# install packages
install.packages('devtools')   ## you need to do this step just once
# running
library("devtools")
install_github('Atlantis-Ecosystem-Model/ReactiveAtlantis', force=TRUE, dependencies=TRUE)
library("ReactiveAtlantis")

nc.current  <- 'your_current_output.nc'
nc.old      <- 'your_previous_output.nc'
grp.csv     <- 'your_groups_definition_file.csv'
bgm.file    <- 'your_spatial_configuration_file.bgm'
cum.depths  <- c(0, 20, 50, 150, 250, 400, 650, 1000, 4300) ## This should be the cummulative depth of your model
## individual file
compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths)
## compare to previuos run
compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths)

biom        <- 'your_BiomIndx.txt'
diet.file   <- 'your_DietCheck.txt'
bio.age     <- 'your_AgeBiomIndx.txt' ## optional file. just if you want to check the predation by age
grp.csv     <- 'your_groups_definition_file.csv'
## Predation by Age
predation(biom, grp.csv, diet.file, bio.age)
## No predation by Age
predation(biom, grp.csv, diet.file, bio.age = NULL)

prm.file    <- 'your_prm_file.prm'
nc.initial  <- 'your_initial_conditions.nc'
grp.csv     <- 'your_groups_definition_file.csv'
bgm.file    <- 'your_spatial_configuration_file.bgm'
cum.depths  <- c(0, 20, 50, 150, 250, 400, 650, 1000, 4300) ## This should be the cummulative depth of your model
feeding.mat(prm.file, grp.file, nc.initial, bgm.file, cum.depths)

grp.csv     <- 'your_groups_definition_file.csv'
prm.file    <- 'your_prm_file.prm'
diet.file   <- 'your_DietCheck.txt'
food.web(diet.file, grp.file)
## optional you can explore the food web by polygon
food.web(diet.file, grp.file, diet.file.bypol)
## diet.file.bypol Detailed diet check file, this can be obtained as an extra output from Atlantis "DetailedDietCheck.txt". To get this file from Atlantis turn on the option "flagdietcheck" on the Run.prm file.

nc.initial  <- 'your_initial_conditions.nc'
nc.current  <- 'your_current_output.nc'
grp.csv     <- 'your_groups_definition_file.csv'
prm.file    <- 'your_prm_file.prm'
growth.pp(nc.initial, grp.csv, prm.file, nc.current)

nc.initial  <- 'your_initial_conditions.nc'
nc.current  <- 'your_current_output.nc'
yoy.file    <- 'your_yoy_file.txt'
grp.csv     <- 'your_groups_definition_file.csv'
prm.file    <- 'your_prm_file.prm'
recruitment.cal(nc.initial, nc.current, yoy.file, grp.file, prm.file)

catch.nc             <- 'your_output_CATCH.nc'
ext.catch.total      <- 'external_catch_time_serie.csv'
ext.catch.by.fleet   <- 'external_catch_time_serie_by_fleets.csv'
cum.depths  <- c(0, 20, 50, 150, 250, 400, 650, 1000, 4300) ## This should be the cummulative depth of your model
fsh.csv     <- 'your_fisheries_definition_file.csv'
bgm.file    <- 'your_spatial_configuration_file.bgm'
grp.csv     <- 'your_groups_definition_file.csv'
catch(grp.csv, fsh.csv, catch.nc, ext.catch.total, ext.catch.total)