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This repository has been archived by the owner on Jun 13, 2023. It is now read-only.
I've got a situation whereby checking the diagnostics related to parameter estimation shows me that the following parameters are hitting their (upper) bounds in the case of some species. Might you have any advice on 1) what to try in order to avoid the problem and 2) what the implications might be?
"logetaE1"
"logetaE2"
"logetaO2"
The upper bounds for each of those seems to have a default value of 3.3396581.
The command used to check the diagnostics table:
print( Opt$diagnostics[, c('Param','Lower', 'MLE', 'Upper', 'final_gradient')] ))
And the instructions that led me to check them: "...print the diagnostics generated during parameter estimation, and I confirm that (1) no parameter is hitting an upper or lower bound and (2) the final gradient for each fixed-effect is close to zero."
Thanks,
Jock
The text was updated successfully, but these errors were encountered:
logeta is the reciprocal of the log-standard deviation for each spatial (O) or spatio-temporal (E) term (1 refers to encounter probability; 2 refers to positive catch rate). When it hits the upper bound, it is essentially driving the SD for that term to zero (i.e., no spatial or spatio-temporal variation in a given model component).
You can do two things:
Turn off the corresponding spatial/spatio-temporal component via FieldConfig. This can of course be automated in the R script
Increase the upper bound by, corresponding to a lower minimum SD, and then not worry about it. If the spatial/spatio-temporal term has a MargSigma below say 0.001, then the maximum likelihood estimate is essentially "turning it off". This can cause problems with estimating standard errors sometimes, but if it doesn't then I think this option is fine.
I include strong advice about not hitting bounds in the markdown document, but it applies more to the range parameters logkappa.
Hi Jim and all
I've got a situation whereby checking the diagnostics related to parameter estimation shows me that the following parameters are hitting their (upper) bounds in the case of some species. Might you have any advice on 1) what to try in order to avoid the problem and 2) what the implications might be?
"logetaE1"
"logetaE2"
"logetaO2"
The upper bounds for each of those seems to have a default value of 3.3396581.
The command used to check the diagnostics table:
print( Opt$diagnostics[, c('Param','Lower', 'MLE', 'Upper', 'final_gradient')] ))
And the instructions that led me to check them: "...print the diagnostics generated during parameter estimation, and I confirm that (1) no parameter is hitting an upper or lower bound and (2) the final gradient for each fixed-effect is close to zero."
Thanks,
Jock
The text was updated successfully, but these errors were encountered: