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R/read_fitted_parameters.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
read_fitted_parameters
#
# read_fitted_parameters.R
#
#' Load fitted parameter values for model
#'
#' Parameters which have been established by the simulated annealing scheme are
#' loaded from a csv file which is made from the last line of the 'accepted parameters'
#' file produced by the annealing programme.
#
#' A variety of other parameters which are not optimized by simulated annealing are
#' hard-wired in this subroutine
#'
#' @param model.path path to model
#'
#' @return list of fitted model parameters
#'
#' @noRd
#
# ------------------------------------------------------------------------------
read_fitted_parameters <- function(model.path) {
preference_matrix_input <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FITTED_PARAMETERS_PREFERENCE, row.names=1) # special
uptake_mort_input <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FITTED_PARAMETERS_UPTAKE_MORT)
microbiology_input <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FITTED_PARAMETERS_MICROBIOLOGY)
#showall("preference_matrix_input",preference_matrix_input)
#showall("PREF_NIT_kelp", preference_matrix_input$kelp[which(rownames(preference_matrix_input)=="nitrate")])
# rownames(preference_matrix_input)
# [1] "ammonia" "nitrate" "suspdet" "seddet" "corpses" "discards"
# [7] "phyt" "omnivzoo" "carnzoo" "fishplar" "fishdlar" "fishp"
# [13] "fishm" "fishd" "benthslar" "benthclar" "benths" "benthc"
# [19] "bird" "seal" "ceta"
# make a linear list of prefs from the matrices:
fitted.parameters <- list(
# PREFS: 79 pars
PREF_NIT_kelp = preference_matrix_input$kelp[which(rownames(preference_matrix_input)=="nitrate")],
PREF_AMM_kelp = preference_matrix_input$kelp[which(rownames(preference_matrix_input)=="ammonia")],
PREF_NIT_phyt = preference_matrix_input$phyt[which(rownames(preference_matrix_input)=="nitrate")],
PREF_AMM_phyt = preference_matrix_input$phyt[which(rownames(preference_matrix_input)=="ammonia")],
PREF_phyt_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="phyt")],
PREF_det_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="suspdet")],
PREF_benthslar_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="benthclar")],
PREF_omni_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_benthslar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="benthclar")],
PREF_fishplar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="fishplar")],
PREF_fishdlar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_omni_fishplar = preference_matrix_input$fishplar[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_benthslar_fishplar = preference_matrix_input$fishplar[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishplar = preference_matrix_input$fishplar[which(rownames(preference_matrix_input)=="benthclar")],
PREF_omni_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_carn_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benthslar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="benthclar")],
PREF_fishdlar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_fishplar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="fishplar")],
PREF_omni_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_carn_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benthslar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="benthclar")],
PREF_fishdlar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_fishplar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="fishplar")],
PREF_omni_fishdlar = preference_matrix_input$fishdlar[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_benthslar_fishdlar = preference_matrix_input$fishdlar[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishdlar = preference_matrix_input$fishdlar[which(rownames(preference_matrix_input)=="benthclar")],
PREF_carn_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishplar_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishplar")],
PREF_fishdlar_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_fishp_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishd")],
PREF_disc_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="discards")],
PREF_corp_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="corpses")],
PREF_phyt_benthslar = preference_matrix_input$benthslar[which(rownames(preference_matrix_input)=="phyt")],
PREF_phyt_benthclar = preference_matrix_input$benthclar[which(rownames(preference_matrix_input)=="phyt")],
PREF_det_benthslar = preference_matrix_input$benthslar[which(rownames(preference_matrix_input)=="suspdet")],
PREF_det_benthclar = preference_matrix_input$benthclar[which(rownames(preference_matrix_input)=="suspdet")],
PREF_phyt_benths = preference_matrix_input$benths[which(rownames(preference_matrix_input)=="phyt")],
PREF_det_benths = preference_matrix_input$benths[which(rownames(preference_matrix_input)=="suspdet")],
PREF_sed_benths = preference_matrix_input$benths[which(rownames(preference_matrix_input)=="seddet")],
PREF_kelp_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="kelp")],
PREF_kelpdebris_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="kelpdebris")],
PREF_benths_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="benths")],
PREF_corp_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="corpses")],
PREF_carn_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishp_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="fishd")],
PREF_disc_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="discards")],
PREF_corp_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="corpses")],
