R/fishing_fleet_model.R
In strathclyde-marine-resource-modelling/StrathE2E2: End-to-end marine food web model
#
# fishing_fleet_model.R
#
#' defines the fishing fleet model
#'
#' returns fishing fleet model
#'
#' @param model model object
#' @param build model build object
#'
#' @return fishing fleet model
#'
#' @export
#
fishing_fleet_model <- function(model, build) {
# Unpack:
data <- elt(model, "data")
initial.state <- elt(data, "initial.state")
fleet.model <- elt(data, "fleet.model")
physical.parameters <- elt(data, "physical.parameters")
habitat_areas <- elt(physical.parameters, "habitat_areas")
gear_activity <- elt(fleet.model, "gear_activity")
gear_group_rel_power <- elt(fleet.model, "gear_group_rel_power")
gear_group_discard <- elt(fleet.model, "gear_group_discard")
gear_group_gutting <- elt(fleet.model, "gear_group_gutting")
gear_ploughing_rate <- elt(fleet.model, "gear_ploughing_rate")
gear_habitat_activity <- elt(fleet.model, "gear_habitat_activity")
HRscale_vector <- elt(fleet.model, "HRscale_vector")
HRscale_vector_muliplier <- elt(fleet.model, "HRscale_vector_multiplier")
gear_mult <- elt(fleet.model, "gear_mult")
quota_nonquota_parms_vector <- elt(fleet.model, "quota_nonquota_parms_vector")
DFsize_SWITCH <- elt(fleet.model, "DFsize_SWITCH")
DFdiscard_SWITCH <- elt(fleet.model, "DFdiscard_SWITCH")
plough_depth_vector <- elt(fleet.model, "plough_depth_vector")
BSmort_gear <- elt(fleet.model, "BSmort_gear")
BCmort_gear <- elt(fleet.model, "BCmort_gear")
offal_prop_live_weight <- elt(fleet.model, "offal_prop_live_weight")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
Last_January <- 0
RESETS <- 0
xstart <- initial.state
out <- 0
HRscale_vector <- HRscale_vector*HRscale_vector_muliplier
## ------- Fishing fleet parameters -------- ##
#INPUTS REQUIRED FROM THE FLEET CONFIGURATION PROGRAMME
#gear_activity
#gear_group_rel_power
#gear_group_discard
#gear_group_gutting
#gear_ploughing_rate
#gear_habitat_activity
#HRscale_vector
#gear_mult
#quota_nonquota_parms_vector
#plough_depth_vector
#BSmort_gear, BCmort_gear
#offal_prop_live_weight
#INPUT REQUIRED FROM THE PHYSICAL CONFIGURATION PROGRAMME
#habitat_areas
#INPUT REQUIRED FROM THE MAIN MODEL MANAGEMENT SCRIPT
#RESETS, Last_January, xstart, out
#OUTPUTS FROM THE FLEET MODEL
#Vector of parameters needed fof the ecology model
#matrix of the proportional distribution of group effort across gears
#matrix of, for each group, the ratio of gear discard rate to the effort-weighted overall discard rate
# ------------------------------
# ------------------------------
# ------------------------------
#THIS BIT IS A PLACE-HOLDER FOR FUTURE DEVELOPMENT INVOLVING MANAGEMENT DECISION RULES
#Grab the 1 January value of any state variables eg. dfish from either the start conditions or the last 1 january row of the model output to date
#Illustrated here with the value of dfish
if(RESETS==0) {
current_dfish<-xstart["fishd"]
} else {
current_dfish<-out$fishd[which(out[,1]==Last_January)]
}
# ------------------------------
################################################## ///
# THE FISHING FLEET MODEL ///
################################################## ///
#Apply the group fishing multiplers - - these are activity scaling factors used to generate scenarios of fishing activity
# The scaling factors are applied across groups of gears which mainly target the same resource groups in the model
gear_activity_mult<-gear_activity * gear_mult
#Activity density - units s/m2/d
#-------------------------------------------------------------
#Divide the activity density between inshore and offshore subregions
#To preserve the activity density units of s/m2/d in each subregion we need to divide by the areas
#4 habitats inshore to account for kelp forests
inshore_gear_activity_mult <- (gear_activity_mult*rowSums(gear_habitat_activity[,1:4]))/sum(habitat_areas[1:4])
offshore_gear_activity_mult <- (gear_activity_mult*rowSums(gear_habitat_activity[,5:8]))/sum(habitat_areas[5:8])
#gear_habitat_activity has rows = gears columns = habitats, cells = proportion of activity by each gear in habitat, rowsums=1
#Units still s/m2/d
#-------------------------------------------------------------
#Derive the effort density for each gear ( = activity density * power)
#Units of group rel power = mMN/sec; rows = gears columns = groups.
