireframe, ?cloud and in scatterplot3d package scatterplot3d. Try example() on each one, e.g. example(image), to get an idea if its what you want. Also google for the R Graph Gallery and look through the charts there. For the second question you can customize the x axis labels by not drawing them in plot and drawing them yourself using axis: tt - 19 + 0:40 plot(tt, tt, xaxt = n) axis(1, tt, paste(tt, 00, sep = :), cex.axis = 0.5) abline(v = tt, col = grey) # optional On 7/16/06, Lorenzo Isella [EMAIL PROTECTED] wrote: Dear All, I am getting some data from fluid dynamics simulations (air mixing in a pipe, 2D axial symmetry, geometry described by a radial coordinate r and an axial coordinate z) which I'd like to plot and analyze with R. Think about slicing the cylinder along its axial direction to get a set of cross sections which are orthogonal to the z axis. For each section, I have a set of velocity readings, i.e. the data I would like to plot are in the form: v_11 v_12 v_13 . v_1n v_21 v_22 v_23 . v_2n .. v_m1 v_m2 v_m3 . v_mn where v_ij is the velocity reading on the i-th position along z and the j-th position along r. Tipically, these sets of data are plotted in 2D with r and z as axis and the velocity field represented by using colours explained by a legenda. Can R do anything like this? Second (and much simpler question): I have a list of data which I can plot easily, but I would like to have the time during the day to label the x axis (starting from 19:00 for forty hours). How can I do that? Many thanks Lorenzo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] put R on a web server
Has anyone put R on a web server any time, recently, please? It depends on what you mean by recently. R 2.3.1 and 1054 packages at http://kryton.cc.unt.edu/cgi-bin/R/Rprog R 2.3.1 and 1046 packages at http://www.unt.edu/rss/Rinterface.htm R 2.3.1 and 499 packages at http://pbil.univ-lyon1.fr/Rweb/ R 2.3.0 and 85 packages at http://rweb.stat.umn.edu/Rweb/ R 2.2.1 and 359 packages at http://actin.ucd.ie/Rweb/ R 2.2.0 and 25 packages at http://www.digitalhermit.com/math/Rweb.html R 2.2.0 and 25 packages at http://r.nakama.ne.jp/Rweb-jp/ R 2.1.0 and 25 packages at http://dssm.unipa.it/R-php/ R 2.1.0 and 25 packages at http://homeworld.rutgers.edu/Rweb/Rweb.general.html R 2.0.1 and 526 packages at http://www.ms.uky.edu/~statweb/ R 1.9.1 and 35 packages at http://origin.scic.ulst.ac.uk/Rweb/ R 1.9.0 and 106 packages at http://hermes.sdu.dk/cgi-bin/go/ R 1.9.0 and 48 packages at http://claree.univ-lille1.fr/Rweb/ R 1.8.1 and 30 packages at http://www.er.uqam.ca/nobel/r17165/Rweb/Rweb.html R 1.8.1 and 30 packages at http://bayes.math.montana.edu/Rweb/ R 1.7.0 and 49 packages at http://bic.uams.edu/Rweb/ R 1.6.1 and 28 packages at http://user.cs.tu-berlin.de/~ulfi/cgi-bin/r-online/r-online.cgi R 1.5.0 and 32 packages at http://www.nku.edu/~longa/Rweb/ R 1.3.0 and 11 packages at http://genome1.beatson.gla.ac.uk/Rweb/ -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 12 87 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem with installation of older R-version
to whom it may concern, i hope that someone might help i do need to install an older base-package R 1.6.2 (January, 2003) on my windows-xp computer. when i try to install the rw1062-1.exe file the following error-message pops up. The setup files are corrupted. Please obtain a new copy of the program. i downloaded the exe-file from various mirror sites, however, unfortunately the same message comes up again and again. has anyone already experiences with this problem? i would very much appreciate your help. with best regards and sunny greets, christoph clases [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ts and stl functions - still a problem
