calculate_consumed_biomass: Calculate the consumed biomass in [t] of prey j by predator...

In alketh/atlantistools: Process and Visualise Output from Atlantis Models

Description

Consumption data is extracted from output[...]PROD.nc. Age based groups are stored as "Eat_" non age based groups as "Grazing_". Units are mg N m^-3 d^-1. Factors are species, time, box and agecl (if present). We will refer to species as pred from here on to indicate the predator perspective. Diet contribution data is extracted from DietCheck.txt. Currently this only works for models based on the trunk code. Units are The consumed biomass is calculated as follows: - Calculate consumed biomass as Eat (or Grazing) * boxvolume per time, pred, agecl, box. - Convert to biomass in [t]. - Combine with diet contributions and calculate consumed biomass of prey species.

Usage

calculate_consumed_biomass(eat, grazing, dm, vol, bio_conv)

Arguments

eat	Dataframe with information about consumption for age-based groups. Should be generated with load_nc.
grazing	Dataframe with information about consumption for non-age-based groups. Should be generated with load_nc.
dm	Dataframe with information about diet contributions per predator. Should be generated with load_dietcheck using convert_names = TRUE.
vol	Dataframe with information about volume per polygon and layer. Should be generated with load_nc_physics.
bio_conv	Numeric value to transform weight in mg N to tonnes. Should be generated with get_conv_mgnbiot.

Value

Dataframe with columns 'pred', 'agecl', 'polygon', 'time', 'prey'. Consumed biomass in [t] is stored in column 'atoutput'.

Examples

# 1. Using built-in datasets.
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
prm_biol <- file.path(d, "VMPA_setas_biol_fishing_Trunk.prm")

bio_conv <- get_conv_mgnbiot(prm_biol = prm_biol)

df <- calculate_consumed_biomass(eat = ref_eat, grazing = ref_grazing, dm = ref_dm,
                                 vol = ref_vol, bio_conv = bio_conv)

# 2. Read in dataframes from existing Atlantis simulation.
bboxes <- get_boundary(boxinfo = load_box(file.path(d, "VMPA_setas.bgm")))
nc_gen <- file.path(d, "outputSETAS.nc")
nc_prod <- file.path(d, "outputSETASPROD.nc")
prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")
init <- file.path(d, "INIT_VMPA_Jan2015.nc")

bps <- load_bps(fgs = fgs, init = init)

groups_age <- c("Planktiv_S_Fish", "Pisciv_S_Fish")
groups_rest <- c("Cephalopod", "Megazoobenthos", "Diatom", "Lab_Det", "Ref_Det")

df_eat <- load_nc(nc = nc_prod, bps = bps, fgs = fgs,
               select_groups = groups_age, select_variable = "Eat",
               prm_run = prm_run, bboxes = bboxes)
df_grz <- load_nc(nc = nc_prod, bps = bps, fgs = fgs,
               select_groups = groups_rest, select_variable = "Grazing",
               prm_run = prm_run, bboxes = bboxes)
df_dm <- load_dietcheck(dietcheck = file.path(d, "outputSETASDietCheck.txt"),
                        fgs = fgs, prm_run = prm_run, version_flag = 2, convert_names = TRUE)
vol <- load_nc_physics(nc = nc_gen, select_physics = "volume",
                       prm_run = prm_run, bboxes = bboxes, aggregate_layers = FALSE)

df <- calculate_consumed_biomass(eat = df_eat, grazing = df_grz, dm = df_dm,
                                 vol = vol, bio_conv = bio_conv)

alketh/atlantistools documentation built on Oct. 30, 2021, 5:46 a.m.