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R/build_model_parameters.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
build_model_parameters
#
# build_model_parameters.R
#
#' Build entire set of model parameters combining fixed, physical, fleet model output, plus some biomass thresholds
#'
#' @param model model object
#' @param uptakes prey uptake levels
#' @param fleet.model.output fleet model output
#'
#' @return model parameter vector
#'
#' @noRd
#
# ------------------------------------------------------------------------------
build_model_parameters <- function(model, uptakes, fleet.model.output) {
# Unpack:
data <- elt(model, "data")
fixed.parms <- elt(data, "fixed.parameters")
xprotect_PF <- elt(fixed.parms, "xprotect_PF") # used in calculations
xprotect_DF <- elt(fixed.parms, "xprotect_DF")
xprotect_MF <- elt(fixed.parms, "xprotect_MF")
xprotect_SB <- elt(fixed.parms, "xprotect_SB")
xprotect_CB <- elt(fixed.parms, "xprotect_CB")
xprotect_CZ <- elt(fixed.parms, "xprotect_CZ")
xprotect_BD <- elt(fixed.parms, "xprotect_BD")
xprotect_SL <- elt(fixed.parms, "xprotect_SL")
xprotect_CT <- elt(fixed.parms, "xprotect_CT")
xprotect_KP <- elt(fixed.parms, "xprotect_KP")
CZ_inedible <- elt(fixed.parms, "CZ_inedible")
physical.parms <- elt(data, "physical.parameters")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
fleet.vector <- elt(fleet.model.output, "fleet_vector")
fitted.parms <- elt(data, "fitted.parameters")
#--------------------------------------------------------------------------
#Load all the parameter values into a single vector which will be passed to the model function.
model.parameters <- c(
#First the parameters for morphological and physical configuration of the model
#These occupy elements 1:55 of parms
thik_so = elt(physical.parms, "so_depth"),
thik_d = elt(physical.parms, "d_depth"),
thik_si = elt(physical.parms, "si_depth"),
thik_b = elt(physical.parms, "bx_depth"),
shallowprop = x_shallowprop,
# volume_s=xs_volume,
# volume_d=xd_volume,
area_s0 = elt(physical.parms, "x_area_s0"),
area_s1 = elt(physical.parms, "x_area_s1"),
area_s2 = elt(physical.parms, "x_area_s2"),
area_s3 = elt(physical.parms, "x_area_s3"),
area_d0 = elt(physical.parms, "x_area_d0"),
area_d1 = elt(physical.parms, "x_area_d1"),
area_d2 = elt(physical.parms, "x_area_d2"),
area_d3 = elt(physical.parms, "x_area_d3"),
rock_s1 = elt(physical.parms, "x_rock_s1"),
rock_s2 = elt(physical.parms, "x_rock_s2"),
rock_s3 = elt(physical.parms, "x_rock_s3"),
rock_d1 = elt(physical.parms, "x_rock_d1"),
rock_d2 = elt(physical.parms, "x_rock_d2"),
rock_d3 = elt(physical.parms, "x_rock_d3"),
nonrock_s = elt(physical.parms, "x_nonrock_s"),
nonrock_d = elt(physical.parms, "x_nonrock_d"),
thik_x_s1 = elt(physical.parms, "x_depth_s1"),
thik_x_s2 = elt(physical.parms, "x_depth_s2"),
thik_x_s3 = elt(physical.parms, "x_depth_s3"),
thik_x_d1 = elt(physical.parms, "x_depth_d1"),
thik_x_d2 = elt(physical.parms, "x_depth_d2"),
thik_x_d3 = elt(physical.parms, "x_depth_d3"),
porosity_s1 = elt(physical.parms, "x_poros_s1"),
porosity_s2 = elt(physical.parms, "x_poros_s2"),
porosity_s3 = elt(physical.parms, "x_poros_s3"),
porosity_d1 = elt(physical.parms, "x_poros_d1"),
porosity_d2 = elt(physical.parms, "x_poros_d2"),
porosity_d3 = elt(physical.parms, "x_poros_d3"),
sed_wat_dif_s1 = elt(physical.parms, "Kxw_s1"),
sed_wat_dif_s2 = elt(physical.parms, "Kxw_s2"),
sed_wat_dif_s3 = elt(physical.parms, "Kxw_s3"),
sed_wat_dif_d1 = elt(physical.parms, "Kxw_d1"),
sed_wat_dif_d2 = elt(physical.parms, "Kxw_d2"),
sed_wat_dif_d3 = elt(physical.parms, "Kxw_d3"),
#Reference value of log10(Kxw) for estimating habitat specific sediment geochemistry rates
sed_ref_Kxw = elt(physical.parms, "ref_Kxw"),
#Bioturbation depth and erosion depths of the sediment as proportions of active sediment layer thickness
bioturb_depth_s1 = elt(physical.parms, "xbioturb_depth_s1"),
bioturb_depth_s2 = elt(physical.parms, "xbioturb_depth_s2"),
bioturb_depth_s3 = elt(physical.parms, "xbioturb_depth_s3"),
bioturb_depth_d1 = elt(physical.parms, "xbioturb_depth_d1"),
bioturb_depth_d2 = elt(physical.parms, "xbioturb_depth_d2"),
bioturb_depth_d3 = elt(physical.parms, "xbioturb_depth_d3"),
erosion_depth_s1 = elt(physical.parms, "xerosion_depth_s1"),
erosion_depth_s2 = elt(physical.parms, "xerosion_depth_s2"),
erosion_depth_s3 = elt(physical.parms, "xerosion_depth_s3"),
erosion_depth_d1 = elt(physical.parms, "xerosion_depth_d1"),
erosion_depth_d2 = elt(physical.parms, "xerosion_depth_d2"),
erosion_depth_d3 = elt(physical.parms, "xerosion_depth_d3"),
lightSPM_intercept = elt(physical.parms, "xlightSPM_intercept"),
lightSPM_slope = elt(physical.parms, "xlightSPM_slope"),
inshore_phyt_prop_depth = elt(physical.parms, "xinshore_phyt_prop_depth"),
inshore_kelp_prop_depth = elt(physical.parms, "xinshore_kelp_prop_depth"),
# parms so far: 56
#------ Parameters transferred in from the fishing fleet model ----------
# The fleet vector has 250 elements, so
# these occupy elemnts 57:307 of the parms vector
#Vector of parameters from the fishing fleet configuration model
fleet.vector,
#----- Ecological model parameters -------
#Q10 temperature coefficients for heteroptophs, autotrophs and reference temperature
qtena = elt(fixed.parms, "qtenauto"),
qtenh = elt(fixed.parms, "qtenhetero"),
qtenm = elt(fixed.parms, "qtenmetabol"),
qtenr = elt(fixed.parms, "qtenrreft"),
#Light saturation parameter for phytoplankton N uptake
Lmaxup_phyt = elt(fixed.parms, "satlight_phyt"),
#Light saturation parameter for kelp C uptake
Lmaxup_kelp = elt(fixed.parms, "satlight_kelp"),
#Maximum and minimum values of NC ratio in kelp
