[R-sig-ME] Nested random factor

[Renwick, A. R.]

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:
1|Farm/Site

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))


summary(mrem)

#part of the summary
#Linear mixed-effects model fit by REML
# Data: all
#       AIC      BIC    logLik
#  106.2403 136.8477 -34.12013
#
#Random effects:
# Formula: ~1 | Farm
#        (Intercept)
#StdDev:   0.1597866
#
# 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.

Many thanks,
Anna

Anna Renwick
Institute of Biological & Environment Sciences
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen
AB24 2TZ


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