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...ls below), eventually get to "/usr/bin/install: cannot create regular file `../../include/Rinternals.h': No such file or directory make[2]: *** [Rinternals.ts] Error 1". Any thoughts about what's going on here or what I can do to further diagnose the problem? thanks Ben Bolker ================== bolker at ubuntu-10:~/R/r-devel$ svn update At revision 58379. cd ../r-build make distclean ../r-devel/configure R is now configured for i686-pc-linux-gnu Source directory: ../r-devel Installation directory: /usr/local C compiler: gcc -std=...

...ring the contribution of R-Core (and I think Peter Dalgaard in particular) in writing the original code. If I add "R Development Core Team" to the author list I feel I am suggesting that they might be responsible for my changes. Neither seems entirely appropriate. Suggestions? Ben Bolker PS this is my current DESCRIPTION file: Package: bbmle Title: Maximum likelihood estimation Version: 0.7 Date: 2007/05/16 Author: Ben Bolker Maintainer: Ben Bolker <bolker at zoo.ufl.edu> Depends: R (>= 2.0.0), methods, stats, graphics Description: Methods and functions for fitting maxim...

All R experts, How do I fit a dynamic Random effects model with a binary dependent variable in R Thanks JCM [[alternative HTML version deleted]]

...l latest rjags (3-5) from CRAN with JAGS 3.2.0 installed on Ubuntu 10.04, with r-devel ... the bottom line is that it fails while loading with /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb Has anyone else seen this or is it a glitch somewhere in my system? thanks Ben Bolker ================== bolker at ubuntu-10-new:~/R/pkgs/rjags$ jags Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod: ok Loading module: bugs: ok . ======================= install.packages("rjags") starts...

...ary(Hmisc) > ?subplot > subplot({plot(x,y2,axes=FALSE); axis(side=4)},x=range(x),y=c(0,0.5)) -------- Original Message -------- Subject: Re: [R-sig-eco] How to create axes in arbitrary positions? Date: Sat, 2 Jan 2010 07:31:51 -0500 From: Zongshan Li <zongshan_li at yahoo.com> To: Bolker,Benjamin Michael <bolker at ufl.edu> References: <831079.35547.qm at web114002.mail.gq1.yahoo.com> <4B3E3C40.9010306 at ufl.edu> Dear Ben Bolker: I appeciate your introducing functions very much for my question, and I am glad that your kindly intention to give me f...

...n construct this matrix using sweep(model.matrix(~z-1,dd),1,dd$x>0,"*") and then stick it into lm.fit -- but is there a more elegant way to do this in general? I haven't found a formula combining (z-1) and I(x>0) that works, although I can imagine there is one. thanks Ben Bolker -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bolker at ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/p...

Does anyone have an address for a maintainer, or know what's going on? cheers Ben Bolker ben at bolker-lap2:~$ ping wiki.r-project.org PING econum.umh.ac.be (193.190.194.5) 56(84) bytes of data. ^C --- econum.umh.ac.be ping statistics --- 8 packets transmitted, 0 received, 100% packet loss, time 6999ms ben at bolker-lap2:~$ traceroute wiki.r-project.org traceroute to wiki.r-project.o...

Hello, I am using rbetabinom ( to generate beta binomial random variables) function available in the "emdbook"package written by Professor. Ben Bolker for my research study. I have no questions with this function. However, I am looking for the theoretical method/algorithm of the function "rbetabinom " . Morris (1997), American Naturalist 150:299-327 is given as the reference in the package, But I couldn't fund any theoretical meth...

...\theta p)}% {\mbox{Beta}(\theta(1-p),\theta p)}}% {p(x) = % (C(N,x)*Beta(N-x+theta*(1-p),x+theta*p))/% Beta(theta*(1-p),theta*p)} The parameters \code{shape1} and \code{shape2} are the more traditional parameterization in terms of the parameters of the per-trial probability distribution. } -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bolker at ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size...

optim ignores misspelled control parameters, so that trying to set (e.g.) "maxint=1000" in the control argument silently does nothing. The patch below (watch out for line breaks! also posted at http://www.zoo.ufl.edu/bolker/optim_patch.R , and http://www.zoo.ufl.edu/bolker/optim_new.R) adds three lines to optim.R that issue a warning if any names of elements of "control" fail to match the internal object that contains the defaults. Here is code that shows the behavior: set.seed(1001) x <- rnorm(10) y...

