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...o understand the situation. I believe R-2.15.2 introduced a tighter requirement for precision, thus triggering longer-lasting calculations in many example scripts. Better algorithms can avoid some of that slowdown, as you see in this test case. Here is the test code you can run to see: http://pj.freefaculty.org/scraps/profile/prof-puzzle-1.R It downloads a data file from that same directory and then runs some multiple imputations with the Amelia package. Here's the output from my computer http://pj.freefaculty.org/scraps/profile/prof-puzzle-1.Rout That includes the profile of the calculations...

...is is handy because, when 1 run in 10,000 on the cluster exhibits some weird behavior, we can easily re-initiate that interactively and see what's going on. I have a vignette "pps" that explains. I dropped a copy of that here in case you don't want to get the package: http://pj.freefaculty.org/scraps/pps.pdf While working on that, I gained a considerably deeper understanding of random generators and seeds. That is what this vignette is about http://pj.freefaculty.org/scraps/PRNG-basics.pdf We've been running simulations on our cluster with the portableParallelSeeds framework...

Greetings. I'm trying to understand a problem on a Dell Laptop. Details below, also uploaded the R working example that I pasted below. http://pj.freefaculty.org/scraps/testSymbols.R > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C...

Hi, everybody I have an account on Dreamhost.com and when I renewed it recently, their message said my usage of storage and bandwidth had been reasonably low. In an idle moment about 3 weeks ago, I followed your instructions to set up a CRAN mirror on their server. Here it is: http://www.freefaculty.org/cran It is not hosted at my University, but it is a working, high availability server. Is there any reason it could not be listed as a CRAN mirror. (Although I really have no idea where these machines exist. I'm pretty sure it is in the USA. I'll try to find out). Maybe you might try...

Greetings, R developers Here are my requests today. 1. Would you care to review this vignette http://pj.freefaculty.org/R/Rchaeology.pdf and tell me if you think it is wrong headed, and 2. Supposing you do not think I'm completely wrong, would you care to point me at more examples of R idioms that lead to deep insights into the nature of R programming? Longer more boring explanation: In the rockchalk pa...

...called "rockchalk". For 3d illustrations, my functions use persp, and I've grown to like working with it. As an example of the kind of things I like to do, you might consult my lecture on multicollinearity, which is by far the most detailed illustration I've prepared. http://pj.freefaculty.org/guides/stat/Regression/Multicollinearity/Multicollinearity-1-lecture.pdf I used persp mainly because I can understand it, and it can be made to work like plot in R, with additional tools like lines and points and such. I don't want to interact with these plots, I just need to put them int...

Here's my little discussion example for a quadratic regression: http://pj.freefaculty.org/R/WorkingExamples/regression-quadratic-1.R Students press me to know the benefits of poly() over the more obvious regression formulas. I think I understand the theory on why poly() should be more numerically stable, but I'm having trouble writing down an example that proves the benefit of...

...d a solution by adding this --with-libpth-prefix=$HOME/packages but still rejection, new zlib not found. -- Paul E. Johnson Professor, Political Science Director 1541 Lilac Lane, Room 504 Center for Research Methods University of Kansas University of Kansas http://pj.freefaculty.org http://crmda.ku.edu

...ot. I can't tell if R runs any faster, but it does run, which is encouraging. Now here's the problem I see. Using Rprof causes R to crash, but only when openblas stuff is in the picture. I wondered what you think? Here's the code to reproduce this: datM <- read.csv("http://pj.freefaculty.org/scraps/profile/missingDat.csv") library(Amelia) set.seed(12345) Rprof("Amelia-1.out") impA <- amelia(datM, m = 5, idvars="group") Rprof(NULL) summaryRprof("Amelia-1.out") Here's the crashed session > datM <- read.csv("http://pj.freefaculty...

...verlapping portions of circles. These illustrations are for Social Choice theory, a field in political science and economics. I've wrestled together some examples so you can see what I mean, but have not mastered the "color overlapping sections" problem (as you will see): http://pj.freefaculty.org/scraps/t-m15g.pdf The shaded area does not overlap perfectly, mainly because I isolated the points manually with locator(). Tedious! I've not found R functions just for this. Are there any packages? You can get an idea of the problem if you run, for example library(plotrix) example(dra...