NCmax_kelp = elt(fixed.parms, "kelp_ncmax"),
NCmin_kelp = elt(fixed.parms, "kelp_ncmin"),
#Then the fitted parameters
#Wave dependent beach-case rate parameter for kelp_debris
wave_beach_kelpdebris = elt(fitted.parms, "xwave_kelpdebris"),
#Maximum uptake rate of carbon by kelp
umaxC_kelp = elt(fitted.parms, "uC_kelp"),
#Density dependent carbon exudation rate parameter for kelp
exudeC_kelp = elt(fitted.parms, "ddexudC_kelp"),
#Density dependent self shading paramater for carbon uptake by kelp
selfshade_kelp = elt(fitted.parms, "xkelpshade"),
#Nutrient uptake by kelp at the reference temperature
uNIT_kelpt = elt(uptakes, "uNIT_kelpt"),
hsNIT_kelp = elt(uptakes, "hsNIT_kelp"),
uAMM_kelpt = elt(uptakes, "uAMM_kelpt"),
hsAMM_kelp = elt(uptakes, "hsAMM_kelp"),
#Nutrient uptake by phytoplankton at the reference temperature
uNIT_phytt = elt(uptakes, "uNIT_phytt"),
hsNIT_phyt = elt(uptakes, "hsNIT_phyt"),
uAMM_phytt = elt(uptakes, "uAMM_phytt"),
hsAMM_phyt = elt(uptakes, "hsAMM_phyt"),
#Feeding by mesozooplankton at the reference temperature
uphyt_omnit = elt(uptakes, "uphyt_omnit"),
hsphyt_omni = elt(uptakes, "hsphyt_omni"),
udet_omnit = elt(uptakes, "udet_omnit"),
hsdet_omni = elt(uptakes, "hsdet_omni"),
ubenthslar_omnit = elt(uptakes, "ubenthslar_omnit"),
hsbenthslar_omni = elt(uptakes, "hsbenthslar_omni"),
ubenthclar_omnit = elt(uptakes, "ubenthclar_omnit"),
hsbenthclar_omni = elt(uptakes, "hsbenthclar_omni"),
#Feeding by carnivorous zooplankton at the reference temperature
uomni_carnt = elt(uptakes, "uomni_carnt"),
hsomni_carn = elt(uptakes, "hsomni_carn"),
ubenthslar_carnt = elt(uptakes, "ubenthslar_carnt"),
hsbenthslar_carn = elt(uptakes, "hsbenthslar_carn"),
ubenthclar_carnt = elt(uptakes, "ubenthclar_carnt"),
hsbenthclar_carn = elt(uptakes, "hsbenthclar_carn"),
ufishplar_carnt = elt(uptakes, "ufishplar_carnt"),
hsfishplar_carn = elt(uptakes, "hsfishplar_carn"),
ufishdlar_carnt = elt(uptakes, "ufishdlar_carnt"),
hsfishdlar_carn = elt(uptakes, "hsfishdlar_carn"),
#Feeding by larvae of pelagic fish at the reference temperature
uomni_fishplart = elt(uptakes, "uomni_fishplart"),
hsomni_fishplar = elt(uptakes, "hsomni_fishplar"),
ubenthslar_fishplart = elt(uptakes, "ubenthslar_fishplart"),
hsbenthslar_fishplar = elt(uptakes, "hsbenthslar_fishplar"),
ubenthclar_fishplart = elt(uptakes, "ubenthclar_fishplart"),
hsbenthclar_fishplar = elt(uptakes, "hsbenthclar_fishplar"),
#Feeding by pelagic fish at the reference temperature
uomni_fishpt = elt(uptakes, "uomni_fishpt"),
hsomni_fishp = elt(uptakes, "hsomni_fishp"),
ucarn_fishpt = elt(uptakes, "ucarn_fishpt"),
hscarn_fishp = elt(uptakes, "hscarn_fishp"),
ubenthslar_fishpt = elt(uptakes, "ubenthslar_fishpt"),
hsbenthslar_fishp = elt(uptakes, "hsbenthslar_fishp"),
ubenthclar_fishpt = elt(uptakes, "ubenthclar_fishpt"),
hsbenthclar_fishp = elt(uptakes, "hsbenthclar_fishp"),
ufishdlar_fishpt = elt(uptakes, "ufishdlar_fishpt"),
hsfishdlar_fishp = elt(uptakes, "hsfishdlar_fishp"),
ufishplar_fishpt = elt(uptakes, "ufishplar_fishpt"),
hsfishplar_fishp = elt(uptakes, "hsfishplar_fishp"),
#Feeding by migratory fish at the reference temperature
uomni_fishmt = elt(uptakes, "uomni_fishmt"),
hsomni_fishm = elt(uptakes, "hsomni_fishm"),
ucarn_fishmt = elt(uptakes, "ucarn_fishmt"),
hscarn_fishm = elt(uptakes, "hscarn_fishm"),
ubenthslar_fishmt = elt(uptakes, "ubenthslar_fishmt"),
hsbenthslar_fishm = elt(uptakes, "hsbenthslar_fishm"),
ubenthclar_fishmt = elt(uptakes, "ubenthclar_fishmt"),
hsbenthclar_fishm = elt(uptakes, "hsbenthclar_fishm"),
ufishdlar_fishmt = elt(uptakes, "ufishdlar_fishmt"),
hsfishdlar_fishm = elt(uptakes, "hsfishdlar_fishm"),
ufishplar_fishmt = elt(uptakes, "ufishplar_fishmt"),
hsfishplar_fishm = elt(uptakes, "hsfishplar_fishm"),
#Feeding by larvae of demersal fish at the reference temperature
uomni_fishdlart = elt(uptakes, "uomni_fishdlart"),
hsomni_fishdlar = elt(uptakes, "hsomni_fishdlar"),
ubenthslar_fishdlart = elt(uptakes, "ubenthslar_fishdlart"),
hsbenthslar_fishdlar = elt(uptakes, "hsbenthslar_fishdlar"),
ubenthclar_fishdlart = elt(uptakes, "ubenthclar_fishdlart"),
hsbenthclar_fishdlar = elt(uptakes, "hsbenthclar_fishdlar"),
#Feeding by demersal fish at the reference temperature
ucarn_fishdt = elt(uptakes, "ucarn_fishdt"),
hscarn_fishd = elt(uptakes, "hscarn_fishd"),
ubenths_fishdt = elt(uptakes, "ubenths_fishdt"),
hsbenths_fishd = elt(uptakes, "hsbenths_fishd"),
ubenthc_fishdt = elt(uptakes, "ubenthc_fishdt"),
hsbenthc_fishd = elt(uptakes, "hsbenthc_fishd"),
ufishplar_fishdt = elt(uptakes, "ufishplar_fishdt"),
hsfishplar_fishd = elt(uptakes, "hsfishplar_fishd"),
ufishdlar_fishdt = elt(uptakes, "ufishdlar_fishdt"),
hsfishdlar_fishd = elt(uptakes, "hsfishdlar_fishd"),
ufishp_fishdt = elt(uptakes, "ufishp_fishdt"),
hsfishp_fishd = elt(uptakes, "hsfishp_fishd"),
ufishm_fishdt = elt(uptakes, "ufishm_fishdt"),
hsfishm_fishd = elt(uptakes, "hsfishm_fishd"),
ufishd_fishdt = elt(uptakes, "ufishd_fishdt"),
hsfishd_fishd = elt(uptakes, "hsfishd_fishd"),
udisc_fishdt = elt(uptakes, "udisc_fishdt"),
hsdisc_fishd = elt(uptakes, "hsdisc_fishd"),
ucorp_fishdt = elt(uptakes, "ucorp_fishdt"),
hscorp_fishd = elt(uptakes, "hscorp_fishd"),
#Feeding by larvae of suspension feeding benthos at the reference temperature
uphyt_benthslart = elt(uptakes, "uphyt_benthslart"),
hsphyt_benthslar = elt(uptakes, "hsphyt_benthslar"),
udet_benthslart = elt(uptakes, "udet_benthslart"),
hsdet_benthslar = elt(uptakes, "hsdet_benthslar"),
#Feeding by larvae of carnivore/scavenge feeding benthos at the reference temperature
uphyt_benthclart = elt(uptakes, "uphyt_benthclart"),
hsphyt_benthclar = elt(uptakes, "hsphyt_benthclar"),
