Sanity check initial conditions file

Usage

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)

Arguments

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.

Value

Dataframe/ Plot.

Examples

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)
#> Read in data from out.nc, init.nc and prm.biol!
if (FALSE) { # \dontrun{
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)
} # }