The 'ts' function retains the 'dim' attribute of 'tkr'. When 'stl' finds this 'dim' attribute, it thinks 'tstkr' is a multivariate time series. This causes it to stop with the error, only univariate series allowed. Consider the following modification of an example from the 'stl' help file: not.1 - stl(nottem, per) Nottem - ts(array(nottem, dim=c(240, 1))) Not.1 - stl(Nottem) Error in stl(Nottem) : only univariate series are allowed Solution: tstkr - ts(as.numeric(tkr), deltat=1/12) After converting tkr and tstkr from a matrix to a vector like this, please try 'stl(tstkr)'. If it doesn't work, please submit another post. Hope this helps. Spencer Graves p.s. Your example was not quite self-contained, because I didn't know for sure the format, class, and attributes of your 'tkr' object. The absence of these details made it harder for me (and, I believe, anyone else) to reply. You might get better replies quicker with greater attention to such details. Daniel sutcliffe wrote: Hi I am still having problems with using the stl function, when I read the csv file into R into a file called tkr and use dim(tkr) the result is 132 x 1 which is fine. When coerce it into a trime series using ts either: tstkr - ts(t(tkr), deltat=1/12) or tstkr - ts(c(tkr), deltat=1/12) and use the stl function I get the following error: Error in stl(tstkr) : only univariate series are allowed id just use the tkr file I get the same error..does anyibe have an idea what to do next, here is my data...it's not sensitive so if anyone wants to try then you are very welcome! Rate184.0222180.517222.5792173.5066192.7852 198.0429182.2696189.28178.7644206.8059236.6 155.9807231.7314249.2868222.9537198.3761201.8872 208.9094242.2646221.1982228.2203245.7757244.0202 194.865239.3664234.0862251.6867235.8463197.1253 237.6063267.5271228.8061241.1264249.9267256.9669 188.325258.8788239.5069214.8518234.2237211.3296 234.2237237.7458156.7361239.5069225.4183257.1177 170.8248230.1611265.3001296.9253193.265233.675 240.7028249.4876205.5637237.1889237.1889289.8975 245.9736283.1755316.3875372.3234234.2316263.9476 314.6395286.6715272.6875323.3795295.4115300.6555 174.7997227.184277.4767317.364234.121286.1478279.2109 280.9452235.8552319.0982 296.5532303.4901173.4229302.6072312.8651389.7991 223.9635254.7371329.9615288.93317.994312.8651381.2509 333.3808194.8996285.5743304.0526335.9698307.4123 346.0489288.934335.9698243.5781384.6854359.4876 357.8078221.74336.3712344.6562389.3952286.6611 338.0282407.6222356.2552241.9221347.9702400.9942 381.1102304.8882383.9077418.5089476.1774331.1822 378.9647375.6694339.4206364.1357420.1565446.5193 410.2705296.5811 Cheers and thanks to everyone who offered suggestions before. Daniel SAULEAU Erik-André [EMAIL PROTECTED] wrote: Perhaps ts(t(tkr))? -Message d'origine- De : Daniel sutcliffe [mailto:[EMAIL PROTECTED] Envoyé : mercredi 12 juillet 2006 15:53 À : r-help@stat.math.ethz.ch Objet : [R] ts and stl functions Hi, I have imported a csv file into R which contains one column (the rate er 100,000 population of a disease, by month over 11 years) I coerced into a time series using the following function, tstkr-ts(tkr,deltat=1/12) This seems to work fine, and when I check for the class of the object using class(tstkr) I get ts as the response. When I try to use the stl function in stats I get the error message: Error in stl(tstkr)only univariate series are allowed I then tried this: tstkr - ts(c(tkr), deltat=1/12) however this made no difference...I still get an error - does anybody know what is wrong? Regards, Daniel - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ** Afin d'eviter toute propagation de virus informatique, et en complement des dispositifs en place, ce message (et ses pieces jointes s'il y en a) a ete automatiquement analyse par un antivirus de messagerie.