gear_group_effort <- gear_activity_mult*gear_group_rel_power
# columns are : pelagic, demersal, migratory, filtben, carnben, carnzoo, bird, seal, ceta, kelp; rows are gears
# comparison between gears (down the columns) is meaningful. Comparison between groups (along rows) is not
group_effort<-colSums(gear_group_effort)
#Units of effort density = mMN/m2/d (for stock abundance during a calibration period when harvest ratio is known)
#Repeat for inshore and offshore
inshore_gear_group_effort <- inshore_gear_activity_mult*gear_group_rel_power
# columns are : pelagic, demersal, migratory, filtben, carnben, carnzoo, bird, seal, ceta, kelp
inshore_group_effort<-colSums(inshore_gear_group_effort)
#Units of effort density = mMN/m2/d
offshore_gear_group_effort <- offshore_gear_activity_mult*gear_group_rel_power
# columns are : pelagic, demersal, migratory, filtben, carnben, carnzoo, bird, seal, ceta, kelp (though kelp not meaningful offshore)
offshore_group_effort<-colSums(offshore_gear_group_effort)
#Units of effort density = mMN/m2/d
#-------------------------------------------------------------
#Derive the proportional distribution of effort density for each group across gears
#needed for disaggregating the simulated total landings and discards after the model run
#rows = gears, columns = groups, colsums = 1
gear_group_prop_effort<-gear_group_effort
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj]>0){
gear_group_prop_effort[,jj]<-gear_group_prop_effort[,jj]/group_effort[jj]
} else {
gear_group_prop_effort[,jj]<-0}
}
#Repeat for inshore and offshore
inshore_gear_group_prop_effort<-inshore_gear_group_effort
for(jj in 1:ncol(inshore_gear_group_effort)){
if(inshore_group_effort[jj]>0){
inshore_gear_group_prop_effort[,jj]<-inshore_gear_group_prop_effort[,jj]/inshore_group_effort[jj]
} else {
inshore_gear_group_prop_effort[,jj]<-0}
}
offshore_gear_group_prop_effort<-offshore_gear_group_effort
for(jj in 1:ncol(offshore_gear_group_effort)){
if(offshore_group_effort[jj]>0){
offshore_gear_group_prop_effort[,jj]<-offshore_gear_group_prop_effort[,jj]/offshore_group_effort[jj]
} else {
offshore_gear_group_prop_effort[,jj]<-0}
}
#-------------------------------------------------------------
#Derive the harvest ratios on each resource group ( = total effort * HRscaling)
Fx_daily<-group_effort * HRscale_vector
#Repeat for inshore and offshore
inshore_Fx_daily <- inshore_group_effort * HRscale_vector
offshore_Fx_daily<- offshore_group_effort * HRscale_vector
#-------------------------------------------------------------
#Calculate the gear effort-weighted overall discard rate of each resource group
gear_group_effort_times_discard<-gear_group_effort * gear_group_discard
gear_group_effortdiscard<-0*gear_group_effort_times_discard
for(jj in 1:ncol(gear_group_effort_times_discard)){
if(group_effort[jj]>0){
gear_group_effortdiscard[,jj]<-gear_group_effort_times_discard[,jj]/group_effort[jj]
} else {
gear_group_effortdiscard[,jj]<-0}
}
group_discard<-colSums(gear_group_effortdiscard)
#Repeat for inshore and offshore
inshore_gear_group_effort_times_discard<-inshore_gear_group_effort * gear_group_discard
inshore_gear_group_effortdiscard<-0*inshore_gear_group_effort_times_discard
for(jj in 1:ncol(inshore_gear_group_effort_times_discard)){
if(inshore_group_effort[jj]>0){
inshore_gear_group_effortdiscard[,jj]<-inshore_gear_group_effort_times_discard[,jj]/inshore_group_effort[jj]
} else {
inshore_gear_group_effortdiscard[,jj]<-0}
}
inshore_group_discard<-colSums(inshore_gear_group_effortdiscard)
offshore_gear_group_effort_times_discard<-offshore_gear_group_effort * gear_group_discard
offshore_gear_group_effortdiscard<-0*offshore_gear_group_effort_times_discard
for(jj in 1:ncol(offshore_gear_group_effort_times_discard)){
if(offshore_group_effort[jj]>0){
offshore_gear_group_effortdiscard[,jj]<-offshore_gear_group_effort_times_discard[,jj]/offshore_group_effort[jj]
} else {
offshore_gear_group_effortdiscard[,jj]<-0}
}
offshore_group_discard<-colSums(offshore_gear_group_effortdiscard)
#-------------------------------------------------------------
#Calculate the gear effort-weighted overall gutting-at-sea rate of each resource group
gear_group_effort_times_gutting<-gear_group_effort * gear_group_gutting
gear_group_effortgutting<-0*gear_group_effort_times_gutting
for(jj in 1:ncol(gear_group_effort_times_gutting)){
if(group_effort[jj]>0){
gear_group_effortgutting[,jj]<-gear_group_effort_times_gutting[,jj]/group_effort[jj]
