Nothing
R/build_annual_drivers.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
build_annual_drivers
#
# build_annual_drivers.R
#
#' uses monthly values of time-series drivers over a climatological annual cycle
#' and makes them into functions for #interpolating values at any given time.
#'
#' returns set of interpolating functions
#'
#' @param run model run object
#' @param fixed.parms fixed parameters
#' @param physical.parms physical parameters
#' @param physics.drivers physics drivers
#' @param chemistry.drivers chemistry drivers
#' @param biological.events biological timing events
#'
#' @return driver functions
#'
#' @importFrom stats rnorm approxfun
#'
#' @noRd
#
# ------------------------------------------------------------------------------
build_annual_drivers <- function(run, fixed.parms, physical.parms, physics.drivers, chemistry.drivers, biological.events) {
# run:
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
drndays <- elt(run, "drndays")
drtimes <- elt(run, "drtimes")
sprectimes <- elt(run, "sprectimes")
# physical.parms:
P_an_fec <- elt(fixed.parms, "P_an_fec")
D_an_fec <- elt(fixed.parms, "D_an_fec")
BC_an_fec <- elt(fixed.parms, "BC_an_fec")
BS_an_fec <- elt(fixed.parms, "BS_an_fec")
# physical.parms:
so_depth <- elt(physical.parms, "so_depth")
si_depth <- elt(physical.parms, "si_depth")
d_depth <- elt(physical.parms, "d_depth")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
physics <- physics.drivers
boundconc <- chemistry.drivers
BETdata <- biological.events
#Annual fecundities need to have alreday been read in from the fixed parameter file
#Set the fish and benthos spawning dates and durations, and recruitment dates and durations, and fecundities (max gonad wt /unit total wt)
#-----------------------------------------------------------------------------------------------------------------------------
#Pelagic fish
P_sp_start<- BETdata[1,1]
P_sp_dur<-BETdata[2,1]
P_rec_start<-BETdata[3,1]
P_rec_dur<-BETdata[4,1]
#P_an_fec<-HWPdata[37,1]
#Demersal fish
D_sp_start<- BETdata[5,1]
D_sp_dur<-BETdata[6,1]
D_rec_start<-BETdata[7,1]
D_rec_dur<-BETdata[8,1]
#D_an_fec<-HWPdata[38,1]
BS_sp_start<-BETdata[9,1]
BS_sp_dur<-BETdata[10,1]
BS_rec_start<-BETdata[11,1]
BS_rec_dur<-BETdata[12,1]
#BS_an_fec<-HWPdata[39,1]
BC_sp_start<-BETdata[13,1]
BC_sp_dur<-BETdata[14,1]
BC_rec_start<-BETdata[15,1]
BC_rec_dur<-BETdata[16,1]
#BC_an_fec<-HWPdata[40,1]
#Set the migratory fish imigration and emigration time and rates
#---------------------------------------------------------------
#SWITCH (value 0 or 1) to turn off or on the code for imigration and emigration
migfish_oceanscale <- BETdata[17,1]
#Compute the nitrogen mass of the large scale population supplying imigrants to the model domain (mMN)
migfish_oceanbio <- BETdata[18,1] # Tonnes wet weight
migfish_C_ww <- BETdata[19,1] # gC/gWW
ssarea <- BETdata[20,1]*1000000 # model domain surface area m2 (North Sea = km2)
migfish_oceanpop <- (migfish_oceanbio*1000000*migfish_C_ww/12)*1000*(16/106) # units mMN
#migfish_oceanpop/ssarea # Test.... mMN/m2
#Proportion of the large scale popualtion migrating into the model domain each year
migfish_ocean_prop_entering <- BETdata[21,1]
#Start date for imigration
migfish_im_start <- BETdata[22,1]
#End day for imigration (must be later than start day even if migration is disabled)
migfish_im_end <- BETdata[23,1]
#Proportion of peak population within the model domain which remains and doe snot emigrate
migfish_ocean_prop_staying <- BETdata[24,1]
#Start date for emigration (emigration can be earlier in the year than imigration - ie immigrants are present across 1 January)
migfish_em_start <- BETdata[25,1]
#End day for emigration (must be later than start day even if migration is disabled)
migfish_em_end <- BETdata[26,1]
#.....................................
#]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
#Generate time dependent interpolation functions for each driver
#The drivers needed are.....
#Light at the sea surface
#SPM in the surface layer"
#vertical exchange coefficient derived from "logkvert","mixlscale"
#sinflow
#dinflow
#rivervol
#stemp
#dtemp
#Proportion upwelling
#Surface outflow
#Deep outflow
#atmnitrate flux
#atmammonia flux
#Boundary concentration values of..
#snitrate
#sammonia
#surface phyto
#surface flag
#surface uzoo
#surface detritus
#dnitrate
#dammonia
#deep phyto
#deep flag
#deep uzoo
#deep detritus
#rivnitrate
#rivammona
#rivdetritus
pdriver<-data.frame(rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),
rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),
rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),
rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays))
#names(pdriver)<-c("sslight","logespm","v_dif","s_inflow","d_inflow","prop_up",
# "river","stemp","dtemp","atm_nit","atm_amm","s1_pd","s2_pd","s3_pd","d1_pd","d2_pd","d3_pd")
names(pdriver)<-c("sslight","so_logespm","si_logespm","so_temp","d_temp","si_temp","river",
"v_dif","prop_up","so_inflow","d_inflow","si_inflow","si_outflow","so_si_flow",
"so_atm_nit","so_atm_amm","si_atm_nit","si_atm_amm",
"d1_pd","d2_pd","d3_pd","s1_pd","s2_pd","s3_pd","s_wave")
cdriver<-data.frame(rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays))
#names(cdriver)<-c("snit","samm","sphyt","sflag","suzoo","sdet","dnit","damm","dphyt","dflag","duzoo","ddet","riv_nit","riv_amm","riv_det")
names(cdriver)<-c("so_nit","so_amm","so_phyt","so_det",
"d_nit","d_amm","d_phyt","d_det",
"si_nit","si_amm","si_phyt","si_det",
"riv_nit","riv_amm","riv_det")
#bdriver<-data.frame(rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays))
#names(bdriver)<-c("pfish_sp","dfish_sp","pfish_rec","dfish_rec")
bdriver<-data.frame(rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays))
names(bdriver)<-c("pfish_sp","dfish_sp","pfish_rec","dfish_rec","bc_sp","bc_rec","bs_sp","bs_rec","migfish_im","migfish_em")
#Light.... and SPM
pdriver$sslight[1:drndays]<-rep(physics$sslight,nyears)
driversslight <- approxfun(drtimes, pdriver$sslight, rule=2)
pdriver$so_logespm[1:drndays]<-rep(physics$so_logespm,nyears)
driverso_logespm <- approxfun(drtimes, pdriver$so_logespm, rule=2)
pdriver$si_logespm[1:drndays]<-rep(physics$si_logespm,nyears)
driversi_logespm <- approxfun(drtimes, pdriver$si_logespm, rule=2)
#Offshore Surface temperature....
