[R] Gee with nested desgin

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Wed Apr 22 11:03:54 CEST 2009


Dear all,

Is it possible to incorporate a nested design in GEE? I have
measurements on trees that where measured in two years. The trees are
nested in plots. Each plot contains 24 trees. The number of plots is 72.
Hence we would expect 2 * 24 * 72 = 3456 data points. A few are missing,
so we end up wih 3431 data points.

This is what I have tried until now.

#assuming independence between trees and thus ignoring the plot level.
library(geepack)
geeglm(formula = Y ~ Year, id = TreeID, family = binomial, corstr =
"exchangeable")

#using waves. But I'm wondering if this is correct.
library(geepack)
geeglm(formula = Y ~ Year, id = PlotID, waves = TreeID, family =
binomial, corstr = "exchangeable")

#using a unstructured correlation on the plot level. geeglm with
unstructured correlation resulted in an out of memory error.
library(Zelig)
zelig(formula = Y ~ Year, model = "logit.gee", id = "PlotID", corstr =
"unstructured")

#Ideally I think I need a correlation matrix structured like below
(given for a plot with 3 trees). Here a1 is the correlation within a
tree, a2 the correlation between trees from the same plot and the same
year and a3 the correlation between trees from the same plot but a
different year. Does it make sense to run the model with a unstructured
correlation, calculate the average a1, a2 and a3 and use that as a fixed
working correlation?

matrix(c(
	1,    "a1", "a2", "a3", "a2", "a3", 
	"a1", 1,    "a3", "a2", "a3", "a2", 
	"a2", "a3", 1,    "a1", "a2", "a3", 
	"a3", "a2", "a1", 1,    "a3", "a2", 
	"a2", "a3", "a2", "a3", 1,    "a1", 
	"a3", "a2", "a3", "a2", "a1", 1    
	), nrow = 6)

Best regards,

Thierry

------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 
www.inbo.be 

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