} else {
gear_group_effortgutting[,jj]<-0}
}
group_gutting<-colSums(gear_group_effortgutting)
#Repeat for inshore and offshore
inshore_gear_group_effort_times_gutting<-inshore_gear_group_effort * gear_group_gutting
inshore_gear_group_effortgutting<-0*inshore_gear_group_effort_times_gutting
for(jj in 1:ncol(inshore_gear_group_effort_times_gutting)){
if(inshore_group_effort[jj]>0){
inshore_gear_group_effortgutting[,jj]<-inshore_gear_group_effort_times_gutting[,jj]/inshore_group_effort[jj]
} else {
inshore_gear_group_effortgutting[,jj]<-0}
}
inshore_group_gutting<-colSums(inshore_gear_group_effortgutting)
offshore_gear_group_effort_times_gutting<-offshore_gear_group_effort * gear_group_gutting
offshore_gear_group_effortgutting<-0*offshore_gear_group_effort_times_gutting
for(jj in 1:ncol(offshore_gear_group_effort_times_gutting)){
if(offshore_group_effort[jj]>0){
offshore_gear_group_effortgutting[,jj]<-offshore_gear_group_effort_times_gutting[,jj]/offshore_group_effort[jj]
} else {
offshore_gear_group_effortgutting[,jj]<-0}
}
offshore_group_gutting<-colSums(offshore_gear_group_effortgutting)
#-------------------------------------------------------------
#Calculate the proportional distribution of discard quantities across gears for each resource group
#Columns sum to 1 in the matrix gear_group_prop_discard
effort_time_discard_colsum <- colSums(gear_group_effort_times_discard)
gear_group_prop_discard<-0*gear_group_effort_times_discard
for(jj in 1:ncol(gear_group_prop_discard)){
if(effort_time_discard_colsum[jj]>0){
gear_group_prop_discard[,jj]<-gear_group_effort_times_discard[,jj]/effort_time_discard_colsum[jj]
} else {
gear_group_prop_discard[,jj]<-0}
}
#Just a bit of plotting for a reality check - compare propn distribution of effort and discards
#cc<-10
#plot(seq(1,12),gear_group_prop_discard[,cc],type="l",ylim=c(0,1))
#lines(rep(1:12),gear_group_prop_effort[,cc],type="p")
#Repeat for inshore and offshore
inshore_effort_time_discard_colsum <- colSums(inshore_gear_group_effort_times_discard)
inshore_gear_group_prop_discard<-0*inshore_gear_group_effort_times_discard
for(jj in 1:ncol(inshore_gear_group_prop_discard)){
if(inshore_effort_time_discard_colsum[jj]>0){
inshore_gear_group_prop_discard[,jj]<-inshore_gear_group_effort_times_discard[,jj]/inshore_effort_time_discard_colsum[jj]
} else {
inshore_gear_group_prop_discard[,jj]<-0}
}
offshore_effort_time_discard_colsum <- colSums(offshore_gear_group_effort_times_discard)
offshore_gear_group_prop_discard<-0*offshore_gear_group_effort_times_discard
for(jj in 1:ncol(offshore_gear_group_prop_discard)){
if(offshore_effort_time_discard_colsum[jj]>0){
offshore_gear_group_prop_discard[,jj]<-offshore_gear_group_effort_times_discard[,jj]/offshore_effort_time_discard_colsum[jj]
} else {
offshore_gear_group_prop_discard[,jj]<-0}
}
#-------------------------------------------------------------
#Generate matrices of the ratio of gear-discard rate to the regional effort weighted all-gear discard rate of each group
gear_to_region_discard_rate_ratio <- gear_group_discard
for(jj in 1:(ncol(gear_group_discard))) {
gear_to_region_discard_rate_ratio[,jj]<-0
}
for(jj in 1:ncol(gear_group_discard)){
if(group_discard[jj]>0){
gear_to_region_discard_rate_ratio[,jj] <- gear_group_discard[,jj] / group_discard[jj]
} else {
gear_to_region_discard_rate_ratio[,jj]<-0
}
}
#Inshore
inshore_gear_to_region_discard_rate_ratio <- gear_group_discard
for(jj in 1:(ncol(gear_group_discard))) {
inshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
for(jj in 1:ncol(gear_group_discard)){
if(inshore_group_discard[jj]>0){
inshore_gear_to_region_discard_rate_ratio[,jj] <- gear_group_discard[,jj] / inshore_group_discard[jj]
} else {
inshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
}
#Offshore
offshore_gear_to_region_discard_rate_ratio <- gear_group_discard
for(jj in 1:(ncol(gear_group_discard))) {
offshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
for(jj in 1:ncol(gear_group_discard)){
if(offshore_group_discard[jj]>0){
offshore_gear_to_region_discard_rate_ratio[,jj] <- gear_group_discard[,jj] / offshore_group_discard[jj]
} else {
offshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
}
#-------------------------------------------------------------
#For each group get the proportion of effort in each habitat
group_effort_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity)))
for(jj in 2:(ncol(gear_group_effort))) {