pdriver$so_temp[1:drndays]<-rep(physics$so_temp,nyears)
driverso_temp <- approxfun(drtimes, pdriver$so_temp, rule=2)
#Deep temperature....
pdriver$d_temp[1:drndays]<-rep(physics$d_temp,nyears)
driverd_temp <- approxfun(drtimes, pdriver$d_temp, rule=2)
#Inshore Surface temperature....
pdriver$si_temp[1:drndays]<-rep(physics$si_temp,nyears)
driversi_temp <- approxfun(drtimes, pdriver$si_temp, rule=2)
#Vertical diffusion...
physics$vdif<-(10^(physics$logkvert))/(physics$mixlscale*(so_depth+d_depth))
pdriver$v_dif[1:drndays]<-rep(physics$vdif,nyears)
driverv_dif <- approxfun(drtimes, pdriver$v_dif, rule=2)
#Offshore Surface inflow volume.....
pdriver$so_inflow[1:drndays]<-rep(physics$so_inflow*so_depth*(1-x_shallowprop),nyears)
driverso_inflow <- approxfun(drtimes, pdriver$so_inflow, rule=2)
#Offshore Deep inflow volume...
pdriver$d_inflow[1:drndays]<-rep(physics$d_inflow*d_depth*(1-x_shallowprop),nyears)
driverd_inflow <- approxfun(drtimes, pdriver$d_inflow, rule=2)
#Inshore Surface inflow volume.....
pdriver$si_inflow[1:drndays]<-rep(physics$si_inflow*si_depth*(x_shallowprop),nyears)
driversi_inflow <- approxfun(drtimes, pdriver$si_inflow, rule=2)
#Inshore Surface outflow volume.....
pdriver$si_outflow[1:drndays]<-rep(physics$si_outflow*si_depth*(x_shallowprop),nyears)
driversi_outflow <- approxfun(drtimes, pdriver$si_outflow, rule=2)
#ORIGINAL VERSION - NEEDS TO BE ATTENUATED TO ACCOUNT FOR MIXING LENGTH SCALE IN INSHORE WATERS
##Offshore-inshore flow volume.....
#pdriver$so_si_flow[1:drndays]<-rep(physics$so_si_flow*si_depth*(x_shallowprop),nyears)
#driverso_si_flow <- approxfun(drtimes, pdriver$so_si_flow, rule=2)
#REVISED VERSION - ACCOUNTING FOR MIXING LENGTH SCALE IN INSHORE WATERS
#ASSUMES INFLOW VOLUME IS ATTENUATED BY THE SQUARE OF THE VOLUME OF INSHORE WATERS
#Offshore-inshore flow volume.....
attenuated_so_si_inflow <- 1/((1/physics$so_si_flow)^2)
pdriver$so_si_flow[1:drndays]<-rep(attenuated_so_si_inflow*si_depth*(x_shallowprop),nyears)
driverso_si_flow <- approxfun(drtimes, pdriver$so_si_flow, rule=2)
#Upwelling fraction of deep inflow....
pdriver$prop_up[1:drndays]<-rep(physics$upwelling,nyears)
drivers_upwell <- approxfun(drtimes, (pdriver$prop_up*pdriver$d_inflow), rule=2)
#Derived outflow from si to so - NOT NEEDED HERE ANY MORE
#driversi_so_flow <- approxfun(drtimes, pdriver$so_si_flow + pdriver$si_inflow - pdriver$si_outflow, rule=2)
#Derived surface and deep boundary outflow volumes...... - NOT NEEDED HERE ANY MORE
#driverso_outflow <- approxfun(drtimes, (pdriver$so_inflow + pdriver$prop_up*pdriver$d_inflow + pdriver$si_inflow - pdriver$si_outflow ), rule=2)
#KEEP THIS
driverd_outflow <- approxfun(drtimes, (1-pdriver$prop_up)*pdriver$d_inflow, rule=2)
#~~~~~~~~~~~~~~~
#Some checking to see if we have volume conservation
# ttt<-seq(1,360)
# driverso_inflow(ttt)
# driverd_inflow(ttt)
# driversi_inflow(ttt)
# driverso_outflow(ttt)
# driverd_outflow(ttt)
# driversi_outflow(ttt)
#Volume conservation for the whole system
# plot( (driverso_inflow(ttt) + driverd_inflow(ttt) + driversi_inflow(ttt) - driverso_outflow(ttt) - driverd_outflow(ttt) - driversi_outflow(ttt)),type="l")
# abline(h=0)
# sum( ( (driverso_inflow(ttt) + driverd_inflow(ttt) + driversi_inflow(ttt) - driverso_outflow(ttt) - driverd_outflow(ttt) - driversi_outflow(ttt)) ) )
#Volume conservation for the offshore surface layer
# plot( (driverso_inflow(ttt) + drivers_upwell(ttt) + driversi_so_flow(ttt) - driverso_outflow(ttt) - driverso_si_flow(ttt)),type="l")
# abline(h=0)
# sum( ( (driverso_inflow(ttt) + drivers_upwell(ttt) + driversi_so_flow(ttt) - driverso_outflow(ttt) - driverso_si_flow(ttt)) ) )
#Volume conservation forthe inshore zone
# plot( (driversi_inflow(ttt) + driverso_si_flow(ttt) - driversi_outflow(ttt) - driversi_so_flow(ttt)),type="l")
# abline(h=0)
# sum( ( (driversi_inflow(ttt) + driverso_si_flow(ttt) - driversi_outflow(ttt) - driversi_so_flow(ttt)) ) )
#Volume conservation fof the ofshore deep layer
# plot( (driverd_inflow(ttt) - drivers_upwell(ttt) - driverd_outflow(ttt)) , type="l")
# abline(h=0)
# sum( ( (driverd_inflow(ttt) - drivers_upwell(ttt) - driverd_outflow(ttt)) ) )
#~~~~~~~~~~~~~~~
#River volume inflow volume...
