OK, now it sounds like the behavior is exactly the same for both of us. I think Gmail sometimes gobbles up newline characters, and that must have messed up the code I sent out before.
Someone pointed out to me that a similar problem was identified before: https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q3/001425.html http://www.mail-archive.com/[email protected]/msg13913.html Does anyone know a strategy for dealing with this or isolating the problem? Thanks again Josh for your help. On Fri, Apr 23, 2010 at 9:44 AM, Joshua Wiley <[email protected]>wrote: > Michael, > > Good news (relatively speaking). I ran your code again, but this time > I actually looked at what I pasted in and noticed some errors. When I > actually pulled your code into a text editor, there was an issue with > one of the comments wrapping to the next line without a new # > (probably an email issue). > > For others if "## BEGIN" is line 1; the comment issue is on line 44 (# > nugget for space is (then the line break) determined by the nugget for > time). > > Once I fixed that, I got slightly different results. > > ########From Rterm######## > > Browse[6]> > debug: space.nug <- temp[2] > Browse[6]> > debug: cor.time <- lapply(attr(object[["time"]], "covariate"), > function(mat) (1 > - > time.nug) * exp(-mat/time.rng)) > Browse[6]> > > Traceback: > 1: FUN(X[[5L]], ...) > 2: lapply(attr(object[["time"]], "covariate"), function(mat) (1 - > time.nug) > * exp(-mat/time.rng)) > 3: corMatrix.corSPT(object) > 4: corMatrix(object) > 5: unlist(corMatrix(object)) > 6: corFactor.corSPT(object) > 7: corFactor(object) > 8: `coef<-.corSPT`(`*tmp*`, value = c(0, 0, 1.49011611938477e-08)) > 9: `coef<-`(`*tmp*`, value = c(0, 0, 1.49011611938477e-08)) > 10: `coef<-.modelStruct`(`*tmp*`, value = c(0.375881355354461, 0, 0, > 1.490116119 > 38477e-08)) > 11: `coef<-`(`*tmp*`, value = c(0.375881355354461, 0, 0, > 1.49011611938477e-08)) > 12: logLik.lmeStruct(lmeSt, lmePars) > 13: logLik(lmeSt, lmePars) > 14: objective(.par, ...) > 15: .Call(R_port_nlminb, obj, grad, hess, rho, low, upp, d = > rep(as.double(scale > ), length.out = length(par)), iv, v) > 16: nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars), > contro > l = list(iter.max = controlvals$msMaxIter, eval.max = > controlvals$msMaxEval, > trace = controlvals$msVerbose)) > 17: lme.formula(fixed = e ~ a, random = ~1 | g, data = df, correlation = > corSPT( > corExp(c(1, 0.5), form = ~t | g, nugget = TRUE), corExp(c(1, 0.5), form > = ~x > + y | g, nugget = TRUE)), control = list(msVerbose = TRUE, opt = > "nlmin > b")) > 18: lme(fixed = e ~ a, random = ~1 | g, data = df, correlation = > corSPT(corExp(c > (1, 0.5), form = ~t | g, nugget = TRUE), corExp(c(1, 0.5), form = ~x + > y > | g, nugget = TRUE)), control = list(msVerbose = TRUE, opt = > "nlminb")) > Error in FUN(X[[5L]], ...) : caught access violation - continue with care > > > > > ########From Rterm (again, but this time running the code from > Xemacs)######## > > Browse[3]> > debug: coef(object[[i]]) <- value[parMap[, i]] > Browse[3]> > > Traceback: > 1: `coef<-.modelStruct`(`*tmp*`, value = c(0.47054905560461, 0, > 1.49011611938477e-08, 0)) > 2: `coef<-`(`*tmp*`, value = c(0.47054905560461, 0, 1.49011611938477e-08, > 0)) > 3: logLik.lmeStruct(lmeSt, lmePars) > 4: logLik(lmeSt, lmePars) > 5: objective(.par, ...) > 6: .Call(R_port_nlminb, obj, grad, hess, rho, low, upp, d = > rep(as.double(scale), length.out = length(par)), iv, v) > 7: nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars), > control = list(iter.max = controlvals$msMaxIter, eval.max = > controlvals$msMaxEval, trace = controlvals$msVerbose)) > 8: lme.formula(fixed = e ~ a, random = ~1 | g, data = df, correlation > = corSPT(corExp(c(1, 0.5), form = ~t | g, nugget = TRUE), > corExp(c(1, 0.5), form = ~x + y | g, nugget = TRUE)), control = > list(msVerbose = TRUE, opt = "nlminb")) > 9: lme(fixed = e ~ a, random = ~1 | g, data = df, correlation = > corSPT(corExp(c(1, 0.5), form = ~t | g, nugget = TRUE), > corExp(c(1, 0.5), form = ~x + y | g, nugget = TRUE)), control = > list(msVerbose = TRUE, opt = "nlminb")) > Error in coef(object[[i]]) <- value[parMap[, i]] : > caught access violation - continue with care > > > > Then it occurred to me that RGui sometimes behaves slightly > differently, and that you might be using the Gui so I ran it again > there and it crashed, froze, and I had to manually kill the process. > > I don't know if that really helps, but at least I (sort of?) > replicated your crashing. > > Josh > > > <snipped a bunch of stuff because I already included a lot of output> > > > -- > Joshua Wiley > Senior in Psychology > University of California, Riverside > http://www.joshuawiley.com/ > [[alternative HTML version deleted]] ______________________________________________ [email protected] 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.