udet_benthclart = elt(uptakes, "udet_benthclart"),
hsdet_benthclar = elt(uptakes, "hsdet_benthclar"),
#Feeding by suspension feeding benthos at the reference temperature
uphyt_benthst = elt(uptakes, "uphyt_benthst"),
hsphyt_benths = elt(uptakes, "hsphyt_benths"),
udet_benthst = elt(uptakes, "udet_benthst"),
hsdet_benths = elt(uptakes, "hsdet_benths"),
used_benthst = elt(uptakes, "used_benthst"),
hssed_benths = elt(uptakes, "hssed_benths"),
#Feeding by carnivorous benthos at the reference temperature
ubenths_benthct = elt(uptakes, "ubenths_benthct"),
hsbenths_benthc = elt(uptakes, "hsbenths_benthc"),
ukelp_benthct = elt(uptakes, "ukelp_benthct"),
hskelp_benthc = elt(uptakes, "hskelp_benthc"),
ukelpdebris_benthct = elt(uptakes, "ukelpdebris_benthct"),
hskelpdebris_benthc = elt(uptakes, "hskelpdebris_benthc"),
ucorp_benthct = elt(uptakes, "ucorp_benthct"),
hscorp_benthc = elt(uptakes, "hscorp_benthc"),
#Feeding by birds and mammals - temperature independent
##uomni_bird = elt(uptakes, "uomni_bird"),
##hsomni_bird = elt(uptakes, "hsomni_bird"),
ucarn_bird = elt(uptakes, "ucarn_bird"),
hscarn_bird = elt(uptakes, "hscarn_bird"),
ubenths_bird = elt(uptakes, "ubenths_bird"),
hsbenths_bird = elt(uptakes, "hsbenths_bird"),
ubenthc_bird = elt(uptakes, "ubenthc_bird"),
hsbenthc_bird = elt(uptakes, "hsbenthc_bird"),
ufishp_bird = elt(uptakes, "ufishp_bird"),
hsfishp_bird = elt(uptakes, "hsfishp_bird"),
ufishm_bird = elt(uptakes, "ufishm_bird"),
hsfishm_bird = elt(uptakes, "hsfishm_bird"),
ufishd_bird = elt(uptakes, "ufishd_bird"),
hsfishd_bird = elt(uptakes, "hsfishd_bird"),
udisc_bird = elt(uptakes, "udisc_bird"),
hsdisc_bird = elt(uptakes, "hsdisc_bird"),
ucorp_bird = elt(uptakes, "ucorp_bird"),
hscorp_bird = elt(uptakes, "hscorp_bird"),
bda_par_bird = elt(fitted.parms, "bda_par_bird"),
ucarn_seal = elt(uptakes, "ucarn_seal"),
hscarn_seal = elt(uptakes, "hscarn_seal"),
ubenths_seal = elt(uptakes, "ubenths_seal"),
hsbenths_seal = elt(uptakes, "hsbenths_seal"),
ubenthc_seal = elt(uptakes, "ubenthc_seal"),
hsbenthc_seal = elt(uptakes, "hsbenthc_seal"),
ufishp_seal = elt(uptakes, "ufishp_seal"),
hsfishp_seal = elt(uptakes, "hsfishp_seal"),
ufishm_seal = elt(uptakes, "ufishm_seal"),
hsfishm_seal = elt(uptakes, "hsfishm_seal"),
ufishd_seal = elt(uptakes, "ufishd_seal"),
hsfishd_seal = elt(uptakes, "hsfishd_seal"),
ubird_seal = elt(uptakes, "ubird_seal"),
hsbird_seal = elt(uptakes, "hsbird_seal"),
udisc_seal = elt(uptakes, "udisc_seal"),
hsdisc_seal = elt(uptakes, "hsdisc_seal"),
ucorp_seal = elt(uptakes, "ucorp_seal"),
hscorp_seal = elt(uptakes, "hscorp_seal"),
bdapar_seal = elt(uptakes, "bdapar_seal"),
uomni_ceta = elt(uptakes, "uomni_ceta"),
hsomni_ceta = elt(uptakes, "hsomni_ceta"),
ucarn_ceta = elt(uptakes, "ucarn_ceta"),
hscarn_ceta = elt(uptakes, "hscarn_ceta"),
ubenths_ceta = elt(uptakes, "ubenths_ceta"),
hsbenths_ceta = elt(uptakes, "hsbenths_ceta"),
ubenthc_ceta = elt(uptakes, "ubenthc_ceta"),
hsbenthc_ceta = elt(uptakes, "hsbenthc_ceta"),
ufishp_ceta = elt(uptakes, "ufishp_ceta"),
hsfishp_ceta = elt(uptakes, "hsfishp_ceta"),
ufishm_ceta = elt(uptakes, "ufishm_ceta"),
hsfishm_ceta = elt(uptakes, "hsfishm_ceta"),
ufishd_ceta = elt(uptakes, "ufishd_ceta"),
hsfishd_ceta = elt(uptakes, "hsfishd_ceta"),
ubird_ceta = elt(uptakes, "ubird_ceta"),
hsbird_ceta = elt(uptakes, "hsbird_ceta"),
useal_ceta = elt(uptakes, "useal_ceta"),
hsseal_ceta = elt(uptakes, "hsseal_ceta"),
udisc_ceta = elt(uptakes, "udisc_ceta"),
hsdisc_ceta = elt(uptakes, "hsdisc_ceta"),
## ucorp_ceta=u_ceta*PREF_corp_ceta,hscorp_ceta=h_ceta,
bdapar_ceta = elt(uptakes, "bdapar_ceta"),
#Proportion of consumption converted to growth - temperature independent
aH = elt(fixed.parms, "asimH"),
aC = elt(fixed.parms, "asimC"),
aBslar = elt(fixed.parms, "asimBslar"),
aBclar = elt(fixed.parms, "asimBclar"),
aBs = elt(fixed.parms, "asimBs"),
aBc = elt(fixed.parms, "asimBc"),
aFplar = elt(fixed.parms, "asimFplar"),
aFdlar = elt(fixed.parms, "asimFdlar"),
aFp = elt(fixed.parms, "asimFp"),
aFm = elt(fixed.parms, "asimFm"),
aFd = elt(fixed.parms, "asimFd"),
abird = elt(fixed.parms, "asimbird"),
aseal = elt(fixed.parms, "asimseal"),
aceta = elt(fixed.parms, "asimceta"),
#Background proportion of biomass converted to ammonia per day at the reference temperature (birds and mammals T independent)
eHt = elt(fixed.parms, "excrHt"),
eCt = elt(fixed.parms, "excrCt"),
eBslart = elt(fixed.parms, "excrBslart"),
eBclart = elt(fixed.parms, "excrBclart"),
eBst = elt(fixed.parms, "excrBst"),
eBct = elt(fixed.parms, "excrBct"),
eFplart = elt(fixed.parms, "excrFplart"),
eFdlart = elt(fixed.parms, "excrFdlart"),
eFpt = elt(fixed.parms, "excrFpt"),
eFmt = elt(fixed.parms, "excrFmt"),
eFdt = elt(fixed.parms, "excrFdt"),
ebirdt = elt(fixed.parms, "excrbird"),
esealt = elt(fixed.parms, "excrseal"),
ecetat = elt(fixed.parms, "excrceta"),
#Mineralisation, nitrification and denitrification raees per day at the reference temperature
xmt = elt(fitted.parms, "xmt"),
xnst = elt(fitted.parms, "xnst"),
xdst = elt(fitted.parms, "xdst"),
xndt = elt(fitted.parms, "xndt"),
xddt = elt(fitted.parms, "xddt"),
xqs_p1 = elt(fitted.parms, "xqs_p1"),
xqs_p2 = elt(fitted.parms, "xqs_p2"),
xqs_p3 = elt(fitted.parms, "xqs_p3"),
xmsedt = elt(fitted.parms, "xmsedt"),
xmsens = elt(fitted.parms, "xmsens"),
xnsedt = elt(fitted.parms, "xnsedt"),
xnsens = elt(fitted.parms, "xnsens"),
xdsedt = elt(fitted.parms, "xdsedt"),
xdsens = elt(fitted.parms, "xdsens"),
#Density and wave dependent destruction rate paramater for kelp
xwave_kelp = elt(fitted.parms, "xxwave_kelp"),
#Death rates of phytoplankton at the reference temperature
xxst = elt(fitted.parms, "xxst"),