pdriver$river[1:drndays]<-rep(physics$rivervol*si_depth*(x_shallowprop),nyears)
driverriver <- approxfun(drtimes, pdriver$river, rule=2)
#Sediment natural disturbance fraction per day deep sediments
pdriver$d1_pd[1:drndays]<-rep(physics$d1_pdist,nyears)
driver_d1_pd <- approxfun(drtimes, pdriver$d1_pd, rule=2)
#Sediment natural disturbance fraction per day deep sediments
pdriver$d2_pd[1:drndays]<-rep(physics$d2_pdist,nyears)
driver_d2_pd <- approxfun(drtimes, pdriver$d2_pd, rule=2)
#Sediment natural disturbance fraction per day deep sediments
pdriver$d3_pd[1:drndays]<-rep(physics$d3_pdist,nyears)
driver_d3_pd <- approxfun(drtimes, pdriver$d3_pd, rule=2)
#Sediment natural disturbance fraction per day shallow sediments
pdriver$s1_pd[1:drndays]<-rep(physics$s1_pdist,nyears)
driver_s1_pd <- approxfun(drtimes, pdriver$s1_pd, rule=2)
#Sediment natural disturbance fraction per day shallow sediments
pdriver$s2_pd[1:drndays]<-rep(physics$s2_pdist,nyears)
driver_s2_pd <- approxfun(drtimes, pdriver$s2_pd, rule=2)
#Sediment natural disturbance fraction per day shallow sediments
pdriver$s3_pd[1:drndays]<-rep(physics$s3_pdist,nyears)
driver_s3_pd <- approxfun(drtimes, pdriver$s3_pd, rule=2)
#Inshore wave height
pdriver$s_wave[1:drndays]<-rep(physics$Inshore_waveheight,nyears)
drivers_wave <- approxfun(drtimes, pdriver$s_wave, rule=2)
#Offshore Atmospheric nitrate flux
pdriver$so_atm_nit[1:drndays]<-rep(boundconc$so_atmnitrate,nyears)
driverso_atm_nit <- approxfun(drtimes, pdriver$so_atm_nit, rule=2)
#Offshore Atmospheric ammonia flux
pdriver$so_atm_amm[1:drndays]<-rep(boundconc$so_atmammonia,nyears)
driverso_atm_amm <- approxfun(drtimes, pdriver$so_atm_amm, rule=2)
#Inshore Atmospheric PLUS OTHER nitrate flux
pdriver$si_atm_nit[1:drndays]<-rep((boundconc$si_atmnitrate+boundconc$si_othernitrate),nyears)
driversi_atm_nit <- approxfun(drtimes, pdriver$si_atm_nit, rule=2)
#Inshore Atmospheric PLUS OTHER ammonia flux
pdriver$si_atm_amm[1:drndays]<-rep((boundconc$si_atmammonia+boundconc$si_otherammonia),nyears)
driversi_atm_amm <- approxfun(drtimes, pdriver$si_atm_amm, rule=2)
#Boundary offshore surface nitrate concentrations
cdriver$so_nit[1:drndays]<-rep(boundconc$so_nitrate,nyears)
driverboundso_nit <- approxfun(drtimes, cdriver$so_nit, rule=2)
#Boundary offshore surface ammonia concentrations
cdriver$so_amm[1:drndays]<-rep(boundconc$so_ammonia,nyears)
driverboundso_amm <- approxfun(drtimes, cdriver$so_amm, rule=2)
#Boundary offshore surface phyt concentrations
cdriver$so_phyt[1:drndays]<-rep(boundconc$so_phyt,nyears)
driverboundso_phyt <- approxfun(drtimes, cdriver$so_phyt, rule=2)
#Boundary offshore surface detritus concentrations
cdriver$so_det[1:drndays]<-rep(boundconc$so_detritus,nyears)
driverboundso_det <- approxfun(drtimes, cdriver$so_det, rule=2)
#Boundary offshore deep nitrate concentrations
cdriver$d_nit[1:drndays]<-rep(boundconc$d_nitrate,nyears)
driverboundd_nit <- approxfun(drtimes, cdriver$d_nit, rule=2)
#Boundary offshore deep ammonia concentrations
cdriver$d_amm[1:drndays]<-rep(boundconc$d_ammonia,nyears)
driverboundd_amm <- approxfun(drtimes, cdriver$d_amm, rule=2)
#Boundary offshore deep phyt concentrations
cdriver$d_phyt[1:drndays]<-rep(boundconc$d_phyt,nyears)
driverboundd_phyt <- approxfun(drtimes, cdriver$d_phyt, rule=2)
#Boundary offshore deep detritus concentrations
cdriver$d_det[1:drndays]<-rep(boundconc$d_detritus,nyears)
driverboundd_det <- approxfun(drtimes, cdriver$d_det, rule=2)
#Boundary inshore surface nitrate concentrations
cdriver$si_nit[1:drndays]<-rep(boundconc$si_nitrate,nyears)
driverboundsi_nit <- approxfun(drtimes, cdriver$si_nit, rule=2)
#Boundary inshore surface ammonia concentrations
cdriver$si_amm[1:drndays]<-rep(boundconc$si_ammonia,nyears)
driverboundsi_amm <- approxfun(drtimes, cdriver$si_amm, rule=2)
#Boundary inshore surface phyt concentrations
cdriver$si_phyt[1:drndays]<-rep(boundconc$si_phyt,nyears)
driverboundsi_phyt <- approxfun(drtimes, cdriver$si_phyt, rule=2)
#Boundary inshore surface detritus concentrations
cdriver$si_det[1:drndays]<-rep(boundconc$si_detritus,nyears)
driverboundsi_det <- approxfun(drtimes, cdriver$si_det, rule=2)
#Boundary river nitrate concentrations
cdriver$riv_nit[1:drndays]<-rep(boundconc$rivnitrate,nyears)
driverboundriv_nit <- approxfun(drtimes, cdriver$riv_nit, rule=2)
#Boundary river ammonia concentrations
cdriver$riv_amm[1:drndays]<-rep(boundconc$rivammonia,nyears)
driverboundriv_amm <- approxfun(drtimes, cdriver$riv_amm, rule=2)
#Boundary river detritus concentrations
cdriver$riv_det[1:drndays]<-rep(boundconc$rivdetritus,nyears)
driverboundriv_det <- approxfun(drtimes, cdriver$riv_det, rule=2)
#Set the fish spawning and recruitment rate driving data
#Spawning first
pspawn<-rep(0,360)
dspawn<-rep(0,360)
#pspawn[P_sp_start:(P_sp_start+P_sp_dur)]<-P_an_fec/P_sp_dur
#dspawn[D_sp_start:(D_sp_start+D_sp_dur)]<-D_an_fec/D_sp_dur
