sc_init: Sanity check initial conditions file
In atlantistools: Process and Visualise Output from Atlantis Models

Description Usage Arguments Value Examples

Sanity check initial conditions file

sc_init(init, prm_biol, fgs, bboxes, pred = NULL, set_avail = NULL,
  version_flag = 2)

plot_sc_init(df, mult_mum, mult_c, pred = NULL)

`init`	Character string giving the connection of the initial conditions netcdf file. The filename usually contains `init` and ends in `.nc`.
`prm_biol`	Character string giving the connection to the biological parameterfile. The filename usually contains `biol_fishing` and does end in `.prm`.
`fgs`	Character string giving the connection to the functional groups file. The filename usually contains `Groups` and does end in `.csv`.
`bboxes`	Integer vector giving the box-id of the boundary boxes. Can be created with `get_boundary`.
`pred`	Vector of predator acronyms to check. If `NULL` (default) all age based predators are selected.
`set_avail`	Numeric value. All present availabilities can be set to a specific value. Default value is `NULL` which results in no changes to the present availability matrix.
`version_flag`	The version of ATLANTIS model. 1 for bec_dev, 2 for trunk. `default is 2.`.
`df`	Dataframe to pass to `plot_sc_init()`. df should be generated with sc_init or read in from *.rda (also generated with sc_init()).
`mult_mum`	Numeric vector of multiplication factors applied to the initial mum values.
`mult_c`	Numeric vector of multiplication factors applied to the initial C values.

Dataframe/ Plot.

d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
init <- file.path(d, "INIT_VMPA_Jan2015.nc")
prm_biol <- file.path(d, "VMPA_setas_biol_fishing_Trunk.prm")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")
bboxes <- get_boundary(load_box(bgm = file.path(d, "VMPA_setas.bgm")))

data1 <- sc_init(init, prm_biol, fgs, bboxes)
## Not run: 
dir <- system.file("extdata", "gns", package = "atlantistools")
fgs <- "functionalGroups.csv"
init <- "init_simple_NorthSea.nc"
prm_biol <- "NorthSea_biol_fishing.prm"
bboxes <- get_boundary(load_box(dir = dir, bgm = "NorthSea.bgm"))
mult_mum <- seq(0.5, 10, by = 1)
mult_c <- seq(0.5, 10, by = 1)
no_avail <- FALSE
save_to_disc <- FALSE
data1 <- sc_init(dir, init, prm_biol, fgs, bboxes, save_to_disc = FALSE)
plot_sc_init(df = data1, mult_mum, mult_c)
plot_sc_init(df = data1, mult_mum, mult_c, pred = "Cod")

data2 <- sc_init(dir, init, prm_biol, fgs, bboxes, pred = "Cod", save_to_disc = FALSE)
plot_sc_init(df = data2, mult_mum, mult_c)

## End(Not run)