PREF_carn_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishp_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="fishd")],
PREF_bird_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="bird")],
PREF_disc_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="discards")],
PREF_corp_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="corpses")],
PREF_omni_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_carn_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishp_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="fishd")],
PREF_bird_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="bird")],
PREF_seal_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="seal")],
PREF_disc_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="discards")],
# uptake_mort_input: 18+19+17+16 = 70 pars
# u_store: 18 pars
uC_kelp = uptake_mort_input$Cumax[which(uptake_mort_input$consumer=="kelp")],
ddexudC_kelp = uptake_mort_input$Cddexud[which(uptake_mort_input$consumer=="kelp")],
u_kelp = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="kelp")],
u_phyt = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="phyt_s")],
u_omni = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="omnivzoo")],
u_carn = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="carnzoo")],
u_fishplar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishplar")],
u_fishp = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishp")],
u_fishm = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishm")],
u_fishdlar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishdlar")],
u_fishd = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishd")],
u_benthslar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benthslar")],
u_benthclar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benthclar")],
u_benths = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benths")],
u_benthc = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benthc")],
u_bird = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="bird")],
u_seal = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="seal")],
u_ceta = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="ceta")],
# h_store: 19 pars
h_kelp = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="kelp")],
h_phyt = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="phyt_s")],
h_omni = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="omnivzoo")],
h_carn = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="carnzoo")],
h_fishplar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishplar")],
h_fishp = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishp")],
h_fishm = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishm")],
h_fishdlar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishdlar")],
h_fishd = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishd")],
h_benthslar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benthslar")],
h_benthclar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benthclar")],
h_benths = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benths")],
h_benthc = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benthc")],
h_bird = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="bird")],
h_seal = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="seal")],
h_ceta = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="ceta")],
bda_par_bird = uptake_mort_input$BdeApar[which(uptake_mort_input$consumer=="bird")],
bda_par_seal = uptake_mort_input$BdeApar[which(uptake_mort_input$consumer=="seal")],
bda_par_ceta = uptake_mort_input$BdeApar[which(uptake_mort_input$consumer=="ceta")],
#Mineralisation, nitrification and denitrification rates per day at the reference temperature
# biogeostore: 22 pars
xmt = microbiology_input$Value[1],
xnst = microbiology_input$Value[2],
xdst = microbiology_input$Value[3],
xndt = microbiology_input$Value[4],
xddt = microbiology_input$Value[5],
xqs_p1 = microbiology_input$Value[6], # proportion of detritus which become refractory when minearlised
xqs_p2 = microbiology_input$Value[7], # ratio of refratory to labile detritus minearalisation rates
xqs_p3 = microbiology_input$Value[8], # proportion of refractory whiuch becomes labile when re-oxygenated
xmsedt = microbiology_input$Value[9],
xmsens = microbiology_input$Value[10],
xnsedt = microbiology_input$Value[11],
xnsens = microbiology_input$Value[12],
xdsedt = microbiology_input$Value[13],
xdsens = microbiology_input$Value[14],
#Proportion of discards sinking to become seabed corpses per day - temperature independent
xdisc_corp = microbiology_input$Value[15],
#Proportion of corpse mass converted to detritus per day at the reference temperature
xxcorp_det = microbiology_input$Value[16], # orginally xcorp_det
xkelpdebris_det = microbiology_input$Value[17],
#Sinking rates and their dependence on mixing - temperature independent
xdsink_s = microbiology_input$Value[18],
xdsink_d = microbiology_input$Value[19],
#Density dependent self shading parameter for kelp
xkelpshade = microbiology_input$Value[20],
#Wave-dependent beach-cast parameter for kelp debris
xwave_kelpdebris = microbiology_input$Value[21],
#Fitting parameter fopr demersal discard rate - expect this to be about 1.0
xdfdp = microbiology_input$Value[22],
# mortstore: 17 pars
#Density dependent parameter linking wave height to kelp destruction rate
xxwave_kelp = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="kelp")],
xxst = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="phyt_s")],
xxdt = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="phyt_d")],
#Death rate of carnivores fish birds and mammals per unit biomass - temperature independent
xxomni = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="omnivzoo")],