pspawn[P_sp_start:(P_sp_start+P_sp_dur)]<-1/P_sp_dur # fecundity transferred to parameter list
dspawn[D_sp_start:(D_sp_start+D_sp_dur)]<-1/D_sp_dur # fecundity transferred to parameter list
bdriver$pfish_sp[1:ndays-1]<-rep(pspawn,nyears)
bdriver$dfish_sp[1:ndays-1]<-rep(dspawn,nyears)
#Set recruitment
prec<-rep(0,360)
drec<-rep(0,360)
prec[P_rec_start:(P_rec_start+P_rec_dur)]<-0.1
drec[D_rec_start:(D_rec_start+D_rec_dur)]<-0.1
bdriver$pfish_rec[1:ndays-1]<-rep(prec,nyears)
bdriver$dfish_rec[1:ndays-1]<-rep(drec,nyears)
driverpfish_sp <- approxfun(sprectimes, bdriver$pfish_sp, rule=2)
driverdfish_sp <- approxfun(sprectimes, bdriver$dfish_sp, rule=2)
driverpfish_rec <- approxfun(sprectimes, bdriver$pfish_rec, rule=2)
driverdfish_rec <- approxfun(sprectimes, bdriver$dfish_rec, rule=2)
#Set the benthos spawning and recruitment rate driving data
#Spawning first
bcspawn<-rep(0,360)
bsspawn<-rep(0,360)
#bcspawn[BC_sp_start:(BC_sp_start+BC_sp_dur)]<-BC_an_fec/BC_sp_dur
#bsspawn[BS_sp_start:(BS_sp_start+BS_sp_dur)]<-BS_an_fec/BS_sp_dur
bcspawn[BC_sp_start:(BC_sp_start+BC_sp_dur)]<-1/BC_sp_dur # fecundity transferred to parameter list
bsspawn[BS_sp_start:(BS_sp_start+BS_sp_dur)]<-1/BS_sp_dur # fecundity transferred to parameter list
bdriver$bc_sp[1:ndays-1]<-rep(bcspawn,nyears)
bdriver$bs_sp[1:ndays-1]<-rep(bsspawn,nyears)
#Set recruitment
#bcrec<-rep(0.05,360)
#bsrec<-rep(0.05,360)
#bcrec[BC_sp_start:(BC_sp_start+BC_sp_dur)]<-0.0
#bcrec[BC_rec_start:(BC_rec_start+BC_rec_dur)]<-0.05
#bsrec[BS_sp_start:(BS_sp_start+BS_sp_dur)]<-0.0
#bsrec[BS_rec_start:(BS_rec_start+BS_rec_dur)]<-0.05
bcrec<-rep(0,360)
bsrec<-rep(0,360)
bcrec[BC_rec_start:(BC_rec_start+BC_rec_dur)]<-0.1
bsrec[BS_rec_start:(BS_rec_start+BS_rec_dur)]<-0.1
bdriver$bc_rec[1:ndays-1]<-rep(bcrec,nyears)
bdriver$bs_rec[1:ndays-1]<-rep(bsrec,nyears)
driverbc_sp <- approxfun(sprectimes, bdriver$bc_sp, rule=2)
driverbs_sp <- approxfun(sprectimes, bdriver$bs_sp, rule=2)
driverbc_rec <- approxfun(sprectimes, bdriver$bc_rec, rule=2)
driverbs_rec <- approxfun(sprectimes, bdriver$bs_rec, rule=2)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Set up the migratory fish imigration rate driving functions
migfish_imig <- rep(0,360)
migfish_imig[migfish_im_start:migfish_im_end]<-(migfish_oceanpop*migfish_oceanscale/ssarea)*migfish_ocean_prop_entering/(migfish_im_end-migfish_im_start)
bdriver$migfish_im[1:ndays-1]<- rep(migfish_imig,nyears)
driver_migfish_imig <- approxfun(sprectimes, bdriver$migfish_im, rule=2)
# ........................
# Set up the migratory fish emigration rate driving functions
migfish_emig <- rep(0,360)
migfish_emig[migfish_em_start:migfish_em_end]<-migfish_oceanscale*(-log(migfish_ocean_prop_staying))/(migfish_em_end-migfish_em_start)
bdriver$migfish_em[1:ndays-1]<- rep(migfish_emig,nyears)
driver_migfish_emig <- approxfun(sprectimes, bdriver$migfish_em, rule=2)
# ........................
drivers <- list(
driversslight = driversslight,
driverso_logespm = driverso_logespm,
driversi_logespm = driversi_logespm,
driverso_temp = driverso_temp,
driverd_temp = driverd_temp,
driversi_temp = driversi_temp,
driverv_dif = driverv_dif,
driverso_inflow = driverso_inflow,
driverd_inflow = driverd_inflow,
driversi_inflow = driversi_inflow,
driversi_outflow = driversi_outflow,
driverso_si_flow = driverso_si_flow,
drivers_upwell = drivers_upwell,
driverd_outflow = driverd_outflow,
driverriver = driverriver,
driver_d1_pd = driver_d1_pd,
driver_d2_pd = driver_d2_pd,
driver_d3_pd = driver_d3_pd,
driver_s1_pd = driver_s1_pd,
driver_s2_pd = driver_s2_pd,
driver_s3_pd = driver_s3_pd,
drivers_wave = drivers_wave,
driverso_atm_nit = driverso_atm_nit,
driverso_atm_amm = driverso_atm_amm,
driversi_atm_nit = driversi_atm_nit,
driversi_atm_amm = driversi_atm_amm,
driverboundso_nit = driverboundso_nit,
driverboundso_amm = driverboundso_amm,
driverboundso_phyt = driverboundso_phyt,
driverboundso_det = driverboundso_det,
driverboundd_nit = driverboundd_nit,
driverboundd_amm = driverboundd_amm,
driverboundd_phyt = driverboundd_phyt,
driverboundd_det = driverboundd_det,
driverboundsi_nit = driverboundsi_nit,
driverboundsi_amm = driverboundsi_amm,
driverboundsi_phyt = driverboundsi_phyt,
driverboundsi_det = driverboundsi_det,
driverboundriv_nit = driverboundriv_nit,
driverboundriv_amm = driverboundriv_amm,
driverboundriv_det = driverboundriv_det,
driverpfish_sp = driverpfish_sp,
driverdfish_sp = driverdfish_sp,
driverpfish_rec = driverpfish_rec,
driverdfish_rec = driverdfish_rec,
driverbc_sp = driverbc_sp,
driverbs_sp = driverbs_sp,
driverbc_rec = driverbc_rec,
driverbs_rec = driverbs_rec,
driver_migfish_imig = driver_migfish_imig,
driver_migfish_emig = driver_migfish_emig
)
}
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Defines functions build_annual_drivers
#
# build_annual_drivers.R
#
#' uses monthly values of time-series drivers over a climatological annual cycle
#' and makes them into functions for #interpolating values at any given time.
