[R] nlme: problem with fitting logistic function

Dieter Menne dieter.menne at menne-biomed.de
Mon Mar 9 18:13:07 CET 2009

jakub kreisinger <jakubkreisinger <at> seznam.cz> writes:

> I am trying to analyze growth data on mice. To do this I attempted to fit
logistic curve using nlme package.
> However, the dataset I use is large (in total ca 20 000 measures on ca 3 000
individuals) with relatively
> complicated structure (several explanatory variables with interactions +
random effect where
> individual offspring are nested within particular litters are nested within
particular parental
> pairs). 
> Although I had no problems to fit models, where the complexity of random
effect was reduce (which is
> conceptually incorrect), the fitting procedure of the full model did not reach
the 1 iteration after
> several hours. Do you have any idea how to solve this problem? 

1) Get better starting values by using nlsList
2) Get still better starting values by fitting a simpler model first with
   nlme. This is VERY successful for me, it made many problems feasibly that 
   blew up otherwise. Good luck in finding the right syntax for complex
   start values, this can be a huge challenge.
3) Use lmer in lme4. Your mileage may vary, I could not find a speedup
   for my problems, but larger problem might give one. 
4) Use C for the core function. This is very effective, and there is at least
   on example coming with nlme (was it SSlogist?).


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