xxcarn = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="carnzoo")],
xxbenthslar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benthslar")],
xxbenthclar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benthclar")],
xxbenths = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benths")],
xxbenthc = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benthc")],
xxpfishlar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishplar")],
xxdfishlar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishdlar")],
xxpfish = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishp")],
xxmfish = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishm")],
xxdfish = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishd")],
xxbird = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="bird")],
xxseal = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="seal")],
xxceta = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="ceta")],
# reststore: 16 pars
#Parameters for food gradient migration rates of pelagic and migratory fish
xpfish_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="fishp")],
xmfish_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="fishm")],
xdfish_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="fishd")],
xbird_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="bird")],
xseal_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="seal")],
xceta_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="ceta")],
#Maximum proportions of the stock biomass which is accessible to the fisheries
#Units proportions
xmax_exploitable_f_KP = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="kelp")],
xmax_exploitable_f_PF = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="fishp")],
xmax_exploitable_f_DF = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="fishd")],
xmax_exploitable_f_MF = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="fishm")],
xmax_exploitable_f_SB = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="benths")],
xmax_exploitable_f_CB = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="benthc")],
xmax_exploitable_f_CZ = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="carnzoo")],
xmax_exploitable_f_BD = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="bird")],
xmax_exploitable_f_SL = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="seal")],
xmax_exploitable_f_CT = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="ceta")]
)
fitted.parameters
}
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Defines functions read_fitted_parameters
#
# read_fitted_parameters.R
#
#' Load fitted parameter values for model
#'
#' Parameters which have been established by the simulated annealing scheme are
#' loaded from a csv file which is made from the last line of the 'accepted parameters'
#' file produced by the annealing programme.
#
#' A variety of other parameters which are not optimized by simulated annealing are
#' hard-wired in this subroutine
#'
#' @param model.path path to model
#'
#' @return list of fitted model parameters
#'
#' @noRd
#
# ------------------------------------------------------------------------------
read_fitted_parameters <- function(model.path) {
preference_matrix_input <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FITTED_PARAMETERS_PREFERENCE, row.names=1) # special
uptake_mort_input <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FITTED_PARAMETERS_UPTAKE_MORT)
microbiology_input <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FITTED_PARAMETERS_MICROBIOLOGY)
#showall("preference_matrix_input",preference_matrix_input)
#showall("PREF_NIT_kelp", preference_matrix_input$kelp[which(rownames(preference_matrix_input)=="nitrate")])
# rownames(preference_matrix_input)
# [1] "ammonia" "nitrate" "suspdet" "seddet" "corpses" "discards"
# [7] "phyt" "omnivzoo" "carnzoo" "fishplar" "fishdlar" "fishp"
# [13] "fishm" "fishd" "benthslar" "benthclar" "benths" "benthc"
# [19] "bird" "seal" "ceta"
# make a linear list of prefs from the matrices:
fitted.parameters <- list(
# PREFS: 79 pars
PREF_NIT_kelp = preference_matrix_input$kelp[which(rownames(preference_matrix_input)=="nitrate")],
PREF_AMM_kelp = preference_matrix_input$kelp[which(rownames(preference_matrix_input)=="ammonia")],
PREF_NIT_phyt = preference_matrix_input$phyt[which(rownames(preference_matrix_input)=="nitrate")],
PREF_AMM_phyt = preference_matrix_input$phyt[which(rownames(preference_matrix_input)=="ammonia")],
PREF_phyt_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="phyt")],
PREF_det_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="suspdet")],
PREF_benthslar_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_omni = preference_matrix_input$omnivzoo[which(rownames(preference_matrix_input)=="benthclar")],
PREF_omni_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_benthslar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="benthclar")],
PREF_fishplar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="fishplar")],
PREF_fishdlar_carn = preference_matrix_input$carnzoo[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_omni_fishplar = preference_matrix_input$fishplar[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_benthslar_fishplar = preference_matrix_input$fishplar[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishplar = preference_matrix_input$fishplar[which(rownames(preference_matrix_input)=="benthclar")],
PREF_omni_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_carn_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benthslar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="benthclar")],
PREF_fishdlar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_fishplar_fishp = preference_matrix_input$fishp[which(rownames(preference_matrix_input)=="fishplar")],
