Hello,
Much like Charlie Wills a year ago, I am trying to run the APE program
COMPAR.GEE with a model containing a categorical response variable and
a continuous variable.
My command code is :
compar.gee(costusdata$Syndrome ~ costusdata$Stamen, phy = costustree,
family = "binomial")
I receive the following output with an error:
Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
(Intercept) costusdata$Stamen18 costusdata$Stamen20.5
costusdata$Stamen22.5 costusdata$Stamen25.5 costusdata$Stamen27.5
costusdata$Stamen28
2.056607e+01 -3.750463e-08
-5.619142e-08 -5.644906e-08 -3.849581e-08
-5.622864e-08 -3.777595e-08
costusdata$Stamen30 costusdata$Stamen31 costusdata$Stamen32
costusdata$Stamen32.5 costusdata$Stamen35 costusdata$Stamen36.5
costusdata$Stamen37
-3.954765e-08 -3.749803e-08 -4.113214e
+01 -1.917977e+01 -3.748004e-08 -4.113214e
+01 -5.282325e-08
costusdata$Stamen37.5 costusdata$Stamen38.5 costusdata$Stamen39
costusdata$Stamen41.3 costusdata$Stamen42.5 costusdata$Stamen45
costusdata$Stamen47.5
-5.584079e-08 -4.113214e+01 -4.113214e
+01 -5.272208e-08 -2.016060e+01 -4.113214e
+01 -4.113214e+01
costusdata$Stamen50 costusdata$Stamen52.5 costusdata$Stamen55
costusdata$Stamen?
-4.113214e+01 -4.113214e+01
-5.309908e-08 -2.264551e+01
Error in gee(costusdata$Syndrome ~ costusdata$Stamen, c(1, 1, 1, 1,
1, :
Cgee: error: logistic model for probability has fitted value very
close to 1.
estimates diverging; iteration terminated.
Simon Blumberg answered Charlie's issue with "My guess is that this
combination of variables produces separation in the data: Too many
(all?) of the response 1's are in at level of VAR3, and the 0's are at
the other level (or vice versa)."
I only have the two variables.
I'm wondering if anyone has encountered this problem and how you went
about solving it. I believe that the problem appears when one has to
low (phylogenetic) replication within each (pollination mode) factor
level. Is there a way to run compar.gee if this is in fact the
problem. From the data, I want to know if there a decrease in the
continuous trait is correlated with a change in the categorical trait.
Any insight is much appreciated.
Thank you,
Jenn
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