Hello,
I was wondering if there’s a way to get trace plots from the multiSpeciesTP model runs? When I try what works with the TPmodel function I get this error message:
adult_models <- multiSpeciesTP(adultList, model = "twoBaselinesFull",
n.adapt = 20000, n.iter = 20000,
burnin = 20000, n.chains = 5, print = FALSE)
posterior.samples <- posteriorTP(model = adult_models, n.iter = 20000,
variable.names = c("TP", "alpha"))
Error in model$iter() : attempt to apply non-function
So then I’m not able to take the next step of:
summary(posterior.samples) #use median values from #1 for estimates
#Diagnostic of model fit, use to check if iterations are enough and model has converged
posterior.combined <- coda::mcmc(do.call(rbind, posterior.samples))
getPosteriorMode(posterior.combined) #central tendency best described by mode, according to example
plot(posterior.samples)
The multiSpeciesTP function is definitely working for me, and I’m getting output in the dataframe that seems good, but I would like to check some diagnostics if possible.
Thank you!
Bethany Bethke
Fisheries Research Scientist | Fish and Wildlife
Minnesota Department of Natural Resources
5351 N Shore Dr
Duluth MN, 55804
https://www.dnr.state.mn.us/fisheries/management/research.html
adult_models <- multiSpeciesTP(adultList, model = "twoBaselinesFull",
n.adapt = 20000, n.iter = 20000,
burnin = 20000, n.chains = 5, print = TRUE)
--
To download tRophicPosition package visit https://github.com/clquezada/tRophicPosition
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