[R] Trailing on r-help messages
I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
Hi, Gabor: Sounds great. May I suggest a minor modification something like the following; R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE include in your post minimal, self-contained, reproducible code as suggested in posting guide, www.R-project.org/posting-guide.html. Posts more consistent with this standard tend to get quicker, more useful replies. I'd also suggest adding something like this to the Special Interest Group posts as well. I also reply to questions on R-sig-finance, and I find myself going to R-help to copy the PLEASE do read the posting guide comment for r-sig-finance. Thanks for suggesting this. Spencer Graves Gabor Grothendieck wrote: I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
Personally, I doubt anyone actually reads the bottom of the emails, and generally it is too late anyway, as they have already sent the message. Much like the opening text in R, details in footer tend to trigger legalese neurons and are largely ignored. I think it would be more useful to radically redesign the signup page so that pertinent information is highlighted and the page made easily scannable. As it is, the eye tends to skip to the action part and fill out name and email address without reading the rest of the page. Hadley On 7/16/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
Or just reminding the rules to the list now and then (as it was done today). I, for one, am happy I got reminded, and appologise for my previous posting. Trying to provide reproductible code forced me to find my own mistake! mihai hadley wickham [EMAIL PROTECTED] wrote: Personally, I doubt anyone actually reads the bottom of the emails, and generally it is too late anyway, as they have already sent the message. Much like the opening text in R, details in footer tend to trigger legalese neurons and are largely ignored. I think it would be more useful to radically redesign the signup page so that pertinent information is highlighted and the page made easily scannable. As it is, the eye tends to skip to the action part and fill out name and email address without reading the rest of the page. Hadley On 7/16/06, Gabor Grothendieck wrote: I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Mihai Nica ITT Tech instructor Jackson State University 170 East Griffith St. G5 Jackson, MS 39201 601-914-0361 - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
On 7/16/06, hadley wickham [EMAIL PROTECTED] wrote: Personally, I doubt anyone actually reads the bottom of the emails, and generally it is too late anyway, as they have already sent the message. Much like the opening text in R, details in footer tend to trigger legalese neurons and are largely ignored. They might read it when reading other people's messages since it would be at the bottom of every single one. I think it would be more useful to radically redesign the signup page so that pertinent information is highlighted and the page made easily scannable. As it is, the eye tends to skip to the action part and fill out name and email address without reading the rest of the page. Good idea. Of course these are not mutually exclusive. Hadley On 7/16/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
I was trying to keep it to 4 lines making it more likely read than a longer description. On 7/16/06, Spencer Graves [EMAIL PROTECTED] wrote: Hi, Gabor: Sounds great. May I suggest a minor modification something like the following; R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE include in your post minimal, self-contained, reproducible code as suggested in posting guide, www.R-project.org/posting-guide.html. Posts more consistent with this standard tend to get quicker, more useful replies. I'd also suggest adding something like this to the Special Interest Group posts as well. I also reply to questions on R-sig-finance, and I find myself going to R-help to copy the PLEASE do read the posting guide comment for r-sig-finance. Thanks for suggesting this. Spencer Graves Gabor Grothendieck wrote: I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] rbind, array
Hello, I'm looping something like rbind for array. More precisely: if I define y-array(c(1:27),dim=c(3,3,3)) and I take 3 matrix: y[,,1], y[,,2], y[,,3] and write rbind(y[,,1], y[,,2], y[,,3]) I get what I want. But what if I have hundreds such matrix. How to do it. Robert [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rbind, array
download library(abind). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rbind, array
Try this: y - array(1:27, c(3, 3, 3)) # test array rbind(y[,,1], y[,,2], y[,,3]) apply(y, 2, I) # verify that last two lines give same result identical(apply(y, 2, I), rbind(y[,,1], y[,,2], y[,,3])) # TRUE On 7/16/06, Robert Mcfadden [EMAIL PROTECTED] wrote: Hello, I'm looping something like rbind for array. More precisely: if I define y-array(c(1:27),dim=c(3,3,3)) and I take 3 matrix: y[,,1], y[,,2], y[,,3] and write rbind(y[,,1], y[,,2], y[,,3]) I get what I want. But what if I have hundreds such matrix. How to do it. Robert [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
