[R-sig-ME] Unrealistic coefficient values from an MCMCglmm mixed model
Ronan James Osullivan
113499328 @end|ng |rom um@||@ucc@|e
Mon Apr 1 13:56:39 CEST 2019
Dear forum,
I am struggling with the interpretation of the coefficients from a glmm
implemented using MCMCglmm. My data set has lifetime reproductive success
(LRS) for individual fish and associated climatic variables (NAO and
Temperature) are indexed to each fish. I also know the genetic type of each
fish (A or B). In total, I have 2938 observations with 1321 A fish and 1671
B fish.
I ran the following model:
model<- MCMCglmm(LRS~GeneticType*NAO+
GeneticType *Temp,
random = ~Year_of_Spawning,
family = "poisson",
data = data,
verbose = TRUE,
nitt = 1010000, burnin = 1000, thin = 1000)
Which gave the following summary:
G-structure: ~Year_of_Spawning
post.mean l-95% CI u-95% CI
eff.samp
Year_of_Spawning 0.792 0.1521 1.934
1111
R-structure: ~units
post.mean l-95% CI u-95% CI
eff.samp
units 1.257 1.029
1.488 1447
Location effects: LRS ~ GeneticType *NAO + GeneticType * Temp-1
post.mean l-95% CI u-95% CI
eff.samp pMCMC
GeneticTypeA 5.5510 -4.5345 15.9627
1009.0 0.2577
GeneticTypeB -2.8334 -10.6020 8.0720
1009.0 0.4916
NAO 0.6995 -0.6520 1.9512
918.3 0.2220
Temp -8.2807 -18.7522 1.8865
1009.0 0.0991 .
GeneticTypeB:NAO -0.7729 -1.2302 -0.3119
1009.0 <0.001 ***
GeneticTypeB:Temp 9.8697 4.7849 15.4317
1009.0 <0.001 ***
My issue is that the predicted LRS values for Genetic Type A are far too
high. The intercept for A fish is 5.551, and exp(5.551) = expected mean for
H fish when Temp=0 and NAO = 0 is 244.7. When I solve for LRS for Type A
fish at a given NAO or temperature (holding the other one constant), I get
incredibly high values.
The predicted LRS for Genetic Type B is exp(-2.8334)=0.05881255 which is
far more realistic for my study system
Am I somehow mis-specifying the model or mis-calculating LRS with respect
to each genetic type?
Cheers,
Ronan
--
Ronan O'Sullivan | Ph.D student | School of Biological, Earth and
Environmental Sciences, University College Cork, Ireland |
http://fisheye.ucc.ie/toms-team/ <http://fisheye.ucc.ie/toms-team/>
Irish Ecological Association - Ordinary Committee Member
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