...k 1.8.92, not the one I uploaded yesterday. So none of the beautiful repairs I implemented show up :( pj -- Paul E. Johnson Professor, Political Science Director 1541 Lilac Lane, Room 504 Center for Research Methods University of Kansas University of Kansas http://pj.freefaculty.org http://crmda.ku.edu

...out as black boxes (as they do for me). If you don't use Sweave, but you have a system with a working version of R and LaTeX, the file gives the instructions you need to use to process the file. The The file itself explains the problem. You can see the flawed output on my web site http://pj.freefaculty.org/latex/foo.pdf I'm running Ubuntu Linux 8.10 with R 2.8.1 and TexLive 2007 (which is provided with the distribution). This is not a new problem, I noticed it two years ago while using TeTeX on Fedora Linux, and so I doubt that this is specific to TeXLive. Back then, I took the path of res...

...the file.exists documentation so Windows users can see how easy this is to avoid? Respectfully yours, pj -- Paul E. Johnson Professor, Political Science Director 1541 Lilac Lane, Room 504 Center for Research Methods University of Kansas University of Kansas http://pj.freefaculty.org http://crmda.ku.edu

...kages were built on a stock Centos 5.2 system, with all components as usual EXCEPT for the ones I provide below or the packages that can be downloaded from EPEL. As far as I can tell, everything works as well as it does on Fedora, no better. Go here in your web browser to look it over. http://pj.freefaculty.org/Centos/ My PGP key is in the top directory http://pj.freefaculty.org/Centos/PaulJohnson-BinaryPackageSigningKey And under i386 you should see I've created an RPM repository. I don't have any i686 machines for which I'm doing this work, sorry. To use yum, I think you should spec...

...brings the output into line with the advice of the help page for "if". The output looks more like the a randomly selected R file from the R source or the recommended packages. I'm teaching new users that they should study the R source code itself as a guide for programming (http://pj.freefaculty.org/R/Rstyle.pdf). My argument there would go more smoothly if print.function obeyed the "} else {" policy that most of your source code and packages adhere to. We do see r-help questions about the problem that user code can't be run line-by-line, even when it is styled like the prin...

...rned last week that I generated a lot of PDFs and forgot to go back and embed the fonts in them. It would be very pleasant for me if pdf.options included an argument to turn on font embedding and have fonts always embedded. Always. Thanks for your time, as always. -- Paul E. Johnson http://pj.freefaculty.org Director, Center for Research Methods and Data Analysis http://crmda.ku.edu I only use this account for email list memberships. To write directly, address me at pauljohn at ku.edu.

...r Windows and Mac users as well? If there is none, don't you think it would be fun if there were? pj -- Paul E. Johnson Professor, Political Science ? ?Assoc. Director 1541 Lilac Lane, Room 504 ? ? Center for Research Methods University of Kansas ? ? ? ? ? ? ? University of Kansas http://pj.freefaculty.org ? ? ? ? ? ?http://quant.ku.edu

...edora Linux 8 and R 2.6.2, something funny happens: the characters "overstrike" each other. The Greek letter "mu" is printed several spaces to the left of the "(" that it is supposed to follow. I made an itty bitty picture of the figure title to show you: http://pj.freefaculty.org/R/plotmath_problem.png I can force in spaces to re-arrange the symbols so they do not overstrike. The following looks fine in the output. t1t2 <- bquote (paste("Normal ( ", mu== .(mu), ' , ', sigma== .(sigma)," )") ) ### Note spaces manually inserted above...

....arg=as.character(testdata$group), main="a=4.0", xlab="Group", ylab="xbar") xvalues <- c(0.7, 1.9, 3.1, 4.3, 5.5) arrows(xvalues, testdata$xbar, xvalues, testdata$xbar+testdata$se, length= 0.4, angle=90, code=3) The best clue I have so far is Rtips #5.9: http://pj.freefaculty.org/R/Rtips.html#5.9 which is what I based my present solution off of. However, I do not understand how this works. It seems like there is no concrete way to determine the arrow drawing parameters x0 and x1 for a barplot. Moreover, the bars seem to be "cut off". [[alternative HTML ve...

Helo everybody, I'm new to R and have some issues with my data in R. My raw data look like that: ID Day size 1 1 7 1 1 7.2 1 1 7.1 2 1 7.3 2 1 7.4 2 1 7.2 3 1 7 3 1 7.1 3 1 7.5 4 1 7.3 4 1 7.2 4 1 7.6 1 2 7 1 2 7.2 1 2 7.1 2 2 7.1 2 2 7.4 2 2 7.2 3 2 7.5 3 2 7.1 3 2 7.5 4 2 7.2 4 2 7.2 4 2 7.3 1 3 7.4 1 3 7.2 1 3 7.1 2 3 7.2 2 3 7.4 2 3 7.2 3 3 7.4 3 3 7.2 3 3 7.5 4 3 7.4 4 3 7.2 4 3 7.7