search for: mstol

...optimRes$message,"\n")) } return(x) } lmerControl <- function(maxIter = 200, # used in ../src/lmer.c only tolerance = sqrt(.Machine$double.eps),# ditto msMaxIter = 200, ## msTol = sqrt(.Machine$double.eps), ## FIXME: should be able to pass tolerances to nlminb() msVerbose = getOption("verbose"), niterEM = 15, EMverbose = getOption("verbose"), PQLmaxIt = 30,# FIXME: unused; PQL currently uses 'm...

...vergence depends on how the method (ML/REM) and which (and how much) parameters will depend randomly on the cluster-variable. How get the bist fit without convergence? I set the parameters msVerbose and returnObject to TRUE: lmeControl(maxIter=50000, msMaxIter=200, tolerance=1e-4, niter=50, msTol=1e-5, nlmStepMax=500, ,msVerbose=TRUE ,returnObject=TRUE ) However, the lme-functions does not produce verbose output, nor does it return the best fit if lme is not converging. It returns only an error: Error in lme.formula(y ~ lndbh + I(lndbh^2) + lnh + I(lnh^2), random = ~lndbh + :...

...I would be happy to hear from anyone who has an idea on what parameters in gnlsControl to change to get convergence. Cheers Dan Coleman Genentech Inc. > gnlsControl function (maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, minScale = 0.001, tolerance = 1e-06, nlsTol = 0.001, msTol = 1e-07, msScale = lmeScale, returnObject = FALSE, msVerbose = FALSE, apVar = TRUE, .relStep = (.Machine$double.eps)^(1/3), nlmStepMax = 100, opt = c("nlminb", "optim"), optimMethod = "BFGS", minAbsParApVar = 0.05) { list(maxIter = maxIter, nls...

...ion: What exactly does "Warning message: Step halving factor reduced below minimum in NLS step in: gnls(model = y ~ 5 + ...)" mean? I have tried to address this by specifying "control = list(maxIter = 1000, pnlsMaxIter = 200, msMaxIter = 1000, tolerance = 1e-06, pnlsTol = 1e-04, msTol = 1e-07, minScale = 1e-10, returnObject = TRUE)" in my model calls, but this does not entirely eliminate the problem (I am running gnls( ) 24 separate times on separate data sets). Much thanks in advance, david paul #Constructing Indicator Variables indicator <- paste( "foo$X...

...ffects are very different. Here is my R code and output, with some columns and rows deleted for space considerations: FOO.lme1 <- lme(fixed = Y ~ X1*X2, random = ~ X2 | X3, data = FOO, method = "REML", control = list(maxIter = 200, msMaxIter = 200, tolerance = 1e-8, niterEM = 200, msTol = 1e-8, msVerbose = TRUE, optimMethod = "Nelder-Mead")) 0 203.991: 0.924323 -0.0884338 0.493897 1 203.991: 0.924323 -0.0884338 0.493897 > summary(FOO.lme1) Linear mixed-effects model fit by REML Data: FOO AIC BIC logLik 357.484 373.6868 -170.7420 Ran...

...ow the actual iterative fitting of the model works mathematically) I was wondering if anyone knew if there was anything else in the control values I should try changing. Below are the defaults.. lmeControl function (maxIter = 50, msMaxIter = 50, tolerance = 1e-06, niterEM = 25, msTol = 1e-07, msScale = lmeScale, msVerbose = FALSE, returnObject = FALSE, gradHess = TRUE, apVar = TRUE, .relStep = (.Machine$double.eps)^(1/3), minAbsParApVar = 0.05, nlmStepMax = 100, optimMethod = "BFGS", natural = TRUE) I was reading on the R listserve that lmer from t...

Dear R community, I'm fitting a complex mixed-effects model that requires numerous iterations and function evaluations. I note that nlminb accepts a list of control parameters, including eval.max. Is there a way to change the default eval.max value for nlminb when it is being called from lme? Thanks for any thoughts, Andrew -- Andrew Robinson Department of Mathematics and Statistics

...)) Maximum number of PQL iterations: 200 iteration 1 iteration 2 Error in MEestimate(lmeSt, grps) : NA/NaN/Inf in foreign function call (arg 1) > gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson", niterPQL=200,control=lmeControl(msTol=0.00000000000000001)) Maximum number of PQL iterations: 200 iteration 1 iteration 2 Error in MEestimate(lmeSt, grps) : NA/NaN/Inf in foreign function call (arg 1) > gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family="poisson", niterPQL=200...

Hi All, I've been having a little trouble with creating a loop that will run a a series of t.tests for inspection, Below is the code i've tried, and some checks i've looked at. I've used the get(paste()) idea as i was told previously that the use of the eval should try and be avoided. I've run a single syntax to check that my systax is correct and works without any problems