Convergence Problems with glmer.nb model
On 25 April 2016 at 13:00, Aoibheann Gaughran <gaughra at tcd.ie> wrote:
Good morning, First time posting so I hope I am including all of the relevant information. I am attempting to analyse the foraging behaviour of a animal in an agricultural landscape. The objective is to identify the factors (habitat type, environmental variables and animal-specific variables) that best predict foraging site preference. Some fields are preferred while others are avoided. The response variable is count data - the number of times a given animal was in a given field in a given month. An animal's home range varies from month to month, so the area available to it and the fields that fall within its home range change somewhat every month. The count data shows an overdispersed, negative binomial distribution, and is zero inflated as fields that fell within the home range where the animal had *not *foraged in that month are also included in the dataset. The individual animal is specified as a random variable to account for pseudoreplication. It should be noted that at the moment I am attempting to run a the model on a subset of the data (n=671) as I had attempted to run the model on the full dataset (n=62,000) but three days later the model (which included interaction terms at this point) had still failed to run, and when stopped, R gave me a multitude of convergence warning messages e.g. 13: In (function (fn, par, lower = rep.int(-Inf, n), upper = rep.int(Inf, ... : failure to converge in 10000 evaluations Simpler iterations of the model, with fewer explanatory terms, and no interaction terms, also gave me convergence and some scaling warnings, which I sought to address using: control=glmerControl(optCtrl=list(maxfun=20000) and by scaling the numeric variables age, slope and aspect as follows:- dframe1$agescale <- scale(dframe1$age, center = TRUE, scale = FALSE) dframe1$slopescale <- scale(dframe1$slope, center = TRUE, scale = FALSE) dframe1$aspectscale <- scale(dframe1$aspect, center = TRUE, scale = FALSE) Currently, the model looks like this:
model1 <- glmer.nb(field_count ~ habitat + + sex+ + agescale+ #+ mon+ + soil+ + slopescale+ + aspectscale+ + offset(log(origarea)) #take into account field size + +(1|animal),+ control=glmerControl(optCtrl=list(maxfun=20000)),+ data = dframe1)
There were 24 warnings (use warnings() to see them)
warnings()Warning messages:
1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, ... : Model is nearly unidentifiable: very large eigenvalue - Rescale variables?;Model is nearly unidentifiable: large eigenvalue ratio - Rescale variables? 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, ... : Model failed to converge with max|grad| = 0.0134799 (tol = 0.001, component 1) 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, ... : Model failed to converge with max|grad| = 0.148644 (tol = 0.001, component 1) 4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, ... : Model is nearly unidentifiable: large eigenvalue ratio - Rescale variables? etc. So the model still fails to converge despite rescaling and altering the number of iterations. I had also received the following error in relation to month (in the reduced dataset there are only *four *months), so Ive had to exclude it for the time being. I am not sure why I am getting this error since the factor has four levels. Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels I do eventually want to include interaction terms as previous analysis on ranging behaviour suggests there is an interaction between age and sex. Summary of dataset attached. Also attached is the .csv file containing the reduced dataset. I have read various suggestions online and have come across the following worrying line "It's perfectly possible that your data is insufficient to support the complexity of the model or the model is incorrectly constructed for the design of the study". I would greatly appreciate any help you could give me with understanding and solving the problems I am encountering with my model. Kind regards, -- Aoibheann Gaughran Behavioural and Evolutionary Ecology Research Group Zoology Building School of Natural Sciences Trinity College Dublin Dublin 2 Ireland Phone: +353 (86) 3812615
Aoibheann Gaughran Behavioural and Evolutionary Ecology Research Group Zoology Building School of Natural Sciences Trinity College Dublin Dublin 2 Ireland Phone: +353 (86) 3812615