[R-sig-ME] Nested random factor
Renwick, A. R.
a.renwick at abdn.ac.uk
Thu Jan 22 18:10:01 CET 2009
I am running a LME with a nested random factor using the 'nlme' package and ahave a query interpreting the varince of the netsed random factor.
My data contains samples from 7 farms, and within these farms I sampled at 2 sites. The total number of sites was therefore 14, of which I sampled 4 times.
I therefore have used the following random effect:
My final model is below:
mrem<-lme(log(Nhat+1)~ Width + crop+sess +Width:sess ,random=~1|Farm/Site,data=all, method="REML",correlation=NULL,weights=varIdent(form=~1|Group3))
#part of the summary
#Linear mixed-effects model fit by REML
# Data: all
# AIC BIC logLik
# 106.2403 136.8477 -34.12013
# Formula: ~1 | Farm
# Formula: ~1 | Site %in% Farm
# (Intercept) Residual
#StdDev: 0.2458009 0.928392
#Number of Observations: 51
#Number of Groups:
# Farm Site %in% Farm
# 7 14
I would like to check that I am interpreting the random effect correctly.
1) The std dev of the between-farm variance is 0.16
2) The std dev of the between-site variance is 0.25
3) The std dev of the within-site variance is 0.93.
However, I think I may have missed out the 'nesting' part,i.e the variance within sites within farms, and the variance between sites within farms.
Any help to clarify this point would be much appreciated.
Institute of Biological & Environment Sciences
University of Aberdeen
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