xxdt = elt(fitted.parms, "xxdt"),
#Death rate per unit biomass for carnivores fish birds and mammals
xxomni = elt(fitted.parms, "xxomni"),
xxcarn = elt(fitted.parms, "xxcarn"),
xxbenthslar = elt(fitted.parms, "xxbenthslar"),
xxbenthclar = elt(fitted.parms, "xxbenthclar"),
xxbenths = elt(fitted.parms, "xxbenths"),
xxbenthc = elt(fitted.parms, "xxbenthc"),
xxpfishlar = elt(fitted.parms, "xxpfishlar"),
xxdfishlar = elt(fitted.parms, "xxdfishlar"),
xxpfish = elt(fitted.parms, "xxpfish"),
xxmfish = elt(fitted.parms, "xxmfish"),
xxdfish = elt(fitted.parms, "xxdfish"),
xxbird = elt(fitted.parms, "xxbird"),
xxseal = elt(fitted.parms, "xxseal"),
xxceta = elt(fitted.parms, "xxceta"),
#Proportion of kelp debris becoming detritus per day
kelpdebris_det = elt(fitted.parms, "xkelpdebris_det"),
#Proportion of seabed corpses becoming seabed detritus per day
xxcorp_det = elt(fitted.parms, "xxcorp_det"),
#Proportion of discarded fish sinking to become seabed corpses per day
xdisc_corp = elt(fitted.parms, "xdisc_corp"),
#deleted
#Bioturbation scaling factor for deposit feeding benthos - scales xdet uptake/xdet to fraction of sedimnent excavated
# xbioturb=xxbioturb,
#Sinking rates for detritus in the surface and deep layers
# dsink_s=xdsink_s,dsink_d_Klow=xdsink_d_Klow,dsink_d_Khi=xdsink_d_Khi,
xdsink_s = elt(fitted.parms, "xdsink_s"),
xdsink_d = elt(fitted.parms, "xdsink_d"),
#Fitting parameter for scaling between whole model region demersal fish N mass and the survey
#index on which the empirical relationships for pNQ and dsacrad ates of Q and NQ species are based.
#Expect this to be abouut 2
xdfdp = elt(fitted.parms, "xdfdp"),
#Fitted parameters for food gradient dependent fish migration rates
xpfish_migcoef = elt(fitted.parms, "xpfish_migcoef"),
xmfish_migcoef = elt(fitted.parms, "xmfish_migcoef"),
xdfish_migcoef = elt(fitted.parms, "xdfish_migcoef"),
xbird_migcoef = elt(fitted.parms, "xbird_migcoef"),
xseal_migcoef = elt(fitted.parms, "xseal_migcoef"),
xceta_migcoef = elt(fitted.parms, "xceta_migcoef"),
#Protected biomass thresholds
protect_PF_o = xprotect_PF * (1-x_shallowprop),
protect_DF_o = xprotect_DF * (1-x_shallowprop),
protect_MF_o = xprotect_MF * (1-x_shallowprop),
protect_SB_o = xprotect_SB * (1-x_shallowprop),
protect_CB_o = xprotect_CB * (1-x_shallowprop),
protect_CZ_o = xprotect_CZ * (1-x_shallowprop),
protect_BD_o = xprotect_BD * (1-x_shallowprop),
protect_SL_o = xprotect_SL * (1-x_shallowprop),
protect_CT_o = xprotect_CT * (1-x_shallowprop),
protect_PF_i = xprotect_PF * (x_shallowprop),
protect_DF_i = xprotect_DF * (x_shallowprop),
protect_MF_i = xprotect_MF * (x_shallowprop),
protect_SB_i = xprotect_SB * (x_shallowprop),
protect_CB_i = xprotect_CB * (x_shallowprop),
protect_CZ_i = xprotect_CZ * (x_shallowprop),
protect_BD_i = xprotect_BD * (x_shallowprop),
protect_SL_i = xprotect_SL * (x_shallowprop),
protect_CT_i = xprotect_CT * (x_shallowprop),
protect_KP_i = xprotect_KP,
xmax_exploitable_f_PF = elt(fitted.parms, "xmax_exploitable_f_PF"),
xmax_exploitable_f_DF = elt(fitted.parms, "xmax_exploitable_f_DF"),
xmax_exploitable_f_MF = elt(fitted.parms, "xmax_exploitable_f_MF"),
xmax_exploitable_f_SB = elt(fitted.parms, "xmax_exploitable_f_SB"),
xmax_exploitable_f_CB = elt(fitted.parms, "xmax_exploitable_f_CB"),
xmax_exploitable_f_CZ = elt(fitted.parms, "xmax_exploitable_f_CZ"),
xmax_exploitable_f_BD = elt(fitted.parms, "xmax_exploitable_f_BD"),
xmax_exploitable_f_SL = elt(fitted.parms, "xmax_exploitable_f_SL"),
xmax_exploitable_f_CT = elt(fitted.parms, "xmax_exploitable_f_CT"),
xmax_exploitable_f_KP = elt(fitted.parms, "xmax_exploitable_f_KP"),
PF_fec = elt(fixed.parms, "P_an_fec"), # annual weight specific fecundities added to the end of the paramer list
DF_fec = elt(fixed.parms, "D_an_fec"),
BS_fec = elt(fixed.parms, "BS_an_fec"),
BC_fec = elt(fixed.parms, "BC_an_fec"),
CZ_inedible_biomass_o = CZ_inedible * (1-x_shallowprop), # residual inedible biomass of carnzoo offshore
CZ_inedible_biomass_i = CZ_inedible * (x_shallowprop) # residual inedible biomass of carnzoo inshore
)
model.parameters
}
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Defines functions build_model_parameters
#
# build_model_parameters.R
#
#' Build entire set of model parameters combining fixed, physical, fleet model output, plus some biomass thresholds
#'
#' @param model model object
#' @param uptakes prey uptake levels
#' @param fleet.model.output fleet model output
#'
#' @return model parameter vector
#'
#' @noRd
#
# ------------------------------------------------------------------------------
build_model_parameters <- function(model, uptakes, fleet.model.output) {
# Unpack:
data <- elt(model, "data")
fixed.parms <- elt(data, "fixed.parameters")
xprotect_PF <- elt(fixed.parms, "xprotect_PF") # used in calculations
xprotect_DF <- elt(fixed.parms, "xprotect_DF")
xprotect_MF <- elt(fixed.parms, "xprotect_MF")
xprotect_SB <- elt(fixed.parms, "xprotect_SB")
xprotect_CB <- elt(fixed.parms, "xprotect_CB")
xprotect_CZ <- elt(fixed.parms, "xprotect_CZ")
xprotect_BD <- elt(fixed.parms, "xprotect_BD")
xprotect_SL <- elt(fixed.parms, "xprotect_SL")
xprotect_CT <- elt(fixed.parms, "xprotect_CT")
xprotect_KP <- elt(fixed.parms, "xprotect_KP")
CZ_inedible <- elt(fixed.parms, "CZ_inedible")
physical.parms <- elt(data, "physical.parameters")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
fleet.vector <- elt(fleet.model.output, "fleet_vector")
fitted.parms <- elt(data, "fitted.parameters")
#--------------------------------------------------------------------------
#Load all the parameter values into a single vector which will be passed to the model function.