group_effort_prop_habitat[,jj]<-0
}
names(group_effort_prop_habitat)<-names(gear_group_effort)
rownames(group_effort_prop_habitat)<-names(gear_habitat_activity)
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj]>0){
group_effort_prop_habitat[,jj]<-(colSums(gear_group_effort[,jj]*gear_habitat_activity)) / group_effort[jj]
} else {
group_effort_prop_habitat[,jj]<-0}
}
#Extract separate matrices for inshore (4 rows) and offshore (4 rows), in which the columns still sum to 1 - ie its
#the proportionm distribution of effort across habitats WITHIN inshore and offshore zones
inshore_group_effort_prop_habitat <- (group_effort_prop_habitat[1:4,])
offshore_group_effort_prop_habitat <- (group_effort_prop_habitat[5:8,])
for(jj in 1:4){
inshore_group_effort_prop_habitat[jj,] <- inshore_group_effort_prop_habitat[jj,]/(colSums(group_effort_prop_habitat[1:4,]))
}
for(jj in 1:4){
offshore_group_effort_prop_habitat[jj,] <- offshore_group_effort_prop_habitat[jj,]/(colSums(group_effort_prop_habitat[5:8,]))
}
#-------------------------------------------------------------
#For each group get the proportion of total quantity discarded over each habitat
#In the matrix group_discard_prop_habitat rows=habitats columns = groups, so colsums = 1
group_discard_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity)))
for(jj in 2:(ncol(gear_group_effort))) {
group_discard_prop_habitat[,jj]<-0
}
names(group_discard_prop_habitat)<-names(gear_group_effort)
rownames(group_discard_prop_habitat)<-names(gear_habitat_activity)
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj] & group_discard[jj] >0){
group_discard_prop_habitat[,jj]<-(colSums(gear_group_effortdiscard[,jj]*gear_habitat_activity)) / group_discard[jj]
} else {
group_discard_prop_habitat[,jj]<-0}
}
#Extract separate matrices for inshore (4 row) and offshore (4 row), in which the columns still sum to 1 - ie its
#the proportional distribution of discard quantity across habitats WITHIN inshore and offshore zones
inshore_group_discard_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,1:4])))
for(jj in 2:(ncol(inshore_gear_group_effort))) {
inshore_group_discard_prop_habitat[,jj]<-0
}
names(inshore_group_discard_prop_habitat)<-names(inshore_gear_group_effort)
rownames(inshore_group_discard_prop_habitat)<-names(gear_habitat_activity[1:4])
for(jj in 1:ncol(inshore_gear_group_effort)){
if(inshore_group_effort[jj] & inshore_group_discard[jj] >0){
inshore_group_discard_prop_habitat[,jj]<-(colSums(inshore_gear_group_effortdiscard[,jj]*gear_habitat_activity[,1:4]/rowSums(gear_habitat_activity[,1:4],na.rm=TRUE),na.rm=TRUE)) / inshore_group_discard[jj]
} else {
inshore_group_discard_prop_habitat[,jj]<-0}
}
offshore_group_discard_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,5:8])))
for(jj in 2:(ncol(offshore_gear_group_effort))) {
offshore_group_discard_prop_habitat[,jj]<-0
}
names(offshore_group_discard_prop_habitat)<-names(offshore_gear_group_effort)
rownames(offshore_group_discard_prop_habitat)<-names(gear_habitat_activity[5:8])
for(jj in 1:ncol(offshore_gear_group_effort)){
if(offshore_group_effort[jj] & offshore_group_discard[jj] >0){
offshore_group_discard_prop_habitat[,jj]<-(colSums(offshore_gear_group_effortdiscard[,jj]*gear_habitat_activity[,5:8]/rowSums(gear_habitat_activity[,5:8],na.rm=TRUE),na.rm=TRUE)) / offshore_group_discard[jj]
} else {
offshore_group_discard_prop_habitat[,jj]<-0}
}
#-------------------------------------------------------------
#For each group get the proportion of total quantity of offal produced over each habitat
#In the matrix group_gutting_prop_habitat rows=habitats columns = groups, so colsums = 1
group_gutting_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity)))
for(jj in 2:(ncol(gear_group_effort))) {
group_gutting_prop_habitat[,jj]<-0
}
names(group_gutting_prop_habitat)<-names(gear_group_effort)
rownames(group_gutting_prop_habitat)<-names(gear_habitat_activity)
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj] & group_gutting[jj] >0){
group_gutting_prop_habitat[,jj]<-(colSums(gear_group_effortgutting[,jj]*gear_habitat_activity)) / group_gutting[jj]
} else {
group_gutting_prop_habitat[,jj]<-0}
}
#Extract separate matrices for inshore (4 row) and offshore (4 row), in which the columns still sum to 1 - ie its
#the proportional distribution of gutting quantity across habitats WITHIN inshore and offshore zones
inshore_group_gutting_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,1:4])))
