Description Usage Arguments Value See Also Examples
View source: R/load-dietcheck.R
Read in the atlantis dietcheck.txt file and perform some basic data transformations.
1 2 | load_dietcheck(dietcheck, fgs, prm_run, convert_names = FALSE,
report = FALSE, version_flag = 2)
|
dietcheck |
Character string giving the connection of the dietcheck file.
The filename usually contains |
fgs |
Character string giving the connection to the functional groups file.
The filename usually contains |
prm_run |
Character string giving the connection of the run parameterfile.
The filename usually contains |
convert_names |
Logical indicating if group codes are transformed to LongNames ( |
report |
Logical indicating if incomplete DietCheck information shall
be printed |
version_flag |
The version of ATLANTIS model. 1 for bec_dev, 2 for trunk. |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # 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)
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