Dear list members, I am starting with generalized mixed models and I am
having some trouble I hope someone could help me with.
We are trying to understand the invasiveness of algae inside and outside
MPA, to do so our sampling was set with a nested desing:
Protected vs nonProtected
4 Locations (protected) vs 4 Locations (nonProtected)
Exposed vs Semiexposed at each location
1 transect per sampling point (total 16)
5 quadrants per transect
str(dataGLMMADMB)
'data.frame': 80 obs. of 4 variables:
$ Location: Factor w/ 4 levels "Cies1","Cies2",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Protection: Factor w/ 2 levels "Control","Protected": 1 1 1 1 1 2 2 2 2
2 ...
$ Exposure: Factor w/ 2 levels "Exposed","Semiexposed": 1 1 1 1 1 1 1 1 1
1 ...
$ Biomass: num 124.8 104.8 139.2 102.6 62.9 ...
First I ran it as a Poission distribution (after round the Biomass values)
to be able to fit a zeroInflation model:
Model_ADMB_P<-glmmadmb(Biomass~Protection+Exposure+
Protection:Exposure+(1|
Protection/Location),data=GLMMADMB_P, zeroInflation=TRUE,
family="Poisson")
Parameters were estimated, but standard errors were not: the most likely
problem is that the curvature at MLE was zero or negative
Error in glmmadmb(Biomass ~ Protection + Exposure + Protection:Exposure +
:
The function maximizer failed (couldn't find parameter file)
Troubleshooting steps include (1) run with 'save.dir' set and inspect
output files; (2) change run parameters: see '?admbControl';(3) re-run with
debug=TRUE for more information on failure mode
Adem?s: Warning message:
comando ejecutado 'C:\WINDOWS\system32\cmd.exe /c glmmadmb -maxfn 500
-maxph 5 -noinit -shess' tiene estatus 1
Then I though that since my data is continuous I'd better run the model
with a gamma family, however, when I do run it with gamma I got the
following error:
Model_ADMB_G<-glmmadmb(Biomass~Protection+Exposure+
Protection:Exposure+(1|
Protection/Location),data=GLMMADMB_P, family="gamma")
Error in glmmadmb(Biomass ~ Protection + Exposure + Protection:Exposure +
:
The function maximizer failed (couldn't find parameter file)
Troubleshooting steps include (1) run with 'save.dir' set and inspect
output files; (2) change run parameters: see '?admbControl';(3) re-run with
debug=TRUE for more information on failure mode
Adem?s: Warning message:
comando ejecutado 'C:\WINDOWS\system32\cmd.exe /c glmmadmb -maxfn 500
-maxph 5 -noinit -shess' tiene estatus 1
However, when I run it as a Poisson distribution with zeroInflated values
but with no nested design and Location effect either, it ran ok
Model_ADMB_P1<-glmmadmb(Biomass~Protection*Exposure,data=GLMMADMB_P,
zeroInflation=TRUE, family="Poisson")
Call:
glmmadmb(formula = Biomass ~ Protection * Exposure, data = GLMMADMB_P,
family = "Poisson", zeroInflation = TRUE)
AIC: 1570.7
Coefficients:
Estimate Std. Error z value
Pr(>|z|)
(Intercept) 4.71e+00 3.18e-02 148.0
<2e-16
ProtectionProtected -5.53e-01 5.00e-02 -11.1
<2e-16
ExposureSemiexposed -3.83e+01 2.22e+05 0.0
1
ProtectionProtected:ExposureSemiexposed 3.64e+01 2.22e+05 0.0
1
(Intercept) ***
ProtectionProtected ***
ExposureSemiexposed
ProtectionProtected:ExposureSemiexposed
---
Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
Number of observations: total=80
Zero-inflation: 0.30908 (std. err.: 0.071433 )
Log-likelihood: -780.37
I can not understat the solutions to these errors, can anyone please help
me out?
I really appreciate it!
Thanks in advance,
--
Andreu Blanco Cartagena
Si no ?s imprescindible, no imprimeixis aquest e-mail. Estalviar paper
ajuda a protegir el medi ambient.
Si no es imprescindible, no imprimas este e-mail. Ahorrar papel ayuda a
proteger el medio ambiente.
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