for(jj in 2:(ncol(inshore_gear_group_effort))) {
inshore_group_gutting_prop_habitat[,jj]<-0
}
names(inshore_group_gutting_prop_habitat)<-names(inshore_gear_group_effort)
rownames(inshore_group_gutting_prop_habitat)<-names(gear_habitat_activity[1:4])
for(jj in 1:ncol(inshore_gear_group_effort)){
if(inshore_group_effort[jj] & inshore_group_gutting[jj] >0){
inshore_group_gutting_prop_habitat[,jj]<-(colSums(inshore_gear_group_effortgutting[,jj]*gear_habitat_activity[,1:4]/rowSums(gear_habitat_activity[,1:4],na.rm=TRUE),na.rm=TRUE)) / inshore_group_gutting[jj]
} else {
inshore_group_gutting_prop_habitat[,jj]<-0}
}
offshore_group_gutting_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,5:8])))
for(jj in 2:(ncol(offshore_gear_group_effort))) {
offshore_group_gutting_prop_habitat[,jj]<-0
}
names(offshore_group_gutting_prop_habitat)<-names(offshore_gear_group_effort)
rownames(offshore_group_gutting_prop_habitat)<-names(gear_habitat_activity[5:8])
for(jj in 1:ncol(offshore_gear_group_effort)){
if(offshore_group_effort[jj] & offshore_group_gutting[jj] >0){
offshore_group_gutting_prop_habitat[,jj]<-(colSums(offshore_gear_group_effortgutting[,jj]*gear_habitat_activity[,5:8]/rowSums(gear_habitat_activity[,5:8],na.rm=TRUE),na.rm=TRUE)) / offshore_group_gutting[jj]
} else {
offshore_group_gutting_prop_habitat[,jj]<-0}
}
#-------------------------------------------------------------
#Calculate the daily ploughing rate in each habitat (proportion of habitat area per day)
#To preserve the activity density units of s/m2/d in each subregion we need to divide by the areas
plough_daily_habitat<-rep(0,ncol(gear_habitat_activity))
for(jj in 1:ncol(gear_habitat_activity)){
if(habitat_areas[jj]>0){
plough_daily_habitat[jj]<-(sum(gear_activity_mult * gear_habitat_activity[,jj] * gear_ploughing_rate)) / habitat_areas[jj]
} else {
plough_daily_habitat[jj]<-0}
}
#-------------------------------------------------------------
# Calculate the mortality of benthos due to damage by passage of the trawl gear
# This is given by the area-weighted mortality per trawl pass x the proportion of total seabed area ploughed per day
bensdamage <- BSmort_gear * sum(plough_daily_habitat * habitat_areas)
bencdamage <- BCmort_gear * sum(plough_daily_habitat * habitat_areas)
#Inshore and offshore
inshore_bensdamage <- BSmort_gear * (sum(plough_daily_habitat[1:4] * habitat_areas[1:4]))/sum(habitat_areas[1:4])
offshore_bensdamage <- BSmort_gear * (sum(plough_daily_habitat[5:8] * habitat_areas[5:8]))/sum(habitat_areas[5:8])
inshore_bencdamage <- BCmort_gear * (sum(plough_daily_habitat[1:4] * habitat_areas[1:4]))/sum(habitat_areas[1:4])
offshore_bencdamage <- BCmort_gear * (sum(plough_daily_habitat[5:8] * habitat_areas[5:8]))/sum(habitat_areas[5:8])
#-------------------------------------------------------------
################################
#STUFF THAT NEEDS TO BE OUTPUT FROM THE ROUTINE AND PASSED TO THE ECOLOGY MODEL
#NEED TO COMPILE COMPOSITE VECTORS OF THE INSHORE AND OFFSHORE HARVEST RATES FOR FISH AND BENTHOS
#Compile a vector of daily harvest ratios - inshore and offshore rates for each group except birtds&mammals
Fx_daily_out<-c(inshore_Fx_daily["pelagic"],offshore_Fx_daily["pelagic"],
inshore_Fx_daily["demersal"],offshore_Fx_daily["demersal"],
inshore_Fx_daily["migratory"],offshore_Fx_daily["migratory"],
inshore_Fx_daily["filtben"],offshore_Fx_daily["filtben"],
inshore_Fx_daily["carnben"],offshore_Fx_daily["carnben"],
inshore_Fx_daily["carnzoo"],offshore_Fx_daily["carnzoo"],
inshore_Fx_daily["bird"],offshore_Fx_daily["bird"],
inshore_Fx_daily["seal"],offshore_Fx_daily["seal"],
inshore_Fx_daily["ceta"],offshore_Fx_daily["ceta"],
inshore_Fx_daily["kelp"],offshore_Fx_daily["kelp"])
#Compile a vector of discard rates - inshore and offshore rates for all group except birtds&mammals, plus whole region for demersal
group_discard_out<-c(inshore_group_discard["pelagic"],offshore_group_discard["pelagic"],
inshore_group_discard["demersal"],offshore_group_discard["demersal"],group_discard["demersal"],
inshore_group_discard["migratory"],offshore_group_discard["migratory"],
inshore_group_discard["filtben"],offshore_group_discard["filtben"],
inshore_group_discard["carnben"],offshore_group_discard["carnben"],
inshore_group_discard["carnzoo"],offshore_group_discard["carnzoo"],
inshore_group_discard["bird"],offshore_group_discard["bird"],
inshore_group_discard["seal"],offshore_group_discard["seal"],