model.parameters <- c(
#First the parameters for morphological and physical configuration of the model
#These occupy elements 1:55 of parms
thik_so = elt(physical.parms, "so_depth"),
thik_d = elt(physical.parms, "d_depth"),
thik_si = elt(physical.parms, "si_depth"),
thik_b = elt(physical.parms, "bx_depth"),
shallowprop = x_shallowprop,
# volume_s=xs_volume,
# volume_d=xd_volume,
area_s0 = elt(physical.parms, "x_area_s0"),
area_s1 = elt(physical.parms, "x_area_s1"),
area_s2 = elt(physical.parms, "x_area_s2"),
area_s3 = elt(physical.parms, "x_area_s3"),
area_d0 = elt(physical.parms, "x_area_d0"),
area_d1 = elt(physical.parms, "x_area_d1"),
area_d2 = elt(physical.parms, "x_area_d2"),
area_d3 = elt(physical.parms, "x_area_d3"),
rock_s1 = elt(physical.parms, "x_rock_s1"),
rock_s2 = elt(physical.parms, "x_rock_s2"),
rock_s3 = elt(physical.parms, "x_rock_s3"),
rock_d1 = elt(physical.parms, "x_rock_d1"),
rock_d2 = elt(physical.parms, "x_rock_d2"),
rock_d3 = elt(physical.parms, "x_rock_d3"),
nonrock_s = elt(physical.parms, "x_nonrock_s"),
nonrock_d = elt(physical.parms, "x_nonrock_d"),
thik_x_s1 = elt(physical.parms, "x_depth_s1"),
thik_x_s2 = elt(physical.parms, "x_depth_s2"),
thik_x_s3 = elt(physical.parms, "x_depth_s3"),
thik_x_d1 = elt(physical.parms, "x_depth_d1"),
thik_x_d2 = elt(physical.parms, "x_depth_d2"),
thik_x_d3 = elt(physical.parms, "x_depth_d3"),
porosity_s1 = elt(physical.parms, "x_poros_s1"),
porosity_s2 = elt(physical.parms, "x_poros_s2"),
porosity_s3 = elt(physical.parms, "x_poros_s3"),
porosity_d1 = elt(physical.parms, "x_poros_d1"),
porosity_d2 = elt(physical.parms, "x_poros_d2"),
porosity_d3 = elt(physical.parms, "x_poros_d3"),
sed_wat_dif_s1 = elt(physical.parms, "Kxw_s1"),
sed_wat_dif_s2 = elt(physical.parms, "Kxw_s2"),
sed_wat_dif_s3 = elt(physical.parms, "Kxw_s3"),
sed_wat_dif_d1 = elt(physical.parms, "Kxw_d1"),
sed_wat_dif_d2 = elt(physical.parms, "Kxw_d2"),
sed_wat_dif_d3 = elt(physical.parms, "Kxw_d3"),
#Reference value of log10(Kxw) for estimating habitat specific sediment geochemistry rates
sed_ref_Kxw = elt(physical.parms, "ref_Kxw"),
#Bioturbation depth and erosion depths of the sediment as proportions of active sediment layer thickness
bioturb_depth_s1 = elt(physical.parms, "xbioturb_depth_s1"),
bioturb_depth_s2 = elt(physical.parms, "xbioturb_depth_s2"),
bioturb_depth_s3 = elt(physical.parms, "xbioturb_depth_s3"),
bioturb_depth_d1 = elt(physical.parms, "xbioturb_depth_d1"),
bioturb_depth_d2 = elt(physical.parms, "xbioturb_depth_d2"),
bioturb_depth_d3 = elt(physical.parms, "xbioturb_depth_d3"),
erosion_depth_s1 = elt(physical.parms, "xerosion_depth_s1"),
erosion_depth_s2 = elt(physical.parms, "xerosion_depth_s2"),
erosion_depth_s3 = elt(physical.parms, "xerosion_depth_s3"),
erosion_depth_d1 = elt(physical.parms, "xerosion_depth_d1"),
erosion_depth_d2 = elt(physical.parms, "xerosion_depth_d2"),
erosion_depth_d3 = elt(physical.parms, "xerosion_depth_d3"),
lightSPM_intercept = elt(physical.parms, "xlightSPM_intercept"),
lightSPM_slope = elt(physical.parms, "xlightSPM_slope"),
inshore_phyt_prop_depth = elt(physical.parms, "xinshore_phyt_prop_depth"),
inshore_kelp_prop_depth = elt(physical.parms, "xinshore_kelp_prop_depth"),
# parms so far: 56
#------ Parameters transferred in from the fishing fleet model ----------
# The fleet vector has 250 elements, so
# these occupy elemnts 57:307 of the parms vector
#Vector of parameters from the fishing fleet configuration model
fleet.vector,
#----- Ecological model parameters -------
#Q10 temperature coefficients for heteroptophs, autotrophs and reference temperature
qtena = elt(fixed.parms, "qtenauto"),
qtenh = elt(fixed.parms, "qtenhetero"),
qtenm = elt(fixed.parms, "qtenmetabol"),
qtenr = elt(fixed.parms, "qtenrreft"),
#Light saturation parameter for phytoplankton N uptake
Lmaxup_phyt = elt(fixed.parms, "satlight_phyt"),
#Light saturation parameter for kelp C uptake
Lmaxup_kelp = elt(fixed.parms, "satlight_kelp"),
#Maximum and minimum values of NC ratio in kelp
NCmax_kelp = elt(fixed.parms, "kelp_ncmax"),
NCmin_kelp = elt(fixed.parms, "kelp_ncmin"),
#Then the fitted parameters
#Wave dependent beach-case rate parameter for kelp_debris
wave_beach_kelpdebris = elt(fitted.parms, "xwave_kelpdebris"),
#Maximum uptake rate of carbon by kelp
umaxC_kelp = elt(fitted.parms, "uC_kelp"),
#Density dependent carbon exudation rate parameter for kelp
exudeC_kelp = elt(fitted.parms, "ddexudC_kelp"),
#Density dependent self shading paramater for carbon uptake by kelp
selfshade_kelp = elt(fitted.parms, "xkelpshade"),
#Nutrient uptake by kelp at the reference temperature
uNIT_kelpt = elt(uptakes, "uNIT_kelpt"),
hsNIT_kelp = elt(uptakes, "hsNIT_kelp"),
uAMM_kelpt = elt(uptakes, "uAMM_kelpt"),
hsAMM_kelp = elt(uptakes, "hsAMM_kelp"),
#Nutrient uptake by phytoplankton at the reference temperature
uNIT_phytt = elt(uptakes, "uNIT_phytt"),