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)

...(newdata,object at data),model.matrix(z)) fails -- because model.matrix() is explicitly evaluating the variables in the formula in the environment of z (i.e., ignoring the first argument of "with" ...) Any advice on how to solve this without making a bigger mess? sincerely Ben Bolker ## set up a data frame for prediction set.seed(1001) f = factor(rep(letters[1:4],each=20)) x = runif(80) u = rnorm(4) y = rnorm(80,mean=2+x*(3+u[f]),sd=0.1) dat = data.frame(f,x,y) ## fit a model ... could easily do by lm() but want to ## demonstrate the problem library(bbmle) m1 = mle2(y~dn...

I'm resending this after a decent interval of 20 days -- any opinions? Should I file it as a bug report? Is it my mistake? cheers Ben Bolker -------- Original Message -------- Subject: buglet (?) in de.restore() Date: Tue, 21 Aug 2007 13:29:33 -0400 From: Ben Bolker <bolker at zoo.ufl.edu> To: r-devel at r-project.org If one calls data.entry() with a matrix: A = matrix(0,2,2) data.entry(A) everything works fine except...

...n system libraries etc. (I don't really know how this is done in FORTRAN). Does anyone out there have experience in porting code from Netlib and ending up with clean, platform-configured code? (I will go look at the deSolve package next, but since this is a bit of a side project ...) Ben Bolker baptiste auguie wrote: > Dear Ben, > > Many thanks for the effort you put into this. Out of curiosity I located > an earlier package (sparma) on your webpage yesterday, but ran into some > problem when installing it, related to 'machcon.f ' . A similar problem > comes u...

...be easy to implement others if that seems necessary. I hereby request comments and suggest that it wouldn't hurt to incorporate it into base R ... (I will write docs for it if necessary, perhaps by modifying ?simulate -- there is no specific documentation for simulate.lm) cheers Ben Bolker simulate.glm <- function (object, nsim = 1, seed = NULL, ...) { ## RNG stuff copied from simulate.lm if (!exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE)) runif(1) if (is.null(seed)) RNGstate <- get(".Random.seed", envir = .GlobalEnv) else {...

...t;..." to every call to the function in Reduce() -- patch is included below my signature ... It's not a big deal -- I could also do Reduce(function(x,y) { merge(x,y,by="state",all=TRUE) }, z) but there doesn't seem to be a good reason not to allow it ... cheers Ben Bolker -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bolker at ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc *** /home/ben/funprog.R.new 2009-06-06 18:30:56.000000000 -0400 --- src/library/base/R/funprog.R 2009-02-12 10:39:32...

...## as numeric (and very ugly) ! ## I don't know how to safely convert the breakpoints ! ## back to a character format (e.g. ! ## levels(res) = [1970-01-01 00:00:00,1970-01-01 12:00:00) ! ## instead of [18000,61200) ! } ! } res } -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bolker at ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size...

..." out of ... 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

I have an optimization question that I was hoping to get some suggestions on how best to go about sovling it. I would think there is probably a package that addresses this problem. This is an ordering optimzation problem. Best to describe it with a simple example. Say I have 100 "bins" each with a ball in it numbered from 1 to 100. Each bin can only hold one ball. This optimization is

...e recommend? Below is an example that hacks (not quite "jitters", because it's systematic) the x locations a bit, but I find it a bit ugly. (I was also hoping that ggplot had some magic to do this automatically, but position_dodge doesn't seem to work in this context ...) Ben Bolker library(ggplot2) nx <- 3 ngrp <- 5 nper <- 4 x <- rep(1:nx,ngrp*nper) y <- runif(nx*ngrp*nper) g <- factor(rep(1:ngrp,each=nx*nper)) dat <- data.frame(x,y,g) se <- with(dat,tapply(y,list(g,x),sd)/table(g,x)) means <- with(dat,tapply(y,list(g,x),mean)) limits <- aes...