inshore_group_discard["ceta"],offshore_group_discard["ceta"],
inshore_group_discard["kelp"],offshore_group_discard["kelp"])
#Compile a vector of gutting rates - inshore and offshore rates for all group except birtds&mammals, plus whole region for demersal
group_gutting_out<-c(inshore_group_gutting["pelagic"],offshore_group_gutting["pelagic"],
inshore_group_gutting["demersal"],offshore_group_gutting["demersal"],
inshore_group_gutting["migratory"],offshore_group_gutting["migratory"],
inshore_group_gutting["filtben"],offshore_group_gutting["filtben"],
inshore_group_gutting["carnben"],offshore_group_gutting["carnben"],
inshore_group_gutting["carnzoo"],offshore_group_gutting["carnzoo"],
inshore_group_gutting["bird"],offshore_group_gutting["bird"],
inshore_group_gutting["seal"],offshore_group_gutting["seal"],
inshore_group_gutting["ceta"],offshore_group_gutting["ceta"],
inshore_group_gutting["kelp"],offshore_group_gutting["kelp"])
#Compile a vector of proportions of discard quantity over each habitat WITHIN the inshore and offshore subregions
#except for birds and mamals where its the proportions across all habitats
discard_map<- c(
inshore_group_discard_prop_habitat[,1], # pelagic fish distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,1], # pelagic fish distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,2], # demersal fish distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,2], # demersal fish distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,3], # migratory fish distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,3], # migratory fish distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,4], # inshire filtben distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,4], # offshore filtben distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,5], # inshore carnben distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,5], # offshore carnben distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,6], # carnzoo distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,6], # carnzoo distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,7], # bird distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,7], # bird distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,8], # seal distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,8], # seal distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,9], # ceta distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,9], # ceta distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,10], # kelp distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,10]) # kelp distribution of discard quantity across 4 offshore habitats
#Compile a vector of proportions of discard quantity over each habitat WITHIN the inshore and offshore subregions
#except for birds and mamals where its the proportions across all habitats
gutting_map<- c(
inshore_group_gutting_prop_habitat[,1], # pelagic fish distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,1], # pelagic fish distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,2], # demersal fish distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,2], # demersal fish distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,3], # migratory fish distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,3], # migratory fish distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,4], # inshire filtben distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,4], # offshore filtben distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,5], # inshore carnben distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,5], # offshore carnben distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,6], # carnzoo distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,6], # carnzoo distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,7], # bird distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,7], # bird distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,8], # seal distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,8], # seal distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,9], # ceta distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,9], # ceta distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,10], # kelp distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,10]) # kelp distribution of gutting offal across 4 offshore habitats
#.........................
