Read in the atlantis dietcheck.txt file and perform some basic data transformations.
load_dietcheck(dietcheck, fgs, prm_run, convert_names = FALSE,
report = FALSE, version_flag = 2)
Character string giving the connection of the dietcheck file.
The filename usually contains Dietcheck
and ends in .txt
".
Character string giving the connection to the functional groups file.
The filename usually contains Groups
and does end in .csv
.
Character string giving the connection of the run parameterfile.
The filename usually contains run_fishing
and ends in .prm
".
Logical indicating if group codes are transformed to LongNames (TRUE
)
or not (default = FALSE
).
Logical indicating if incomplete DietCheck information shall
be printed TRUE
or not FALSE
.
The version of ATLANTIS model. 1 for bec_dev, 2 for trunk. default is 2.
.
A data.frame
in long format with the following column names:
time, pred, habitat, prey and atoutput (i.e., variable).
Other load functions: load_box
,
load_bps
, load_fgs
,
load_init_age
, load_init
,
load_nc_physics
, load_nc
,
load_rec
, load_spec_mort
,
load_txt
# NOT RUN {
# Apply to bec-dev models.
d <- system.file("extdata", "setas-model-new-becdev", package = "atlantistools")
dietcheck <- file.path(d, "outputSETASDietCheck.txt")
fgs <- file.path(d, "SETasGroups.csv")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_New.prm")
diet <- load_dietcheck(dietcheck, fgs, prm_run, version_flag = 1)
head(diet, n = 10)
# Apply to trunk models.
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
dietcheck <- file.path(d, "outputSETASDietCheck.txt")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
diet <- load_dietcheck(dietcheck, fgs, prm_run)
head(diet, n = 10)
# }
Run the code above in your browser using DataLab