PREF_omni_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_carn_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benthslar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="benthclar")],
PREF_fishdlar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_fishplar_fishm = preference_matrix_input$fishm[which(rownames(preference_matrix_input)=="fishplar")],
PREF_omni_fishdlar = preference_matrix_input$fishdlar[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_benthslar_fishdlar = preference_matrix_input$fishdlar[which(rownames(preference_matrix_input)=="benthslar")],
PREF_benthclar_fishdlar = preference_matrix_input$fishdlar[which(rownames(preference_matrix_input)=="benthclar")],
PREF_carn_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishplar_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishplar")],
PREF_fishdlar_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishdlar")],
PREF_fishp_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="fishd")],
PREF_disc_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="discards")],
PREF_corp_fishd = preference_matrix_input$fishd[which(rownames(preference_matrix_input)=="corpses")],
PREF_phyt_benthslar = preference_matrix_input$benthslar[which(rownames(preference_matrix_input)=="phyt")],
PREF_phyt_benthclar = preference_matrix_input$benthclar[which(rownames(preference_matrix_input)=="phyt")],
PREF_det_benthslar = preference_matrix_input$benthslar[which(rownames(preference_matrix_input)=="suspdet")],
PREF_det_benthclar = preference_matrix_input$benthclar[which(rownames(preference_matrix_input)=="suspdet")],
PREF_phyt_benths = preference_matrix_input$benths[which(rownames(preference_matrix_input)=="phyt")],
PREF_det_benths = preference_matrix_input$benths[which(rownames(preference_matrix_input)=="suspdet")],
PREF_sed_benths = preference_matrix_input$benths[which(rownames(preference_matrix_input)=="seddet")],
PREF_kelp_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="kelp")],
PREF_kelpdebris_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="kelpdebris")],
PREF_benths_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="benths")],
PREF_corp_benthc = preference_matrix_input$benthc[which(rownames(preference_matrix_input)=="corpses")],
PREF_carn_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishp_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="fishd")],
PREF_disc_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="discards")],
PREF_corp_bird = preference_matrix_input$bird[which(rownames(preference_matrix_input)=="corpses")],
PREF_carn_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishp_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="fishd")],
PREF_bird_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="bird")],
PREF_disc_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="discards")],
PREF_corp_seal = preference_matrix_input$seal[which(rownames(preference_matrix_input)=="corpses")],
PREF_omni_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="omnivzoo")],
PREF_carn_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="carnzoo")],
PREF_benths_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="benths")],
PREF_benthc_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="benthc")],
PREF_fishp_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="fishp")],
PREF_fishm_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="fishm")],
PREF_fishd_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="fishd")],
PREF_bird_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="bird")],
PREF_seal_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="seal")],
PREF_disc_ceta = preference_matrix_input$ceta[which(rownames(preference_matrix_input)=="discards")],
# uptake_mort_input: 18+19+17+16 = 70 pars
# u_store: 18 pars
uC_kelp = uptake_mort_input$Cumax[which(uptake_mort_input$consumer=="kelp")],
ddexudC_kelp = uptake_mort_input$Cddexud[which(uptake_mort_input$consumer=="kelp")],
u_kelp = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="kelp")],
u_phyt = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="phyt_s")],
u_omni = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="omnivzoo")],
u_carn = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="carnzoo")],
u_fishplar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishplar")],
u_fishp = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishp")],
u_fishm = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishm")],
u_fishdlar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishdlar")],
u_fishd = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="fishd")],
u_benthslar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benthslar")],
u_benthclar = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benthclar")],
u_benths = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benths")],
u_benthc = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="benthc")],
u_bird = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="bird")],
u_seal = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="seal")],
u_ceta = uptake_mort_input$Numax[which(uptake_mort_input$consumer=="ceta")],
# h_store: 19 pars
h_kelp = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="kelp")],
h_phyt = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="phyt_s")],
h_omni = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="omnivzoo")],
h_carn = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="carnzoo")],
h_fishplar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishplar")],
h_fishp = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishp")],