#Compile all the above elements into a single vector that will be piped into the ecology model (6 more elements than the orignal version)
fleet_vector<-c(
Fx_daily_out,
quota_nonquota_parms_vector,
group_discard_out,
group_gutting_out,
DFsize_SWITCH,
DFdiscard_SWITCH,
discard_map,
gutting_map,
plough_daily_habitat,
inshore_bensdamage,
offshore_bensdamage,
inshore_bencdamage,
offshore_bencdamage,
offal_prop_live_weight,
plough_depth_vector
)
names(fleet_vector)<-c(
"F_inshore_pelagic","F_offshore_pelagic",
"F_inshore_demersal","F_offshore_demersal",
"F_inshore_migratory","F_offshore_migratory",
"F_inshore_filtben","F_offshore_filtben",
"F_inshore_carnben","F_offshore_carnben",
"F_inshore_carnzoo","F_offshore_carnzoo",
"F_inshore_bird","F_offshore_bird",
"F_inshore_seal","F_offshore_seal",
"F_inshore_ceta","F_offshore_ceta",
"F_inshore_kelp","F_offshore_kelp",
"QnQ_coef","QnQ_exp","NQus_coef","NQus_exp","QLus_coef","QLus_exp",
"D_inshore_pelagic","D_offshore_pelagic",
"D_inshore_demersal","D_offshore_demersal","D_demersal",
"D_inshore_migratory","D_offshore_migratory",
"D_inshore_filtben","D_offshore_filtben",
"D_inshore_carnben","D_offshore_carnben",
"D_inshore_carnzoo","D_offshore_carnzoo",
"D_inshore_bird","D_offshore_bird",
"D_inshore_seal","D_offshore_seal",
"D_inshore_ceta","D_offshore_ceta",
"D_inshore_kelp","D_offshore_kelp",
"G_inshore_pelagic","G_offshore_pelagic",
"G_inshore_demersal","G_offshore_demersal",
"G_inshore_migratory","G_offshore_migratory",
"G_inshore_filtben","G_offshore_filtben",
"G_inshore_carnben","G_offshore_carnben",
"G_inshore_carnzoo","G_offshore_carnzoo",
"G_inshore_bird","G_offshore_bird",
"G_inshore_seal","G_offshore_seal",
"G_inshore_ceta","G_offshore_ceta",
"G_inshore_kelp","G_offshore_kelp",
"Undersizeswitch",
"Discardswitch",
"PelpD_S0","PelpD_S1","PelpD_S2","PelpD_S3","PelpD_D0","PelpD_D1","PelpD_D2","PelpD_D3",
"DempD_S0","DempD_S1","DempD_S2","DempD_S3","DempD_D0","DempD_D1","DempD_D2","DempD_D3",
"MigpD_S0","MigpD_S1","MigpD_S2","MigpD_S3","MigpD_D0","MigpD_D1","MigpD_D2","MigpD_D3",
"IBfpD_S0","IBfpD_S1","IBfpD_S2","IBfpD_S3","OBfpD_D0","OBfpD_D1","OBfpD_D2","OBfpD_D3",
"IBcpD_S0","IBcpD_S1","IBcpD_S2","IBcpD_S3","OBcpD_D0","OBcpD_D1","OBcpD_D2","OBcpD_D3",
"CzopD_S0","CzopD_S1","CzopD_S2","CzopD_S3","CzopD_D0","CzopD_D1","CzopD_D2","CzopD_D3",
"BirpD_S0","BirpD_S1","BirpD_S2","BirpD_S3","BirpD_D0","BirpD_D1","BirpD_D2","BirpD_D3",
"SeapD_S0","SeapD_S1","SeapD_S2","SeapD_S3","SeapD_D0","SeapD_D1","SeapD_D2","SeapD_D3",
"CetpD_S0","CetpD_S1","CetpD_S2","CetpD_S3","CetpD_D0","CetpD_D1","CetpD_D2","CetpD_D3",
"KelpD_S0","KelpD_S1","KelpD_S2","KelpD_S3","KelpD_D0","KelpD_D1","KelpD_D2","KelpD_D3",
"PelpG_S0","PelpG_S1","PelpG_S2","PelpG_S3","PelpG_D0","PelpG_D1","PelpG_D2","PelpG_D3",
"DempG_S0","DempG_S1","DempG_S2","DempG_S3","DempG_D0","DempG_D1","DempG_D2","DempG_D3",
"MigpG_S0","MigpG_S1","MigpG_S2","MigpG_S3","MigpG_D0","MigpG_D1","MigpG_D2","MigpG_D3",
"IBfpG_S0","IBfpG_S1","IBfpG_S2","IBfpG_S3","OBfpG_D0","OBfpG_D1","OBfpG_D2","OBfpG_D3",
