Question NicheMapR - Run a DEB simulation with the NicheMapR ectotherm model

[Luisa Diele-Viegas]

Hey all,

I hope you are doing well!

I've been working on gathering data on the Golden Frog to run a DEB model for the species. Although there's not a huge amount of data available, I managed to find some helpful info and ran the MATLAB routine for the species. My goal, however, is to run the NicheMapR's Ectotherm model with the DEB model on, but the routine for that indicates that the species must be in the AmP collection, which is not the case for my species. In this sense, is there a way of inputting the species' parameters manually in R, so that I can proceed with the analysis? 

Thank you in advance for your help!

Sincerely

--

Luisa M. Diele-Viegas, Ph. D.

Ecology and Evolution

she/her

Researcher at the University of Mississippi, United States

Permanent Professor at the Graduate Program of Ecology, Federal University of Bahia, Brazil
Collaborator Professor at the Graduate Program of Zoology, State University of Santa Cruz, Brazil

Coordinator of the Laboratory of (Bio)Diversity in the Anthropocene - BioDivA Lab
Chair of the Brazilian Chapter of the Organization for Women in Science for the Developing World (OWSD)

Chair of the Kunhã Asé Network of Women in Science

Chair of the Brazilian Association of Ecological and Conservation Sciences (ABECO)

Council Member of the European Society for Evolutionary Biology

Member of the Global Young Academy

Young Affiliate of The World Academy of Sciences

Contact: +55 (82) 9.9193-3600

Lattes: http://lattes.cnpq.br/9032844663306862

ORCID: https://orcid.org/0000-0002-9225-4678

"May the desire to see something not obscure what the data reveals"  - TC Ávila-Pires

[NicheMapR]

Hi Luisa,

At the end of your run file paste

load('results_Your_species.mat');
[stat, txtStat] = statistics_st(metaPar.model, par);
save('stat_Your_species.mat', 'stat')

pars <- readMat('DEB models/Your_species/results_Your_species.mat')
par.names <- unlist(labels(pars$par))
for(i in 1:length(par.names)){
  assign(par.names[i], unlist(pars$par[i]))
}
stat <- readMat('DEB models/Your_species/stat_Your_species.mat')
stat.names <- unlist(labels(stat$stat))
for(i in 1:length(stat.names)){
  assign(stat.names[i], unlist(stat$stat[i]))
}

Also, as I might have mentioned, the amphibian functionality isn't working yet in the ectotherm model so you'd have to manually alter the microclimate input to make it aquatic initially if you're working on a species with an aquatic tadpole/eggs, and then restart at metamorphosis under terrestrial microclimate conditions.

All the best,
Mike

[Luisa Diele-Viegas]

Thank you Mike! It worked :)

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