hsNIT_phyt = elt(uptakes, "hsNIT_phyt"),
uAMM_phytt = elt(uptakes, "uAMM_phytt"),
hsAMM_phyt = elt(uptakes, "hsAMM_phyt"),
#Feeding by mesozooplankton at the reference temperature
uphyt_omnit = elt(uptakes, "uphyt_omnit"),
hsphyt_omni = elt(uptakes, "hsphyt_omni"),
udet_omnit = elt(uptakes, "udet_omnit"),
hsdet_omni = elt(uptakes, "hsdet_omni"),
ubenthslar_omnit = elt(uptakes, "ubenthslar_omnit"),
hsbenthslar_omni = elt(uptakes, "hsbenthslar_omni"),
ubenthclar_omnit = elt(uptakes, "ubenthclar_omnit"),
hsbenthclar_omni = elt(uptakes, "hsbenthclar_omni"),
#Feeding by carnivorous zooplankton at the reference temperature
uomni_carnt = elt(uptakes, "uomni_carnt"),
hsomni_carn = elt(uptakes, "hsomni_carn"),
ubenthslar_carnt = elt(uptakes, "ubenthslar_carnt"),
hsbenthslar_carn = elt(uptakes, "hsbenthslar_carn"),
ubenthclar_carnt = elt(uptakes, "ubenthclar_carnt"),
hsbenthclar_carn = elt(uptakes, "hsbenthclar_carn"),
ufishplar_carnt = elt(uptakes, "ufishplar_carnt"),
hsfishplar_carn = elt(uptakes, "hsfishplar_carn"),
ufishdlar_carnt = elt(uptakes, "ufishdlar_carnt"),
hsfishdlar_carn = elt(uptakes, "hsfishdlar_carn"),
#Feeding by larvae of pelagic fish at the reference temperature
uomni_fishplart = elt(uptakes, "uomni_fishplart"),
hsomni_fishplar = elt(uptakes, "hsomni_fishplar"),
ubenthslar_fishplart = elt(uptakes, "ubenthslar_fishplart"),
hsbenthslar_fishplar = elt(uptakes, "hsbenthslar_fishplar"),
ubenthclar_fishplart = elt(uptakes, "ubenthclar_fishplart"),
hsbenthclar_fishplar = elt(uptakes, "hsbenthclar_fishplar"),
#Feeding by pelagic fish at the reference temperature
uomni_fishpt = elt(uptakes, "uomni_fishpt"),
hsomni_fishp = elt(uptakes, "hsomni_fishp"),
ucarn_fishpt = elt(uptakes, "ucarn_fishpt"),
hscarn_fishp = elt(uptakes, "hscarn_fishp"),
ubenthslar_fishpt = elt(uptakes, "ubenthslar_fishpt"),
hsbenthslar_fishp = elt(uptakes, "hsbenthslar_fishp"),
ubenthclar_fishpt = elt(uptakes, "ubenthclar_fishpt"),
hsbenthclar_fishp = elt(uptakes, "hsbenthclar_fishp"),
ufishdlar_fishpt = elt(uptakes, "ufishdlar_fishpt"),
hsfishdlar_fishp = elt(uptakes, "hsfishdlar_fishp"),
ufishplar_fishpt = elt(uptakes, "ufishplar_fishpt"),
hsfishplar_fishp = elt(uptakes, "hsfishplar_fishp"),
#Feeding by migratory fish at the reference temperature
uomni_fishmt = elt(uptakes, "uomni_fishmt"),
hsomni_fishm = elt(uptakes, "hsomni_fishm"),
ucarn_fishmt = elt(uptakes, "ucarn_fishmt"),
hscarn_fishm = elt(uptakes, "hscarn_fishm"),
ubenthslar_fishmt = elt(uptakes, "ubenthslar_fishmt"),
hsbenthslar_fishm = elt(uptakes, "hsbenthslar_fishm"),
ubenthclar_fishmt = elt(uptakes, "ubenthclar_fishmt"),
hsbenthclar_fishm = elt(uptakes, "hsbenthclar_fishm"),
ufishdlar_fishmt = elt(uptakes, "ufishdlar_fishmt"),
hsfishdlar_fishm = elt(uptakes, "hsfishdlar_fishm"),
ufishplar_fishmt = elt(uptakes, "ufishplar_fishmt"),
hsfishplar_fishm = elt(uptakes, "hsfishplar_fishm"),
#Feeding by larvae of demersal fish at the reference temperature
uomni_fishdlart = elt(uptakes, "uomni_fishdlart"),
hsomni_fishdlar = elt(uptakes, "hsomni_fishdlar"),
ubenthslar_fishdlart = elt(uptakes, "ubenthslar_fishdlart"),
hsbenthslar_fishdlar = elt(uptakes, "hsbenthslar_fishdlar"),
ubenthclar_fishdlart = elt(uptakes, "ubenthclar_fishdlart"),
hsbenthclar_fishdlar = elt(uptakes, "hsbenthclar_fishdlar"),
#Feeding by demersal fish at the reference temperature
ucarn_fishdt = elt(uptakes, "ucarn_fishdt"),
hscarn_fishd = elt(uptakes, "hscarn_fishd"),
ubenths_fishdt = elt(uptakes, "ubenths_fishdt"),
hsbenths_fishd = elt(uptakes, "hsbenths_fishd"),
ubenthc_fishdt = elt(uptakes, "ubenthc_fishdt"),
hsbenthc_fishd = elt(uptakes, "hsbenthc_fishd"),
ufishplar_fishdt = elt(uptakes, "ufishplar_fishdt"),
hsfishplar_fishd = elt(uptakes, "hsfishplar_fishd"),
ufishdlar_fishdt = elt(uptakes, "ufishdlar_fishdt"),
hsfishdlar_fishd = elt(uptakes, "hsfishdlar_fishd"),
ufishp_fishdt = elt(uptakes, "ufishp_fishdt"),
hsfishp_fishd = elt(uptakes, "hsfishp_fishd"),
ufishm_fishdt = elt(uptakes, "ufishm_fishdt"),
hsfishm_fishd = elt(uptakes, "hsfishm_fishd"),
ufishd_fishdt = elt(uptakes, "ufishd_fishdt"),
hsfishd_fishd = elt(uptakes, "hsfishd_fishd"),
udisc_fishdt = elt(uptakes, "udisc_fishdt"),
hsdisc_fishd = elt(uptakes, "hsdisc_fishd"),
ucorp_fishdt = elt(uptakes, "ucorp_fishdt"),
hscorp_fishd = elt(uptakes, "hscorp_fishd"),
#Feeding by larvae of suspension feeding benthos at the reference temperature
uphyt_benthslart = elt(uptakes, "uphyt_benthslart"),
hsphyt_benthslar = elt(uptakes, "hsphyt_benthslar"),
udet_benthslart = elt(uptakes, "udet_benthslart"),
hsdet_benthslar = elt(uptakes, "hsdet_benthslar"),
#Feeding by larvae of carnivore/scavenge feeding benthos at the reference temperature
uphyt_benthclart = elt(uptakes, "uphyt_benthclart"),
hsphyt_benthclar = elt(uptakes, "hsphyt_benthclar"),
udet_benthclart = elt(uptakes, "udet_benthclart"),