h_fishm = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishm")],
h_fishdlar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishdlar")],
h_fishd = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="fishd")],
h_benthslar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benthslar")],
h_benthclar = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benthclar")],
h_benths = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benths")],
h_benthc = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="benthc")],
h_bird = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="bird")],
h_seal = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="seal")],
h_ceta = uptake_mort_input$Nhsat[which(uptake_mort_input$consumer=="ceta")],
bda_par_bird = uptake_mort_input$BdeApar[which(uptake_mort_input$consumer=="bird")],
bda_par_seal = uptake_mort_input$BdeApar[which(uptake_mort_input$consumer=="seal")],
bda_par_ceta = uptake_mort_input$BdeApar[which(uptake_mort_input$consumer=="ceta")],
#Mineralisation, nitrification and denitrification rates per day at the reference temperature
# biogeostore: 22 pars
xmt = microbiology_input$Value[1],
xnst = microbiology_input$Value[2],
xdst = microbiology_input$Value[3],
xndt = microbiology_input$Value[4],
xddt = microbiology_input$Value[5],
xqs_p1 = microbiology_input$Value[6], # proportion of detritus which become refractory when minearlised
xqs_p2 = microbiology_input$Value[7], # ratio of refratory to labile detritus minearalisation rates
xqs_p3 = microbiology_input$Value[8], # proportion of refractory whiuch becomes labile when re-oxygenated
xmsedt = microbiology_input$Value[9],
xmsens = microbiology_input$Value[10],
xnsedt = microbiology_input$Value[11],
xnsens = microbiology_input$Value[12],
xdsedt = microbiology_input$Value[13],
xdsens = microbiology_input$Value[14],
#Proportion of discards sinking to become seabed corpses per day - temperature independent
xdisc_corp = microbiology_input$Value[15],
#Proportion of corpse mass converted to detritus per day at the reference temperature
xxcorp_det = microbiology_input$Value[16], # orginally xcorp_det
xkelpdebris_det = microbiology_input$Value[17],
#Sinking rates and their dependence on mixing - temperature independent
xdsink_s = microbiology_input$Value[18],
xdsink_d = microbiology_input$Value[19],
#Density dependent self shading parameter for kelp
xkelpshade = microbiology_input$Value[20],
#Wave-dependent beach-cast parameter for kelp debris
xwave_kelpdebris = microbiology_input$Value[21],
#Fitting parameter fopr demersal discard rate - expect this to be about 1.0
xdfdp = microbiology_input$Value[22],
# mortstore: 17 pars
#Density dependent parameter linking wave height to kelp destruction rate
xxwave_kelp = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="kelp")],
xxst = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="phyt_s")],
xxdt = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="phyt_d")],
#Death rate of carnivores fish birds and mammals per unit biomass - temperature independent
xxomni = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="omnivzoo")],
xxcarn = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="carnzoo")],
xxbenthslar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benthslar")],
xxbenthclar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benthclar")],
xxbenths = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benths")],
xxbenthc = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="benthc")],
xxpfishlar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishplar")],
xxdfishlar = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishdlar")],
xxpfish = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishp")],
xxmfish = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishm")],
xxdfish = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="fishd")],
xxbird = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="bird")],
xxseal = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="seal")],
xxceta = uptake_mort_input$ddmort[which(uptake_mort_input$consumer=="ceta")],
# reststore: 16 pars
#Parameters for food gradient migration rates of pelagic and migratory fish
xpfish_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="fishp")],
xmfish_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="fishm")],
xdfish_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="fishd")],
xbird_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="bird")],
xseal_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="seal")],
xceta_migcoef = uptake_mort_input$migration_coef[which(uptake_mort_input$consumer=="ceta")],
#Maximum proportions of the stock biomass which is accessible to the fisheries
#Units proportions
xmax_exploitable_f_KP = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="kelp")],
xmax_exploitable_f_PF = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="fishp")],
xmax_exploitable_f_DF = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="fishd")],
xmax_exploitable_f_MF = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="fishm")],
xmax_exploitable_f_SB = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="benths")],
xmax_exploitable_f_CB = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="benthc")],
xmax_exploitable_f_CZ = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="carnzoo")],
xmax_exploitable_f_BD = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="bird")],
xmax_exploitable_f_SL = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="seal")],
xmax_exploitable_f_CT = uptake_mort_input$max_exploitable_f[which(uptake_mort_input$consumer=="ceta")]
)
fitted.parameters
}
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