Hi, Gabor: Yes. Saying more often communicates less. Spencer Graves Gabor Grothendieck wrote: I was trying to keep it to 4 lines making it more likely read than a longer description. On 7/16/06, Spencer Graves [EMAIL PROTECTED] wrote: Hi, Gabor: Sounds great. May I suggest a minor modification something like the following; R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE include in your post minimal, self-contained, reproducible code as suggested in posting guide, www.R-project.org/posting-guide.html. Posts more consistent with this standard tend to get quicker, more useful replies. I'd also suggest adding something like this to the Special Interest Group posts as well. I also reply to questions on R-sig-finance, and I find myself going to R-help to copy the PLEASE do read the posting guide comment for r-sig-finance. Thanks for suggesting this. Spencer Graves Gabor Grothendieck wrote: I would like to propose that we change the trailer on r-help messages which is currently: R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html to add the following 4th line: and provide minimal, self-contained, reproducible code. The posting guide is so long that I suspect few people really read it so at least this way the most important part of the message about posting would be readily visible without further user action. Of course minimal refers to cutting the code down to remove anything not related to the question at hand while self-contained and reproducible refer to being able to copy the code from the post and paste it into an R session to reproduce the problem. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
They might read it when reading other people's messages since it would be at the bottom of every single one. Perhaps, it might also trigger same-blindness: seeing the same thing again and again makes it less and less likely to really percieve it. Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Trailing on r-help messages
On 7/16/06, hadley wickham [EMAIL PROTECTED] wrote: They might read it when reading other people's messages since it would be at the bottom of every single one. Perhaps, it might also trigger same-blindness: seeing the same thing again and again makes it less and less likely to really percieve it. Hadley I think that is likely true but it would at least mean that they had seen it repeatedly and there would really be no excuse for not following it (unlike the current situation where one needs to take action to follow the posting guide link and then read a lengthy page). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] install.packages for local zip files
O/S: Linux R version : 2.2.1 The R server doesn't have http internet access. And the sys admins will not install the R libraries that I requested. So I have downloaded the packages that I want to intall and have moved them into my home directory on the server. These are a series of *.tar.gz files. I want to install the R libraries in my home directory, but I can't get it to work. According to the install.packages documentation : install.packages(pkgs, lib, repos = getOption(repos), contriburl = contrib.url(repos, type), method, available = NULL, destdir = NULL, installWithVers = FALSE, dependencies = FALSE, type = getOption(pkgType)) repos: character vector, the base URL(s) of the repositories to use, i.e., Can be 'NULL' to install from local '.tar.gz' files. contriburl: URL(s) of the contrib section of the repositories. .. Can be 'NULL' to install from local '.tar.gz' files. pkgs: character vector of the short names of packages/bundles whose current versions should be downloaded from the repositories. If 'repos = NULL', a character vector of file paths of '.tar.gz' files. These can be source archives or binary package/bundle archive files (as created by 'R CMD build --binary'). .. lib: character vector giving the library directories where to install the packages. Recycled as needed. So I have issued a command like this: install.packages(pkgs=~/Rdownloads/hgug4112a_1.12.0.tar.gz, lib = ~/Rlib, repos=NULL, contriburl=NULL) Warning in download.packages(pkgs, destdir = tmpd, available = available, : no package '~/Rdownloads/hgug4112a_1.12.0.tar.gz' at the repositories As far as I can tell, I've given it the full path to the zip file, the directory in which to install the library and I've set the repository path to 'NULL' to indicate that I'm installing from an already downloaded zip file. But I'm missing something. Any ideas? Thanks, Dan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Manipulation involving arrays
Hi,
I have the following piece of code that is part of a larger function. This
piece is the most time consuming part of the function, and I would like to make
this a bit more efficient. Could anyone suggest a way to do this faster?
In particular, I would like to replace the nested for loop with a faster
construct. I tried things like kronecker and outer combined with apply,
but couldn't get it to work.
Here is a sample code:
##
n - 120
sigerr - 5
covmat - diag(c(8,6,3.5))
mu - c(105,12,10)
mcsamp - 1
Tbar - array(0, dim=c(3,3,n))
# theta is a mcsamp x 3 matrix
theta - mvrnorm(mcsamp, mu = mu, Sigma = covmat)
wt - matrix(runif(n*mcsamp),n,mcsamp)
wti - apply(wt,1,sum)
tarray - array(apply(theta,1,function(x)outer(x,x)),dim=c(3,3,mcsamp))
for (i in 1:n) {
for (k in 1:mcsamp) {
Tbar[,,i] - Tbar[,,i] + wt[i,k] * tarray[,,k]
}
Tbar[,,i] - Tbar[,,i] / wti[i]
}
###
Thanks very much,
Ravi.
