Fix for error in pre-process (Antarctic model)

[jessmt]

#bps <- load_bps(dir, fgs, init)
bps <- c("Ice_Diatoms","Ice_Mixotrophs","Ice_Zoobiota",
         "Macrobenthos","Benthic_Filter_feeders","Ice_Bacteria")

[jessmt]

Additional error is at line

  biomass_age   <- bio_sp %>% filter(agecl > 2) %>% agg_data(groups = c("species", "agecl", "time"), fun = sum)

 Error in filter(., agecl > 2) : object 'agecl' not found 

[jporobicg]

Hi Jess,
I modified the code, So you can add the extra FGs as a Vector in the arguments of the pre.Atlantis.tools() function.
Something like this:

results <- pre.Atlantis.tools(dir         = "/home/demiurgo/Documents/2016/Oficina/ANTARCTIC-ATLANTIS-files/",
                              nc_gen      =  "output/output.nc",
                              nc_prod     =  "output/outputPROD.nc",
                              dietcheck   =  "output/outputDietCheck.txt",
                              yoy         =  "output/outputYOY.txt",
                              ssb         =  "output/outputSSB.txt",
                              version_flag =  2,
                              prm_run     =  "SO28_run.prm",
                              prm_biol    =  "SO28_biol.prm",
                              fgs         =  "AntarcticGroupsnew.csv",
                              bgm         =  "Antarctica_28.bgm",
                              init        =  "input.nc",
                              extraFG     =  c("Ice_Diatoms","Ice_Mixotrophs","Ice_Zoobiota","Ice_Bacteria")
                              )

Cheers,
Javier

[jessmt]

Oh excellent! That looks great. I will try it once I see a new commit of Output_Atlantis_tool.R. Thanks!