atlantistools (version 0.4.3)

sc_init: Sanity check initial conditions file

Description

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

# NOT RUN {
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)
# }