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[R] Hmisc xYplot
Dear R community, I am having trouble with a particular plot that I am trying to produce using Hmisc's xYplot function. I've been using primarily lattice and Hmisc packages for my plotting needs for the past few years, with great success. However, what I want to do now with xYplot is plot more than one data trend in the same panel, much as I would use xyplot from package lattice in conjunction with superpose, with type=b. My problem is I can't get the error bars to plot when I use xYplot this way. I've attached my data set for reference. Here are my inputs: p1sum-read.csv(file=p1sum.csv, header=T) library(Hmisc) xYplot(Cbind(DRP, SE) + Cbind(Fe, FeSE) ~ Day | Group + Port, p1sum, type='b') The plotted result is two lines per panel, one labeled Cbind(DRP, SE) and the other labeled Cbind(Fe, FeSE). However, the error bars are not plotted at all (I want the error bars to be DRP +/- SE, and Fe +/- FeSE). Any advice on this is greatly appreciated. Thank you, Erin Erin Berryman ***PLEASE- NOTE NEW EMAIL [EMAIL PROTECTED]__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Manipulation involving arrays
The double loop is the same as:
Tbar[] - matrix(tarray, 9) %*% t(wt) / rep(wti, each = 9)
On 7/16/06, RAVI VARADHAN [EMAIL PROTECTED] wrote:
Hi,
I have the following piece of code that is part of a larger function. This
piece is the most time consuming part of the function, and I would like to
make this a bit more efficient. Could anyone suggest a way to do this faster?
In particular, I would like to replace the nested for loop with a faster
construct. I tried things like kronecker and outer combined with apply,
but couldn't get it to work.
Here is a sample code:
##
n - 120
sigerr - 5
covmat - diag(c(8,6,3.5))
mu - c(105,12,10)
mcsamp - 1
Tbar - array(0, dim=c(3,3,n))
# theta is a mcsamp x 3 matrix
theta - mvrnorm(mcsamp, mu = mu, Sigma = covmat)
wt - matrix(runif(n*mcsamp),n,mcsamp)
wti - apply(wt,1,sum)
tarray - array(apply(theta,1,function(x)outer(x,x)),dim=c(3,3,mcsamp))
for (i in 1:n) {
for (k in 1:mcsamp) {
Tbar[,,i] - Tbar[,,i] + wt[i,k] * tarray[,,k]
}
Tbar[,,i] - Tbar[,,i] / wti[i]
}
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Re: [R] sem question
MODEL UNDERIDENTIFIED? I've looked at 'sem' for many years but never found that application that seemed to me to require that machinery. However, I know that it's very easy to get models that are underidentified. One of the simplest cases is the classical errors in x regression problem: Observe: X = xi + e.x, e.x~N(0, s2.x) Y = eta + e.y, e.y~N(0, s2.y) Model: eta = a+b*xi If I'm not mistaken, I believe that it is theoretically impossible to estimate a, b, s2.x, and s2.y without additional information, like for example the ratio between s2.x and s2.y. LAGS IN BOTH TIME AND SPACE? I've copied John Fox, the 'sem' package author and maintainer, on this reply. He might educate us both on how to include lags in both time and space into an 'sem' model. Failing that, are you familiar with Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer). This book and the companion 'nlme' packages include facilities for linear and nonlinear models in both space and time. The follow-on 'lme4' package and accompanying 'lmer' function will also handle non-normal response distributions. I'm a firm believer in trying the simple things first, and I think the mixed-effects models are simpler than 'sem', though Prof. Fox may wish to disabuse me of my ignorance on that point. MORE HELP? If you would like more from this listserve than just this, please submit another post. When you do, however, please include a simple, self contained example to illustrate briefly what you want, what you tried, and the deficiencies with what you tried, as suggested in the posting guide! www.R-project.org/posting-guide.html. Hope this helps. Spencer Graves Denis Fomchenko wrote: Dear all, I am trying to estimate simultaneous equation model concerning growth in russian regions. I run the analysis by means of FIML in R sem package. I am not familiar with SEM yet, but I've just got several suitable estimated specifications. Nevertheless, sometimes R gives the following warning message: Warning message: Negative parameter variances. Model is probably underidentified. in: sem.default(ram = ram, S = S, N = N, param.names = pars, var.names = vars, I check for rank condition - all three equations in the system are turned out to be exact... Does anybody know what it means? and how to handle with that problem? P.S. Do you know any examples of models estimated in SEM by means of FIML, incorporating spatial lag on endogenous variable? Thanks, in advance Denis Fomchenko research fellow Department for Economic Development Problems Institute for the Economy in Transition 5, Gazetny lane, Moscow 125993, Russia e-mail: [EMAIL PROTECTED] http://www.iet.ru [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MLE and QR classes
