multimodelTP - what's missing?

[Isa Wallin Kihlberg]

Dear Dr. Quezada-Romegialli,

I am currently trying to establish the trophic position of an invasive fish species, using your package tRophicPosition. The data is from two different areas, and for each area I have two years of data. There are two different baseline species, one suspension-filter feeder and one suspension-deposit feeder. I use your vignette and an online tutorial and everything works fine until I’m running the actual model – then nothing happens. I understand that I’m probably missing something in a previous step, but I can’t identify what’s missing.

 

rg_tp_list <- extractIsotopeData(rg_tp_data,

                               consumersColumn = "class",

                               b1 = "Macoma",

                               b2 = "Mytilus",

                               baselineColumn = "species",

                               groupsColumn = "site",

                               deltaC = TDF_values$deltaC,

                               deltaN = TDF_values$deltaN)

 

for (site in rg_tp_list){

  plot(site)

  print(summary(site))

}                     #everything works fine until here (as far as I can tell)

 

# but here nothing really happens

cluster <- parallel::makePSOCKcluster(parallel::detectCores())

 

system.time(rg_TPmodels <- parallel::parLapply(cluster,

                                                    rg_tp_list,

                                                    multiModelTP,

                                                    lambda = 2, #Trophic position of source

                                                    adapt = 20000,

                                                    n.iter = 20000,

                                                    burnin = 2000,

                                                    n.chains = 5,

                                                    model = "twoBaselinesFull"))

 

#parallel::stopCluster(cluster)

 

 

The only output I get is

user  system elapsed

0.02    0.00   87.29

 

I attach two of the density plots and a few rows of my data.

 

Any help or guidance would be highly appreciated!

 

Best wishes,

Isa

 

Isa Wallin Kihlberg
PhD Student

Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences

Department of Aquatic Resources (SLU Aqua)

Institute of Coastal Research
Skolgatan 6, 742 42 Öregrund, Sweden

Phone: +46 (0)10 478 4162
isa.w...@slu.se, www.slu.se/akvatiskaresurser

 

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