hsdet_benthclar = elt(uptakes, "hsdet_benthclar"),
#Feeding by suspension feeding benthos at the reference temperature
uphyt_benthst = elt(uptakes, "uphyt_benthst"),
hsphyt_benths = elt(uptakes, "hsphyt_benths"),
udet_benthst = elt(uptakes, "udet_benthst"),
hsdet_benths = elt(uptakes, "hsdet_benths"),
used_benthst = elt(uptakes, "used_benthst"),
hssed_benths = elt(uptakes, "hssed_benths"),
#Feeding by carnivorous benthos at the reference temperature
ubenths_benthct = elt(uptakes, "ubenths_benthct"),
hsbenths_benthc = elt(uptakes, "hsbenths_benthc"),
ukelp_benthct = elt(uptakes, "ukelp_benthct"),
hskelp_benthc = elt(uptakes, "hskelp_benthc"),
ukelpdebris_benthct = elt(uptakes, "ukelpdebris_benthct"),
hskelpdebris_benthc = elt(uptakes, "hskelpdebris_benthc"),
ucorp_benthct = elt(uptakes, "ucorp_benthct"),
hscorp_benthc = elt(uptakes, "hscorp_benthc"),
#Feeding by birds and mammals - temperature independent
##uomni_bird = elt(uptakes, "uomni_bird"),
##hsomni_bird = elt(uptakes, "hsomni_bird"),
ucarn_bird = elt(uptakes, "ucarn_bird"),
hscarn_bird = elt(uptakes, "hscarn_bird"),
ubenths_bird = elt(uptakes, "ubenths_bird"),
hsbenths_bird = elt(uptakes, "hsbenths_bird"),
ubenthc_bird = elt(uptakes, "ubenthc_bird"),
hsbenthc_bird = elt(uptakes, "hsbenthc_bird"),
ufishp_bird = elt(uptakes, "ufishp_bird"),
hsfishp_bird = elt(uptakes, "hsfishp_bird"),
ufishm_bird = elt(uptakes, "ufishm_bird"),
hsfishm_bird = elt(uptakes, "hsfishm_bird"),
ufishd_bird = elt(uptakes, "ufishd_bird"),
hsfishd_bird = elt(uptakes, "hsfishd_bird"),
udisc_bird = elt(uptakes, "udisc_bird"),
hsdisc_bird = elt(uptakes, "hsdisc_bird"),
ucorp_bird = elt(uptakes, "ucorp_bird"),
hscorp_bird = elt(uptakes, "hscorp_bird"),
bda_par_bird = elt(fitted.parms, "bda_par_bird"),
ucarn_seal = elt(uptakes, "ucarn_seal"),
hscarn_seal = elt(uptakes, "hscarn_seal"),
ubenths_seal = elt(uptakes, "ubenths_seal"),
hsbenths_seal = elt(uptakes, "hsbenths_seal"),
ubenthc_seal = elt(uptakes, "ubenthc_seal"),
hsbenthc_seal = elt(uptakes, "hsbenthc_seal"),
ufishp_seal = elt(uptakes, "ufishp_seal"),
hsfishp_seal = elt(uptakes, "hsfishp_seal"),
ufishm_seal = elt(uptakes, "ufishm_seal"),
hsfishm_seal = elt(uptakes, "hsfishm_seal"),
ufishd_seal = elt(uptakes, "ufishd_seal"),
hsfishd_seal = elt(uptakes, "hsfishd_seal"),
ubird_seal = elt(uptakes, "ubird_seal"),
hsbird_seal = elt(uptakes, "hsbird_seal"),
udisc_seal = elt(uptakes, "udisc_seal"),
hsdisc_seal = elt(uptakes, "hsdisc_seal"),
ucorp_seal = elt(uptakes, "ucorp_seal"),
hscorp_seal = elt(uptakes, "hscorp_seal"),
bdapar_seal = elt(uptakes, "bdapar_seal"),
uomni_ceta = elt(uptakes, "uomni_ceta"),
hsomni_ceta = elt(uptakes, "hsomni_ceta"),
ucarn_ceta = elt(uptakes, "ucarn_ceta"),
hscarn_ceta = elt(uptakes, "hscarn_ceta"),
ubenths_ceta = elt(uptakes, "ubenths_ceta"),
hsbenths_ceta = elt(uptakes, "hsbenths_ceta"),
ubenthc_ceta = elt(uptakes, "ubenthc_ceta"),
hsbenthc_ceta = elt(uptakes, "hsbenthc_ceta"),
ufishp_ceta = elt(uptakes, "ufishp_ceta"),
hsfishp_ceta = elt(uptakes, "hsfishp_ceta"),
ufishm_ceta = elt(uptakes, "ufishm_ceta"),
hsfishm_ceta = elt(uptakes, "hsfishm_ceta"),
ufishd_ceta = elt(uptakes, "ufishd_ceta"),
hsfishd_ceta = elt(uptakes, "hsfishd_ceta"),
ubird_ceta = elt(uptakes, "ubird_ceta"),
hsbird_ceta = elt(uptakes, "hsbird_ceta"),
useal_ceta = elt(uptakes, "useal_ceta"),
hsseal_ceta = elt(uptakes, "hsseal_ceta"),
udisc_ceta = elt(uptakes, "udisc_ceta"),
hsdisc_ceta = elt(uptakes, "hsdisc_ceta"),
## ucorp_ceta=u_ceta*PREF_corp_ceta,hscorp_ceta=h_ceta,
bdapar_ceta = elt(uptakes, "bdapar_ceta"),
#Proportion of consumption converted to growth - temperature independent
aH = elt(fixed.parms, "asimH"),
aC = elt(fixed.parms, "asimC"),
aBslar = elt(fixed.parms, "asimBslar"),
aBclar = elt(fixed.parms, "asimBclar"),
aBs = elt(fixed.parms, "asimBs"),
aBc = elt(fixed.parms, "asimBc"),
aFplar = elt(fixed.parms, "asimFplar"),
aFdlar = elt(fixed.parms, "asimFdlar"),
aFp = elt(fixed.parms, "asimFp"),
aFm = elt(fixed.parms, "asimFm"),
aFd = elt(fixed.parms, "asimFd"),
abird = elt(fixed.parms, "asimbird"),
aseal = elt(fixed.parms, "asimseal"),
aceta = elt(fixed.parms, "asimceta"),
#Background proportion of biomass converted to ammonia per day at the reference temperature (birds and mammals T independent)
eHt = elt(fixed.parms, "excrHt"),
eCt = elt(fixed.parms, "excrCt"),
eBslart = elt(fixed.parms, "excrBslart"),
eBclart = elt(fixed.parms, "excrBclart"),
eBst = elt(fixed.parms, "excrBst"),
eBct = elt(fixed.parms, "excrBct"),
eFplart = elt(fixed.parms, "excrFplart"),
eFdlart = elt(fixed.parms, "excrFdlart"),
eFpt = elt(fixed.parms, "excrFpt"),
eFmt = elt(fixed.parms, "excrFmt"),
eFdt = elt(fixed.parms, "excrFdt"),
ebirdt = elt(fixed.parms, "excrbird"),
esealt = elt(fixed.parms, "excrseal"),
ecetat = elt(fixed.parms, "excrceta"),
#Mineralisation, nitrification and denitrification raees per day at the reference temperature