#'
#' returns set of interpolating functions
#'
#' @param run model run object
#' @param fixed.parms fixed parameters
#' @param physical.parms physical parameters
#' @param physics.drivers physics drivers
#' @param chemistry.drivers chemistry drivers
#' @param biological.events biological timing events
#'
#' @return driver functions
#'
#' @importFrom stats rnorm approxfun
#'
#' @noRd
#
# ------------------------------------------------------------------------------
build_annual_drivers <- function(run, fixed.parms, physical.parms, physics.drivers, chemistry.drivers, biological.events) {
# run:
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
drndays <- elt(run, "drndays")
drtimes <- elt(run, "drtimes")
sprectimes <- elt(run, "sprectimes")
# physical.parms:
P_an_fec <- elt(fixed.parms, "P_an_fec")
D_an_fec <- elt(fixed.parms, "D_an_fec")
BC_an_fec <- elt(fixed.parms, "BC_an_fec")
BS_an_fec <- elt(fixed.parms, "BS_an_fec")
# physical.parms:
so_depth <- elt(physical.parms, "so_depth")
si_depth <- elt(physical.parms, "si_depth")
d_depth <- elt(physical.parms, "d_depth")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
physics <- physics.drivers
boundconc <- chemistry.drivers
BETdata <- biological.events
#Annual fecundities need to have alreday been read in from the fixed parameter file
#Set the fish and benthos spawning dates and durations, and recruitment dates and durations, and fecundities (max gonad wt /unit total wt)
#-----------------------------------------------------------------------------------------------------------------------------
#Pelagic fish
P_sp_start<- BETdata[1,1]
P_sp_dur<-BETdata[2,1]
P_rec_start<-BETdata[3,1]
P_rec_dur<-BETdata[4,1]
#P_an_fec<-HWPdata[37,1]
#Demersal fish
D_sp_start<- BETdata[5,1]
D_sp_dur<-BETdata[6,1]
D_rec_start<-BETdata[7,1]
D_rec_dur<-BETdata[8,1]
#D_an_fec<-HWPdata[38,1]
BS_sp_start<-BETdata[9,1]
BS_sp_dur<-BETdata[10,1]
BS_rec_start<-BETdata[11,1]
BS_rec_dur<-BETdata[12,1]
#BS_an_fec<-HWPdata[39,1]
BC_sp_start<-BETdata[13,1]
BC_sp_dur<-BETdata[14,1]
BC_rec_start<-BETdata[15,1]
BC_rec_dur<-BETdata[16,1]
#BC_an_fec<-HWPdata[40,1]
#Set the migratory fish imigration and emigration time and rates
#---------------------------------------------------------------
#SWITCH (value 0 or 1) to turn off or on the code for imigration and emigration
migfish_oceanscale <- BETdata[17,1]
#Compute the nitrogen mass of the large scale population supplying imigrants to the model domain (mMN)
migfish_oceanbio <- BETdata[18,1] # Tonnes wet weight
migfish_C_ww <- BETdata[19,1] # gC/gWW
ssarea <- BETdata[20,1]*1000000 # model domain surface area m2 (North Sea = km2)
migfish_oceanpop <- (migfish_oceanbio*1000000*migfish_C_ww/12)*1000*(16/106) # units mMN
#migfish_oceanpop/ssarea # Test.... mMN/m2
#Proportion of the large scale popualtion migrating into the model domain each year
migfish_ocean_prop_entering <- BETdata[21,1]
#Start date for imigration
migfish_im_start <- BETdata[22,1]
#End day for imigration (must be later than start day even if migration is disabled)
migfish_im_end <- BETdata[23,1]
#Proportion of peak population within the model domain which remains and doe snot emigrate
migfish_ocean_prop_staying <- BETdata[24,1]
#Start date for emigration (emigration can be earlier in the year than imigration - ie immigrants are present across 1 January)
migfish_em_start <- BETdata[25,1]
#End day for emigration (must be later than start day even if migration is disabled)
migfish_em_end <- BETdata[26,1]
#.....................................
#]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
#Generate time dependent interpolation functions for each driver
#The drivers needed are.....
#Light at the sea surface
#SPM in the surface layer"
#vertical exchange coefficient derived from "logkvert","mixlscale"
#sinflow
#dinflow
#rivervol
#stemp
#dtemp
#Proportion upwelling
#Surface outflow
#Deep outflow
#atmnitrate flux
#atmammonia flux
#Boundary concentration values of..
#snitrate
#sammonia
#surface phyto
#surface flag
#surface uzoo
#surface detritus
#dnitrate
#dammonia
#deep phyto
#deep flag
#deep uzoo
#deep detritus
#rivnitrate
#rivammona
#rivdetritus
pdriver<-data.frame(rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),
rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),
rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),
rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays))
#names(pdriver)<-c("sslight","logespm","v_dif","s_inflow","d_inflow","prop_up",
# "river","stemp","dtemp","atm_nit","atm_amm","s1_pd","s2_pd","s3_pd","d1_pd","d2_pd","d3_pd")
names(pdriver)<-c("sslight","so_logespm","si_logespm","so_temp","d_temp","si_temp","river",
"v_dif","prop_up","so_inflow","d_inflow","si_inflow","si_outflow","so_si_flow",
"so_atm_nit","so_atm_amm","si_atm_nit","si_atm_amm",
"d1_pd","d2_pd","d3_pd","s1_pd","s2_pd","s3_pd","s_wave")
cdriver<-data.frame(rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays),rep(0,drndays))
#names(cdriver)<-c("snit","samm","sphyt","sflag","suzoo","sdet","dnit","damm","dphyt","dflag","duzoo","ddet","riv_nit","riv_amm","riv_det")
names(cdriver)<-c("so_nit","so_amm","so_phyt","so_det",
"d_nit","d_amm","d_phyt","d_det",
"si_nit","si_amm","si_phyt","si_det",
"riv_nit","riv_amm","riv_det")
#bdriver<-data.frame(rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays))
#names(bdriver)<-c("pfish_sp","dfish_sp","pfish_rec","dfish_rec")
bdriver<-data.frame(rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays),rep(0,ndays))
names(bdriver)<-c("pfish_sp","dfish_sp","pfish_rec","dfish_rec","bc_sp","bc_rec","bs_sp","bs_rec","migfish_im","migfish_em")
#Light.... and SPM
pdriver$sslight[1:drndays]<-rep(physics$sslight,nyears)
driversslight <- approxfun(drtimes, pdriver$sslight, rule=2)
pdriver$so_logespm[1:drndays]<-rep(physics$so_logespm,nyears)
driverso_logespm <- approxfun(drtimes, pdriver$so_logespm, rule=2)
pdriver$si_logespm[1:drndays]<-rep(physics$si_logespm,nyears)
driversi_logespm <- approxfun(drtimes, pdriver$si_logespm, rule=2)
#Offshore Surface temperature....