I don't understand your question. First, I'm not familiar with the 'wls' package; I found no such package by that name via www.r-project.org - CRAN - (select a local mirror) - Packages. The 'qr' function in the 'quandreg' package looks straightforward to me. Have you worked through the examples in the 'qr' help page? The look to me like they follow the standard syntax of 'lm'. If you don't understand the 'lm' syntax, I encourage you to spend some quality time with appropriate sections of Venables and Ripley (2003) Modern Applied Statistics with S, 4th ed. (Springer). If you'd like more help from this listserve, please submit another question. However, please include a simple, self-contained example of something you tried to help illustrate your question (as suggested in the posting guide! www.R-project.org/posting-guide.html). Hope this helps. Spencer Graves [EMAIL PROTECTED] wrote: Hi, I load my data set and separate it as folowing: presu - read.table(C:/_Ricardo/Paty/qtdata_f.txt, header=TRUE, sep=\t, na.strings=NA, dec=., strip.white=TRUE) dep-presu[,3]; exo-presu[,4:92]; Now, I want to use it using the wls and quantreg packages. How I change the data classes for mle and rq objects? Thanks a lot, Ricardo Gonçalves Silva, M. Sc. Apoio aos Processos de Modelagem Matemática Econometria Inadimplência Serasa S.A. (11) - 6847-8889 [EMAIL PROTECTED] ** As informações contidas nesta mensagem e no(s) arquivo(s) anexo(s) são endereçadas exclusivamente à(s) pessoa(s) e/ou instituição(ões) acima indicada(s), podendo conter dados confidenciais, os quais não podem, sob qualquer forma ou pretexto, ser utilizados, divulgados, alterados, impressos ou copiados, total ou parcialmente, por pessoas não autorizadas. Caso não seja o destinatário, favor providenciar sua exclusão e notificar o remetente imediatamente. O uso impróprio será tratado conforme as normas da empresa e da legislação em vigor. Esta mensagem expressa o posicionamento pessoal do subscritor e não reflete necessariamente a opinião da Serasa. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] sem question
Dear Spencer and Denis, I've been traveling for a while and away from r-help, so I didn't see Denis's question until now. I'm not familiar with applications of SEMs that have lags in time and space. As to the identification status of Denis's model, it's hard to know about that in the abstract. What's the model? Regards, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: Spencer Graves [mailto:[EMAIL PROTECTED] Sent: Sunday, July 16, 2006 7:29 PM To: Denis Fomchenko Cc: r-help@stat.math.ethz.ch; John Fox Subject: Re: [R] sem question MODEL UNDERIDENTIFIED? I've looked at 'sem' for many years but never found that application that seemed to me to require that machinery. However, I know that it's very easy to get models that are underidentified. One of the simplest cases is the classical errors in x regression problem: Observe: X = xi + e.x, e.x~N(0, s2.x) Y = eta + e.y, e.y~N(0, s2.y) Model: eta = a+b*xi If I'm not mistaken, I believe that it is theoretically impossible to estimate a, b, s2.x, and s2.y without additional information, like for example the ratio between s2.x and s2.y. LAGS IN BOTH TIME AND SPACE? I've copied John Fox, the 'sem' package author and maintainer, on this reply. He might educate us both on how to include lags in both time and space into an 'sem' model. Failing that, are you familiar with Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer). This book and the companion 'nlme' packages include facilities for linear and nonlinear models in both space and time. The follow-on 'lme4' package and accompanying 'lmer' function will also handle non-normal response distributions. I'm a firm believer in trying the simple things first, and I think the mixed-effects models are simpler than 'sem', though Prof. Fox may wish to disabuse me of my ignorance on that point. MORE HELP? If you would like more from this listserve than just this, please submit another post. When you do, however, please include a simple, self contained example to illustrate briefly what you want, what you tried, and the deficiencies with what you tried, as suggested in the posting guide! www.R-project.org/posting-guide.html. Hope this helps. Spencer Graves Denis Fomchenko wrote: Dear all, I am trying to estimate simultaneous equation model concerning growth in russian regions. I run the analysis by means of FIML in R sem package. I am not familiar with SEM yet, but I've just got several suitable estimated specifications. Nevertheless, sometimes R gives the following warning message: Warning message: Negative parameter variances. Model is probably underidentified. in: sem.default(ram = ram, S = S, N = N, param.names = pars, var.names = vars, I check for rank condition - all three equations in the system are turned out to be exact... Does anybody know what it means? and how to handle with that problem? P.S. Do you know any examples of models estimated in SEM by means of FIML, incorporating spatial lag on endogenous variable? Thanks, in advance Denis Fomchenko research fellow Department for Economic Development Problems Institute for the Economy in Transition 5, Gazetny lane, Moscow 125993, Russia e-mail: [EMAIL PROTECTED] http://www.iet.ru [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Getting rid of for loops
Hello R-users!
