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...... myself (and make a note to that effect in the documentation)? (I guess another general solution to this is to ask for lists of arguments, like MoreArgs in mapply(). Another would be to go back and change spheres3d to make size a synonym for radius ... ) any thoughts? Ben Bolker -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

Please, I would like to know how to generate a truncated multivariate normal distribution k - dimensional, X ~ NT(mu, Sigma), where the elements of X to be non-negative (except the first), and the first dimension is strictly larger than zero. Example: X ~ NT_2(mu, Sigma), where mu=c(0.5, 0.5) and Sigma=c([120, 191], [191,154]), with X_1>0 and X_2>=0 Could anybody help

...[i], wid=width[i], stats= z$stats[,i], out = z$out[z$group==i], conf = z$conf[,i], notch= notch, xlog = xlog, i = i) ! axes <- is.null(pars$axes) if(!axes) { axes <- pars$axes; pars$axes <- NULL } if(axes) { -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

Dear all, I have the following output generated by linear regression. Since there is only one regression intercept and one slope for one set of data, what is the meaning of std. error for intercept and that of slope? Thanks in advance. Sincerely, Minghua > data(thuesen) > attach(thuesen) > lm(short.velocity~blood.glucose) Call: lm(formula = short.velocity ~ blood.glucose)

R help list subscribers, I am a new user of R. I am attempting to use R to explore a set of equations specifying the dynamics of a three trophic level food chain. I have put together this code for the function that is to be evaluted by LSODA. My equations Rprime, Cprime, and Pprime are meant to describe the actual equation of the derivative. When I run LSODA, I do not get the output that

Hi, I would like to know how to extract the data from Excel Spreadsheet. Thank you very much. Melissa ************************************************************ JLT Risk Solutions Ltd 6 Crutched Friars, London EC3N 2PH. Co Reg No 1536540 Tel: (44) (0)20 7528 4000 Fax: (44) (0)20 7528 4500 http://www.jltgroup.com Lloyd's Broker. Regulated by the General Insurance Standards Council

...the code, also gets rid of the problem. Apparently (I surmise) R does find the binary (replacing system("test.bin") with system("junk") produces a warning message), but the file that gets created gets cleaned up or put somewhere other than the current working directory. -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...n -s /usr/lib/atlas/libblas.so.3 libblas-3.so # ln -s /usr/lib/atlas/liblapack.so.3 liblapack-3.so Otherwise compilation couldn't find -lblas-3 or -llapack-3 (I could have gotten away with the links in /usr/lib/atlas instead of /usr/lib, as /usr/lib/atlas was listed in /etc/ld.so.conf) -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...work with commas as well, haven't tried it) will give you a list of t-test results. If all you want is the t-statistic, something like sapply(m1,"[[","statistic") should do it. Poke around in the documentation (?mapply, ?sapply, etc.) to see why this all works. -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...t;- seq(mmin,17.5,by=0.5) else { mile <- seq(mmin,17.5,length=n) } mean <- 3000-50*(mile-10)^2 v <- sd^2 dist <- abs(outer(mile,mile,"-")) Sigma <- v*exp(-dist/range) X <- mvrnorm(1,mu=mean,Sigma=Sigma) data.frame(mile=mile,X=X,mean=mean) } -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...confidence limits); I also have opinions about some of the defaults, and I can certainly help test it ... I don't know who the primary developer is beyond "R-core" ... if whoever's working on it would like to take me up on the offer, can you let me know? Ben Bolker -- 620B Bartram Hall bolker@zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...see where the ^H was coming from. I was going to suggest testing interactive() to see if the code was running in batch mode or not, but I just tried that with Sweave() and it thinks that interactive() is TRUE when running Sweave. Oh well. Any one else have a solution? Ben Bolker -- 620B Bartram Hall bolker@zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...is that I like to keep using the same version of R as my classes are currently using, and I haven't yet gone to the trouble of maintaining different versions on my system. [did anyone have any thoughts on my 4 Nov query about errors vs warnings in dgamma?] cheers Ben Bolker -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...f$trace <- mf$model <- ## mf$lower <- mf$upper <- NULL ## add "mynls <- " at the beginning, delete namespace code at the end source("mynls.R") mynls(y~a+b*x+c*I(x^2),start=c(a=1,b=1,c=0.1),algorithm="port",lower=c(0,0,0)) ## works beautifully -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...2)) confint(m2) m2b = mle(minuslogl=mfun, fixed=list(b=0),start=list(a=1,s=0.1), method="L-BFGS-B",lower=c(0.002,0.002,0.002)) ## set boundary slightly above zero to avoid ## boundary cases dev <- 2*(-logLik(m2b)+logLik(m2)) as.numeric(pchisq(dev,lower.tail=FALSE,df=1)) -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...mplain about a recent seminar about nanotechnology using the terms nanofluidics, nanofactory, nano-this, and nano-that ... I found myself thinking "well the speaker should just have said with(nano, ...) Un(?)fortunately there's no-one here I can share that thought with. -- 620B Bartram Hall bolker at zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

...there were a succinct list of these differences, with a disclaimer ... I would be willing to maintain such a list, but since I don't ever use S-PLUS it would be a little bit hard ... http://www.math.uwaterloo.ca/~dbabinea/webpage/function.htm gives a few differences. Ben Bolker -- 620B Bartram Hall bolker@zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704 ---------- Forwarded message -------...

...ew() if (horizontal) plot.window(ylim = xlim, xlim = ylim, log = log) else plot.window(xlim = xlim, ylim = ylim, log = log) } b <- boxplot(split(mf[[response]], f),at=at, horizontal=horizontal, boxwex=boxwex, add=TRUE, ...) invisible(b) } -- 620B Bartram Hall bolker@zoo.ufl.edu Zoology Department, University of Florida http://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704

Dear list members, I want to fit a nonlinear mixed model using the nlme command. My dependent variable takes the form of event counts for different countries over a number of years, and hence I was going to fit a mixed effects negative binomial model. The problem, as far as I can glean from Pinheiro & Bates 2000, is that I need a model that is not normal in the errors. All the models they

Dear Colleagues, I have x, y data (pollen and seed dispersal from oaks !) that I would like to fit with a function which look like this: p(a,b,x,y)=b/(2*pi*a?gamma(2/b))*exp(-(square_root(x?+y?)/a)power(b)) I am looking for a and b values that fit my data at best. Can someone give me hints to perform such an analysis with R ? Thanks a lot Sophie Sophie Gerber