pdriver$so_temp[1:drndays]<-rep(physics$so_temp,nyears)
driverso_temp <- approxfun(drtimes, pdriver$so_temp, rule=2)
#Deep temperature....
pdriver$d_temp[1:drndays]<-rep(physics$d_temp,nyears)
driverd_temp <- approxfun(drtimes, pdriver$d_temp, rule=2)
#Inshore Surface temperature....
pdriver$si_temp[1:drndays]<-rep(physics$si_temp,nyears)
driversi_temp <- approxfun(drtimes, pdriver$si_temp, rule=2)
#Vertical diffusion...
physics$vdif<-(10^(physics$logkvert))/(physics$mixlscale*(so_depth+d_depth))
pdriver$v_dif[1:drndays]<-rep(physics$vdif,nyears)
driverv_dif <- approxfun(drtimes, pdriver$v_dif, rule=2)
#Offshore Surface inflow volume.....
pdriver$so_inflow[1:drndays]<-rep(physics$so_inflow*so_depth*(1-x_shallowprop),nyears)
driverso_inflow <- approxfun(drtimes, pdriver$so_inflow, rule=2)
#Offshore Deep inflow volume...
pdriver$d_inflow[1:drndays]<-rep(physics$d_inflow*d_depth*(1-x_shallowprop),nyears)
driverd_inflow <- approxfun(drtimes, pdriver$d_inflow, rule=2)
#Inshore Surface inflow volume.....
pdriver$si_inflow[1:drndays]<-rep(physics$si_inflow*si_depth*(x_shallowprop),nyears)
driversi_inflow <- approxfun(drtimes, pdriver$si_inflow, rule=2)
#Inshore Surface outflow volume.....
pdriver$si_outflow[1:drndays]<-rep(physics$si_outflow*si_depth*(x_shallowprop),nyears)
driversi_outflow <- approxfun(drtimes, pdriver$si_outflow, rule=2)
#ORIGINAL VERSION - NEEDS TO BE ATTENUATED TO ACCOUNT FOR MIXING LENGTH SCALE IN INSHORE WATERS
##Offshore-inshore flow volume.....
#pdriver$so_si_flow[1:drndays]<-rep(physics$so_si_flow*si_depth*(x_shallowprop),nyears)
#driverso_si_flow <- approxfun(drtimes, pdriver$so_si_flow, rule=2)
#REVISED VERSION - ACCOUNTING FOR MIXING LENGTH SCALE IN INSHORE WATERS
#ASSUMES INFLOW VOLUME IS ATTENUATED BY THE SQUARE OF THE VOLUME OF INSHORE WATERS
#Offshore-inshore flow volume.....
attenuated_so_si_inflow <- 1/((1/physics$so_si_flow)^2)
pdriver$so_si_flow[1:drndays]<-rep(attenuated_so_si_inflow*si_depth*(x_shallowprop),nyears)
driverso_si_flow <- approxfun(drtimes, pdriver$so_si_flow, rule=2)
#Upwelling fraction of deep inflow....
pdriver$prop_up[1:drndays]<-rep(physics$upwelling,nyears)
drivers_upwell <- approxfun(drtimes, (pdriver$prop_up*pdriver$d_inflow), rule=2)
#Derived outflow from si to so - NOT NEEDED HERE ANY MORE
#driversi_so_flow <- approxfun(drtimes, pdriver$so_si_flow + pdriver$si_inflow - pdriver$si_outflow, rule=2)
#Derived surface and deep boundary outflow volumes...... - NOT NEEDED HERE ANY MORE
#driverso_outflow <- approxfun(drtimes, (pdriver$so_inflow + pdriver$prop_up*pdriver$d_inflow + pdriver$si_inflow - pdriver$si_outflow ), rule=2)
#KEEP THIS
driverd_outflow <- approxfun(drtimes, (1-pdriver$prop_up)*pdriver$d_inflow, rule=2)
#~~~~~~~~~~~~~~~
#Some checking to see if we have volume conservation
# ttt<-seq(1,360)
# driverso_inflow(ttt)
# driverd_inflow(ttt)
# driversi_inflow(ttt)
# driverso_outflow(ttt)
# driverd_outflow(ttt)
# driversi_outflow(ttt)
#Volume conservation for the whole system
# plot( (driverso_inflow(ttt) + driverd_inflow(ttt) + driversi_inflow(ttt) - driverso_outflow(ttt) - driverd_outflow(ttt) - driversi_outflow(ttt)),type="l")
# abline(h=0)
# sum( ( (driverso_inflow(ttt) + driverd_inflow(ttt) + driversi_inflow(ttt) - driverso_outflow(ttt) - driverd_outflow(ttt) - driversi_outflow(ttt)) ) )
#Volume conservation for the offshore surface layer
# plot( (driverso_inflow(ttt) + drivers_upwell(ttt) + driversi_so_flow(ttt) - driverso_outflow(ttt) - driverso_si_flow(ttt)),type="l")
# abline(h=0)
# sum( ( (driverso_inflow(ttt) + drivers_upwell(ttt) + driversi_so_flow(ttt) - driverso_outflow(ttt) - driverso_si_flow(ttt)) ) )
#Volume conservation forthe inshore zone
# plot( (driversi_inflow(ttt) + driverso_si_flow(ttt) - driversi_outflow(ttt) - driversi_so_flow(ttt)),type="l")
# abline(h=0)
# sum( ( (driversi_inflow(ttt) + driverso_si_flow(ttt) - driversi_outflow(ttt) - driversi_so_flow(ttt)) ) )
#Volume conservation fof the ofshore deep layer
# plot( (driverd_inflow(ttt) - drivers_upwell(ttt) - driverd_outflow(ttt)) , type="l")
# abline(h=0)
# sum( ( (driverd_inflow(ttt) - drivers_upwell(ttt) - driverd_outflow(ttt)) ) )
#~~~~~~~~~~~~~~~
#River volume inflow volume...