I have a style question. I know that for loops are somewhat frowned upon in
R, and I was trying to figure out a nice way to do something without using
loops, but figured that i could get it done quickly using them. I am now
looking to see what kind of tricks I can use to make this code a bit more
aesthetically appealing to other R users (and learn something about R along
the way...).
Here's the problem. I have a data.frame with 4 columns of dependent
variables and then ~35 columns of predictor variables (factors) [for those
interested, it is a qtl problem, where the predictors are genotypes at DNA
markers and the dependent variable is a biological trait]. I want to go
through all pairwise combinations of predictor variables and perform an
anova with two predictors and their interaction on a given dependent
variable. I then want to store the p.value of the interaction term, along
with the predictor variable information. So I want to end up with a
dataframe at the end with the two variable names and the interaction p value
in each row, for all pairwise combinations of predictors. I used the
following code:
# qtl is the original data.frame, and my dependent var in this case is
# qtl$CPP.
marker1 - NULL
marker2 - NULL
p.interaction - NULL
for ( i in 5:40) { # cols 5 - 41 are the predictor factors
for (j in (i+1):41) {
marker1 - rbind(marker1,names(qtl)[i])
marker2 - rbind(marker2,names(qtl)[j])
tmp2 - summary(aov(tmp$CPP ~ tmp[,i] * tmp[,j]))[[1]]
p.interaction - rbind(p.interaction, tmp2$Pr(F)[3])
}
}
I have two questions:
(1) is there a nicer way to do this without having to invoke for loops?
(2) my other dependent variables are categorical in nature. I need
basically the same information - I am looking for information regarding the
interaction of predictors on a categorical variable. Any ideas on what
tests to use? (I am new to analysis of all-categorical data).
Thanks in advance!
Kevin
--
--
Kevin Emerson
Center for Ecology and Evolutionary Biology
1210 University of Oregon
Eugene, OR 97403
USA
[EMAIL PROTECTED]
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[R] a question about data combination
Hello sir: Here's the data: a b c d 1 2 3 4 I wanna know how to get: ab ac ad bc bd cd 12 13 14 23 24 34 Thanks a lot! My best -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ols/gls or systemfit (OLS, WLS, SUR) give identical results
I can't say without more information. If the system were saturated (i.e., has as many equations as unknowns), you should get the same answer from all the different methods. However, I just tried a saturated model in 'systemfit', with the following results: DF2 - data.frame(y=1:2, x=3:4) lm(y~x, DF2) Call: lm(formula = y ~ x, data = DF2) Coefficients: (Intercept)x -21 library(systemfit) systemfit(OLS, list(eqn=y~x), data=DF2) Error in solve.default(sigma, tol = solvetol) : system is computationally singular: reciprocal condition number = 0 If you'd like more help from this listserve, please supply a simple, self-contained example to illustrate your question (as suggested in the posting guide! www.R-project.org/posting-guide.html). Hope this helps. Spencer Graves Mihai Nica wrote: I might be sorry for asking this question :-) I have two equations and I tried to estimate them individually with lm and gls, and then in a system (using systemfit) with OLS, WLS and SUR. Quite surprisingly (for myself at least) the results are identical to the last digit. Could someone (please!) give a hint as to what am I doing wrong? Thanks, mihai - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Correlation Mapping
On the cover of Zivot and Wang's Modeling Financial Time Series with S Plus, there is a correlation plot that seems to indicate the strength of correlation with color-coded squares, so that more highly correlated stocks appear darker red. If anybody out there is familiar with the book or understands what I am talking about, I am curious as to whether or not there is a similar function in R and how I can call it up. Thank you. jdr __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] planned comparisons for ANOVA