xmt = elt(fitted.parms, "xmt"),
xnst = elt(fitted.parms, "xnst"),
xdst = elt(fitted.parms, "xdst"),
xndt = elt(fitted.parms, "xndt"),
xddt = elt(fitted.parms, "xddt"),
xqs_p1 = elt(fitted.parms, "xqs_p1"),
xqs_p2 = elt(fitted.parms, "xqs_p2"),
xqs_p3 = elt(fitted.parms, "xqs_p3"),
xmsedt = elt(fitted.parms, "xmsedt"),
xmsens = elt(fitted.parms, "xmsens"),
xnsedt = elt(fitted.parms, "xnsedt"),
xnsens = elt(fitted.parms, "xnsens"),
xdsedt = elt(fitted.parms, "xdsedt"),
xdsens = elt(fitted.parms, "xdsens"),
#Density and wave dependent destruction rate paramater for kelp
xwave_kelp = elt(fitted.parms, "xxwave_kelp"),
#Death rates of phytoplankton at the reference temperature
xxst = elt(fitted.parms, "xxst"),
xxdt = elt(fitted.parms, "xxdt"),
#Death rate per unit biomass for carnivores fish birds and mammals
xxomni = elt(fitted.parms, "xxomni"),
xxcarn = elt(fitted.parms, "xxcarn"),
xxbenthslar = elt(fitted.parms, "xxbenthslar"),
xxbenthclar = elt(fitted.parms, "xxbenthclar"),
xxbenths = elt(fitted.parms, "xxbenths"),
xxbenthc = elt(fitted.parms, "xxbenthc"),
xxpfishlar = elt(fitted.parms, "xxpfishlar"),
xxdfishlar = elt(fitted.parms, "xxdfishlar"),
xxpfish = elt(fitted.parms, "xxpfish"),
xxmfish = elt(fitted.parms, "xxmfish"),
xxdfish = elt(fitted.parms, "xxdfish"),
xxbird = elt(fitted.parms, "xxbird"),
xxseal = elt(fitted.parms, "xxseal"),
xxceta = elt(fitted.parms, "xxceta"),
#Proportion of kelp debris becoming detritus per day
kelpdebris_det = elt(fitted.parms, "xkelpdebris_det"),
#Proportion of seabed corpses becoming seabed detritus per day
xxcorp_det = elt(fitted.parms, "xxcorp_det"),
#Proportion of discarded fish sinking to become seabed corpses per day
xdisc_corp = elt(fitted.parms, "xdisc_corp"),
#deleted
#Bioturbation scaling factor for deposit feeding benthos - scales xdet uptake/xdet to fraction of sedimnent excavated
# xbioturb=xxbioturb,
#Sinking rates for detritus in the surface and deep layers
# dsink_s=xdsink_s,dsink_d_Klow=xdsink_d_Klow,dsink_d_Khi=xdsink_d_Khi,
xdsink_s = elt(fitted.parms, "xdsink_s"),
xdsink_d = elt(fitted.parms, "xdsink_d"),
#Fitting parameter for scaling between whole model region demersal fish N mass and the survey
#index on which the empirical relationships for pNQ and dsacrad ates of Q and NQ species are based.
#Expect this to be abouut 2
xdfdp = elt(fitted.parms, "xdfdp"),
#Fitted parameters for food gradient dependent fish migration rates
xpfish_migcoef = elt(fitted.parms, "xpfish_migcoef"),
xmfish_migcoef = elt(fitted.parms, "xmfish_migcoef"),
xdfish_migcoef = elt(fitted.parms, "xdfish_migcoef"),
xbird_migcoef = elt(fitted.parms, "xbird_migcoef"),
xseal_migcoef = elt(fitted.parms, "xseal_migcoef"),
xceta_migcoef = elt(fitted.parms, "xceta_migcoef"),
#Protected biomass thresholds
protect_PF_o = xprotect_PF * (1-x_shallowprop),
protect_DF_o = xprotect_DF * (1-x_shallowprop),
protect_MF_o = xprotect_MF * (1-x_shallowprop),
protect_SB_o = xprotect_SB * (1-x_shallowprop),
protect_CB_o = xprotect_CB * (1-x_shallowprop),
protect_CZ_o = xprotect_CZ * (1-x_shallowprop),
protect_BD_o = xprotect_BD * (1-x_shallowprop),
protect_SL_o = xprotect_SL * (1-x_shallowprop),
protect_CT_o = xprotect_CT * (1-x_shallowprop),
protect_PF_i = xprotect_PF * (x_shallowprop),
protect_DF_i = xprotect_DF * (x_shallowprop),
protect_MF_i = xprotect_MF * (x_shallowprop),
protect_SB_i = xprotect_SB * (x_shallowprop),
protect_CB_i = xprotect_CB * (x_shallowprop),
protect_CZ_i = xprotect_CZ * (x_shallowprop),
protect_BD_i = xprotect_BD * (x_shallowprop),
protect_SL_i = xprotect_SL * (x_shallowprop),
protect_CT_i = xprotect_CT * (x_shallowprop),
protect_KP_i = xprotect_KP,
xmax_exploitable_f_PF = elt(fitted.parms, "xmax_exploitable_f_PF"),
xmax_exploitable_f_DF = elt(fitted.parms, "xmax_exploitable_f_DF"),
xmax_exploitable_f_MF = elt(fitted.parms, "xmax_exploitable_f_MF"),
xmax_exploitable_f_SB = elt(fitted.parms, "xmax_exploitable_f_SB"),
xmax_exploitable_f_CB = elt(fitted.parms, "xmax_exploitable_f_CB"),
xmax_exploitable_f_CZ = elt(fitted.parms, "xmax_exploitable_f_CZ"),
xmax_exploitable_f_BD = elt(fitted.parms, "xmax_exploitable_f_BD"),
xmax_exploitable_f_SL = elt(fitted.parms, "xmax_exploitable_f_SL"),
xmax_exploitable_f_CT = elt(fitted.parms, "xmax_exploitable_f_CT"),
xmax_exploitable_f_KP = elt(fitted.parms, "xmax_exploitable_f_KP"),
PF_fec = elt(fixed.parms, "P_an_fec"), # annual weight specific fecundities added to the end of the paramer list
DF_fec = elt(fixed.parms, "D_an_fec"),
BS_fec = elt(fixed.parms, "BS_an_fec"),
BC_fec = elt(fixed.parms, "BC_an_fec"),
CZ_inedible_biomass_o = CZ_inedible * (1-x_shallowprop), # residual inedible biomass of carnzoo offshore
CZ_inedible_biomass_i = CZ_inedible * (x_shallowprop) # residual inedible biomass of carnzoo inshore
)
model.parameters
}
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