pdriver$river[1:drndays]<-rep(physics$rivervol*si_depth*(x_shallowprop),nyears)
driverriver <- approxfun(drtimes, pdriver$river, rule=2)
#Sediment natural disturbance fraction per day deep sediments
pdriver$d1_pd[1:drndays]<-rep(physics$d1_pdist,nyears)
driver_d1_pd <- approxfun(drtimes, pdriver$d1_pd, rule=2)
#Sediment natural disturbance fraction per day deep sediments
pdriver$d2_pd[1:drndays]<-rep(physics$d2_pdist,nyears)
driver_d2_pd <- approxfun(drtimes, pdriver$d2_pd, rule=2)
#Sediment natural disturbance fraction per day deep sediments
pdriver$d3_pd[1:drndays]<-rep(physics$d3_pdist,nyears)
driver_d3_pd <- approxfun(drtimes, pdriver$d3_pd, rule=2)
#Sediment natural disturbance fraction per day shallow sediments
pdriver$s1_pd[1:drndays]<-rep(physics$s1_pdist,nyears)
driver_s1_pd <- approxfun(drtimes, pdriver$s1_pd, rule=2)
#Sediment natural disturbance fraction per day shallow sediments
pdriver$s2_pd[1:drndays]<-rep(physics$s2_pdist,nyears)
driver_s2_pd <- approxfun(drtimes, pdriver$s2_pd, rule=2)
#Sediment natural disturbance fraction per day shallow sediments
pdriver$s3_pd[1:drndays]<-rep(physics$s3_pdist,nyears)
driver_s3_pd <- approxfun(drtimes, pdriver$s3_pd, rule=2)
#Inshore wave height
pdriver$s_wave[1:drndays]<-rep(physics$Inshore_waveheight,nyears)
drivers_wave <- approxfun(drtimes, pdriver$s_wave, rule=2)
#Offshore Atmospheric nitrate flux
pdriver$so_atm_nit[1:drndays]<-rep(boundconc$so_atmnitrate,nyears)
driverso_atm_nit <- approxfun(drtimes, pdriver$so_atm_nit, rule=2)
#Offshore Atmospheric ammonia flux
pdriver$so_atm_amm[1:drndays]<-rep(boundconc$so_atmammonia,nyears)
driverso_atm_amm <- approxfun(drtimes, pdriver$so_atm_amm, rule=2)
#Inshore Atmospheric PLUS OTHER nitrate flux
pdriver$si_atm_nit[1:drndays]<-rep((boundconc$si_atmnitrate+boundconc$si_othernitrate),nyears)
driversi_atm_nit <- approxfun(drtimes, pdriver$si_atm_nit, rule=2)
#Inshore Atmospheric PLUS OTHER ammonia flux
pdriver$si_atm_amm[1:drndays]<-rep((boundconc$si_atmammonia+boundconc$si_otherammonia),nyears)
driversi_atm_amm <- approxfun(drtimes, pdriver$si_atm_amm, rule=2)
#Boundary offshore surface nitrate concentrations
cdriver$so_nit[1:drndays]<-rep(boundconc$so_nitrate,nyears)
driverboundso_nit <- approxfun(drtimes, cdriver$so_nit, rule=2)
#Boundary offshore surface ammonia concentrations
cdriver$so_amm[1:drndays]<-rep(boundconc$so_ammonia,nyears)
driverboundso_amm <- approxfun(drtimes, cdriver$so_amm, rule=2)
#Boundary offshore surface phyt concentrations
cdriver$so_phyt[1:drndays]<-rep(boundconc$so_phyt,nyears)
driverboundso_phyt <- approxfun(drtimes, cdriver$so_phyt, rule=2)
#Boundary offshore surface detritus concentrations
cdriver$so_det[1:drndays]<-rep(boundconc$so_detritus,nyears)
driverboundso_det <- approxfun(drtimes, cdriver$so_det, rule=2)
#Boundary offshore deep nitrate concentrations
cdriver$d_nit[1:drndays]<-rep(boundconc$d_nitrate,nyears)
driverboundd_nit <- approxfun(drtimes, cdriver$d_nit, rule=2)
#Boundary offshore deep ammonia concentrations
cdriver$d_amm[1:drndays]<-rep(boundconc$d_ammonia,nyears)
driverboundd_amm <- approxfun(drtimes, cdriver$d_amm, rule=2)
#Boundary offshore deep phyt concentrations
cdriver$d_phyt[1:drndays]<-rep(boundconc$d_phyt,nyears)
driverboundd_phyt <- approxfun(drtimes, cdriver$d_phyt, rule=2)
#Boundary offshore deep detritus concentrations
cdriver$d_det[1:drndays]<-rep(boundconc$d_detritus,nyears)
driverboundd_det <- approxfun(drtimes, cdriver$d_det, rule=2)
#Boundary inshore surface nitrate concentrations
cdriver$si_nit[1:drndays]<-rep(boundconc$si_nitrate,nyears)
driverboundsi_nit <- approxfun(drtimes, cdriver$si_nit, rule=2)
#Boundary inshore surface ammonia concentrations
cdriver$si_amm[1:drndays]<-rep(boundconc$si_ammonia,nyears)
driverboundsi_amm <- approxfun(drtimes, cdriver$si_amm, rule=2)
#Boundary inshore surface phyt concentrations
cdriver$si_phyt[1:drndays]<-rep(boundconc$si_phyt,nyears)
driverboundsi_phyt <- approxfun(drtimes, cdriver$si_phyt, rule=2)
#Boundary inshore surface detritus concentrations
cdriver$si_det[1:drndays]<-rep(boundconc$si_detritus,nyears)
driverboundsi_det <- approxfun(drtimes, cdriver$si_det, rule=2)
#Boundary river nitrate concentrations
cdriver$riv_nit[1:drndays]<-rep(boundconc$rivnitrate,nyears)
driverboundriv_nit <- approxfun(drtimes, cdriver$riv_nit, rule=2)
#Boundary river ammonia concentrations
cdriver$riv_amm[1:drndays]<-rep(boundconc$rivammonia,nyears)
driverboundriv_amm <- approxfun(drtimes, cdriver$riv_amm, rule=2)
#Boundary river detritus concentrations
cdriver$riv_det[1:drndays]<-rep(boundconc$rivdetritus,nyears)
driverboundriv_det <- approxfun(drtimes, cdriver$riv_det, rule=2)
#Set the fish spawning and recruitment rate driving data
#Spawning first
pspawn<-rep(0,360)
dspawn<-rep(0,360)
#pspawn[P_sp_start:(P_sp_start+P_sp_dur)]<-P_an_fec/P_sp_dur
