Some Basic lmer Questions
Hi Kevin, welcome to the wonderful world of mixed-models! I heartily recommend that you read the following books: Gelman and Hill, and Pinehiro and Bates.
On Mon, Jan 14, 2008 at 03:21:20PM -0500, Kevin E. Thorpe wrote:
I am taking my first cautious steps into the mixed-models pool and I have a few, probably basic questions. The data I am faced with are lab values taken at regular time intervals (0, 4, 8, 12 and 24 hours) following a surgery.
str(trop)
'data.frame': 790 obs. of 6 variables: $ pid : int 0 0 0 0 0 1 1 1 1 1 ... $ ittrx: int 1 1 1 1 1 2 2 2 2 2 ... $ pprx : int 1 1 1 1 1 2 2 2 2 2 ... $ rx3 : Factor w/ 3 levels "On","Off","Converted": 1 1 1 1 1 2 2 2 2 2 ... $ hours: num 0 4 8 12 24 0 4 8 12 24 ... $ trop : num 2.12 9.51 5.79 4.37 1.8 NA NA NA NA NA ... - attr(*, "reshapeLong")=List of 4 ..$ varying:List of 1 .. ..$ : chr "Trop0" "Trop4" "Trop8" "Trop12" ... ..$ v.names: chr "trop" ..$ idvar : chr "pid" ..$ timevar: chr "hours" Of interest is whether or not there are differences among the groups represented by rx3 above. If we pretend for the moment that the time effect is linear and there is no treatment by time interaction, I would be inclined to test for differences as follows (also ignoring any correlation structure). trop.lme0 <- lmer(trop~hours+(1|pid),data=trop,method="ML") trop.lme1 <- lmer(trop~rx3+hours+(1|pid),data=trop,method="ML") anova(trop.lme0,trop.lme1) I seem to recall hearing/reading that the LRT from anova() is appropriate for maximum-likelihood but not REML which is why I used method="ML". So, is this the right approach or have I seriously misunderstood something?
It's under discussion. The current recommendation is to use mcmcsamp to sample the posterior distribution.
Next, assuming I have not done anything egregious, I want to turn to the non-linearity of the time effect. I found that I can use ns() in the splines package to include a spline term for hours, but is this the right approach? I could also see making hours a factor to allow for non-linearity as well.
It's plausible. You could also try GAMM in mgcv.
Finally, (and feel free to point me at suitable references) how does one determine the appropriate correlation structure to use in these models?
See above! Andrew
Andrew Robinson Department of Mathematics and Statistics Tel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/