Hi, we need some help to define planned comparisons. I've based my understanding of the problem on reading Tabachnick and Fidell (2006), ie: http://www.ablongman.com/catalog/academic/product/0,1144,0205459382,00.html I don't understand how to specify planned comparisons in R. I've not found explanations for this in MASS or elsewhere. There is only discussion of the contrast option to ANOVA in general terms, there are no examples for the analysis of planned comparisons. I have an ANOVA design, described as a factorial design, with both between-subjects and within-subjects factors. There are 2 subject groups. Although there are matched individuals across groups (matched for extraneous demographic variables), we consider them a between-subject factor with 2 categorical levels (controls, patients). The dependent variable is a multivariate recording from 124 electrodes on the scalp, to measure electric potential from the scalp surface. These recordings are summarised into regional activity for the left and right hemisphere. So hemisphere is a within-subjects factor that has 2 levels (left and right). The last factor is an experimental manipulation, a visual task contains three types of events. This is a within-subjects factor with three levels (S1, S2, S3). Our planned comparisons are: 1. test the group mean difference for S1 vs S2 (in the absence of S3) 2. test the group mean difference for S2 vs S3 (in the absence of S1) This is the current form of the ANOVA specification for R: aov( Y ~ (Task*Hemisphere*Group) + Error( Subject/(Task*Hemisphere) ) How can we add planned comparisons to this specification? Can we add just one planned comparison matrix, with rows for 1 2 above, or do we need to run the model twice, once for each planned comparison? Alternatively, is there a function to compute the planned comparisons after running the full ANOVA model? Thanks, Darren PS, I was trained well on using SPSS, but I am trying to make a switch to R. You help with this would be really appreciated. We need to get our results revised and published soon. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Handshake exception in Rserve
Hello,
We are facing some problem while calling a Rserve API from our Java client.
The details are as below:
1) We have installed Rserve on linux machine Nagarajan(Port: 6311) and
related modules.
2) We have started the Rserve in daemon mode perfectly by executing the
comman R CMD Rserve on the linux machine.
But when the Java client executes the statement: Rconnection c = new
Rconnection (Nagrajan, 6311), we are getting an exception: handshake
exception: expected 32 bytes received -1 byte.
It would be really great if you could help us out to resolve the issue or
provide a probable root cause of the problem.
Thank you,
Jaydeep
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Re: [R] planned comparisons for ANOVA
Darren Weber wrote: [snip] Our planned comparisons are: 1. test the group mean difference for S1 vs S2 (in the absence of S3) 2. test the group mean difference for S2 vs S3 (in the absence of S1) This is the current form of the ANOVA specification for R: aov( Y ~ (Task*Hemisphere*Group) + Error( Subject/(Task*Hemisphere) ) How can we add planned comparisons to this specification? Can we add just one planned comparison matrix, with rows for 1 2 above, or do we need to run the model twice, once for each planned comparison? There are a couple of ways to do this in R. Perhaps the easiest is to use make.contrasts in the gmodels package. cmat - rbind(S1 v S2 = c(1, -1, 0), S2 v S3 = c(0, 1, -1)) library(gmodels) fit - aov( Y ~ Task*Hemisphere*Group + Error( Subject/(Task*Hemisphere), contrasts=list(Task=make.contrasts(cmat ))) summary(fit) Alternatively, is there a function to compute the planned comparisons after running the full ANOVA model? see ?fit.contrast in gmodels for this. HTH, Simon. Thanks, Darren PS, I was trained well on using SPSS, but I am trying to make a switch to R. You help with this would be really appreciated. We need to get our results revised and published soon. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat. Centre for Resource and Environmental Studies The Australian National University Canberra ACT 0200 Australia T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au F: +61 2 6125 0757 CRICOS Provider # 00120C __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Correlation Mapping
I have not seen that book cover but I assume the question is how to plot the cells of a correlation matrix in different colors. Try heatmap or the gplot package function heatmap.2 . For example, we create a correlation matrix, K, from the first 4 columns of the iris data set and create a heatmap using the bluered color scheme: # heatmap.2 library(gplots) K - cor(iris[,1:4]) heatmap.2(K, col = bluered(16), cexRow = .7, cexCol = .7, symm = TRUE, dend = row, trace = none, main = Iris Data) balloonplot, also in the gplots package, and image in graphics (i.e. core R) might be other functions to look at. On 7/16/06, justin rapp [EMAIL PROTECTED] wrote: On the cover of Zivot and Wang's Modeling Financial Time Series with S Plus, there is a correlation plot that seems to indicate the strength of correlation with color-coded squares, so that more highly correlated stocks appear darker red. If anybody out there is familiar with the book or understands what I am talking about, I am curious as to whether or not there is a similar function in R and how I can call it up. Thank you. jdr __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