#dspawn[D_sp_start:(D_sp_start+D_sp_dur)]<-D_an_fec/D_sp_dur
pspawn[P_sp_start:(P_sp_start+P_sp_dur)]<-1/P_sp_dur # fecundity transferred to parameter list
dspawn[D_sp_start:(D_sp_start+D_sp_dur)]<-1/D_sp_dur # fecundity transferred to parameter list
bdriver$pfish_sp[1:ndays-1]<-rep(pspawn,nyears)
bdriver$dfish_sp[1:ndays-1]<-rep(dspawn,nyears)
#Set recruitment
prec<-rep(0,360)
drec<-rep(0,360)
prec[P_rec_start:(P_rec_start+P_rec_dur)]<-0.1
drec[D_rec_start:(D_rec_start+D_rec_dur)]<-0.1
bdriver$pfish_rec[1:ndays-1]<-rep(prec,nyears)
bdriver$dfish_rec[1:ndays-1]<-rep(drec,nyears)
driverpfish_sp <- approxfun(sprectimes, bdriver$pfish_sp, rule=2)
driverdfish_sp <- approxfun(sprectimes, bdriver$dfish_sp, rule=2)
driverpfish_rec <- approxfun(sprectimes, bdriver$pfish_rec, rule=2)
driverdfish_rec <- approxfun(sprectimes, bdriver$dfish_rec, rule=2)
#Set the benthos spawning and recruitment rate driving data
#Spawning first
bcspawn<-rep(0,360)
bsspawn<-rep(0,360)
#bcspawn[BC_sp_start:(BC_sp_start+BC_sp_dur)]<-BC_an_fec/BC_sp_dur
#bsspawn[BS_sp_start:(BS_sp_start+BS_sp_dur)]<-BS_an_fec/BS_sp_dur
bcspawn[BC_sp_start:(BC_sp_start+BC_sp_dur)]<-1/BC_sp_dur # fecundity transferred to parameter list
bsspawn[BS_sp_start:(BS_sp_start+BS_sp_dur)]<-1/BS_sp_dur # fecundity transferred to parameter list
bdriver$bc_sp[1:ndays-1]<-rep(bcspawn,nyears)
bdriver$bs_sp[1:ndays-1]<-rep(bsspawn,nyears)
#Set recruitment
#bcrec<-rep(0.05,360)
#bsrec<-rep(0.05,360)
#bcrec[BC_sp_start:(BC_sp_start+BC_sp_dur)]<-0.0
#bcrec[BC_rec_start:(BC_rec_start+BC_rec_dur)]<-0.05
#bsrec[BS_sp_start:(BS_sp_start+BS_sp_dur)]<-0.0
#bsrec[BS_rec_start:(BS_rec_start+BS_rec_dur)]<-0.05
bcrec<-rep(0,360)
bsrec<-rep(0,360)
bcrec[BC_rec_start:(BC_rec_start+BC_rec_dur)]<-0.1
bsrec[BS_rec_start:(BS_rec_start+BS_rec_dur)]<-0.1
bdriver$bc_rec[1:ndays-1]<-rep(bcrec,nyears)
bdriver$bs_rec[1:ndays-1]<-rep(bsrec,nyears)
driverbc_sp <- approxfun(sprectimes, bdriver$bc_sp, rule=2)
driverbs_sp <- approxfun(sprectimes, bdriver$bs_sp, rule=2)
driverbc_rec <- approxfun(sprectimes, bdriver$bc_rec, rule=2)
driverbs_rec <- approxfun(sprectimes, bdriver$bs_rec, rule=2)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Set up the migratory fish imigration rate driving functions
migfish_imig <- rep(0,360)
migfish_imig[migfish_im_start:migfish_im_end]<-(migfish_oceanpop*migfish_oceanscale/ssarea)*migfish_ocean_prop_entering/(migfish_im_end-migfish_im_start)
bdriver$migfish_im[1:ndays-1]<- rep(migfish_imig,nyears)
driver_migfish_imig <- approxfun(sprectimes, bdriver$migfish_im, rule=2)
# ........................
# Set up the migratory fish emigration rate driving functions
migfish_emig <- rep(0,360)
migfish_emig[migfish_em_start:migfish_em_end]<-migfish_oceanscale*(-log(migfish_ocean_prop_staying))/(migfish_em_end-migfish_em_start)
bdriver$migfish_em[1:ndays-1]<- rep(migfish_emig,nyears)
driver_migfish_emig <- approxfun(sprectimes, bdriver$migfish_em, rule=2)
# ........................
drivers <- list(
driversslight = driversslight,
driverso_logespm = driverso_logespm,
driversi_logespm = driversi_logespm,
driverso_temp = driverso_temp,
driverd_temp = driverd_temp,
driversi_temp = driversi_temp,
driverv_dif = driverv_dif,
driverso_inflow = driverso_inflow,
driverd_inflow = driverd_inflow,
driversi_inflow = driversi_inflow,
driversi_outflow = driversi_outflow,
driverso_si_flow = driverso_si_flow,
drivers_upwell = drivers_upwell,
driverd_outflow = driverd_outflow,
driverriver = driverriver,
driver_d1_pd = driver_d1_pd,
driver_d2_pd = driver_d2_pd,
driver_d3_pd = driver_d3_pd,
driver_s1_pd = driver_s1_pd,
driver_s2_pd = driver_s2_pd,
driver_s3_pd = driver_s3_pd,
drivers_wave = drivers_wave,
driverso_atm_nit = driverso_atm_nit,
driverso_atm_amm = driverso_atm_amm,
driversi_atm_nit = driversi_atm_nit,
driversi_atm_amm = driversi_atm_amm,
driverboundso_nit = driverboundso_nit,
driverboundso_amm = driverboundso_amm,
driverboundso_phyt = driverboundso_phyt,
driverboundso_det = driverboundso_det,
driverboundd_nit = driverboundd_nit,
driverboundd_amm = driverboundd_amm,
driverboundd_phyt = driverboundd_phyt,
driverboundd_det = driverboundd_det,
driverboundsi_nit = driverboundsi_nit,
driverboundsi_amm = driverboundsi_amm,
driverboundsi_phyt = driverboundsi_phyt,
driverboundsi_det = driverboundsi_det,
driverboundriv_nit = driverboundriv_nit,
driverboundriv_amm = driverboundriv_amm,
driverboundriv_det = driverboundriv_det,
driverpfish_sp = driverpfish_sp,
driverdfish_sp = driverdfish_sp,
driverpfish_rec = driverpfish_rec,
driverdfish_rec = driverdfish_rec,
driverbc_sp = driverbc_sp,
driverbs_sp = driverbs_sp,
driverbc_rec = driverbc_rec,
driverbs_rec = driverbs_rec,
driver_migfish_imig = driver_migfish_imig,
driver_migfish_emig = driver_migfish_emig
)
}
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