"IBcpG_S0","IBcpG_S1","IBcpG_S2","IBcpG_S3","OBcpG_D0","OBcpG_D1","OBcpG_D2","OBcpG_D3",
"CzopG_S0","CzopG_S1","CzopG_S2","CzopG_S3","CzopG_D0","CzopG_D1","CzopG_D2","CzopG_D3",
"BirpG_S0","BirpG_S1","BirpG_S2","BirpG_S3","BirpG_D0","BirpG_D1","BirpG_D2","BirpG_D3",
"SeapG_S0","SeapG_S1","SeapG_S2","SeapG_S3","SeapG_D0","SeapG_D1","SeapG_D2","SeapG_D3",
"CetpG_S0","CetpG_S1","CetpG_S2","CetpG_S3","CetpG_D0","CetpG_D1","CetpG_D2","CetpG_D3",
"KelpG_S0","KelpG_S1","KelpG_S2","KelpG_S3","KelpG_D0","KelpG_D1","KelpG_D2","KelpG_D3",
"ploughdaily_S0","ploughdaily_S1","ploughdaily_S2","ploughdaily_S3","ploughdaily_D0","ploughdaily_D1","ploughdaily_D2","ploughdaily_D3",
"inshore_bensdamage","offshore_bensdamage",
"inshore_bencdamage","offshore_bencdamage",
"offal_prop_live_weight",
"ploughdepth_S0","ploughdepth_S1","ploughdepth_S2","ploughdepth_S3","ploughdepth_D0","ploughdepth_D1","ploughdepth_D2","ploughdepth_D3"
)
#STUFF THAT NEEDS TO BE SAVED FOR POST-PROCESSING OF THE ECOLOGY MODEL OUTPUT
#gear_group_prop_effort_out
#gear_group_prop_discard_out
#Compile the gear_group_prop_effort_out matrix
#gear_group_prop_effort_out<-cbind(
# offshore_gear_group_prop_effort[,1],inshore_gear_group_prop_effort[,1],
# offshore_gear_group_prop_effort[,2],inshore_gear_group_prop_effort[,2],
# offshore_gear_group_prop_effort[,3],inshore_gear_group_prop_effort[,2],
# offshore_gear_group_prop_effort[,4],inshore_gear_group_prop_effort[,4],
# offshore_gear_group_prop_effort[,5],inshore_gear_group_prop_effort[,5],
# offshore_gear_group_prop_effort[,6],inshore_gear_group_prop_effort[,6],
# offshore_gear_group_prop_effort[,7],inshore_gear_group_prop_effort[,7],
# offshore_gear_group_prop_effort[,8],inshore_gear_group_prop_effort[,8],
# offshore_gear_group_prop_effort[,9],inshore_gear_group_prop_effort[,9],
# offshore_gear_group_prop_effort[,10],inshore_gear_group_prop_effort[,10])
#colnames(gear_group_prop_effort_out)<-c("offshore_pelagic","inshore_pelagic",
# "offshore_demersal","inshore_demersal",
# "offshore_migratory","inshore_migratory",
# "offshore_filtben","inshore_filtben",
# "offshore_carnben","inshore_carnben",
# "offshore_carnzoo","inshore_carnzoo",
# "offshore_bird","inshore_bird",
# "offshore_seal","inshore_seal",
# "offshore_ceta","inshore_ceta",
# "offshore_kelp","inshore_kelp")
#Compile the gear_group_prop_discard_out matrix
#gear_group_prop_discard_out<-cbind(
# offshore_gear_group_prop_discard[,1],inshore_gear_group_prop_discard[,1],
# offshore_gear_group_prop_discard[,2],inshore_gear_group_prop_discard[,2],
# offshore_gear_group_prop_discard[,3],inshore_gear_group_prop_discard[,3],
# offshore_gear_group_prop_discard[,4],inshore_gear_group_prop_discard[,4],
# offshore_gear_group_prop_discard[,5],inshore_gear_group_prop_discard[,5],
# offshore_gear_group_prop_discard[,6],inshore_gear_group_prop_discard[,6],
# offshore_gear_group_prop_discard[,7],inshore_gear_group_prop_discard[,7],
# offshore_gear_group_prop_discard[,8],inshore_gear_group_prop_discard[,8],
# offshore_gear_group_prop_discard[,9],inshore_gear_group_prop_discard[,9],
# offshore_gear_group_prop_discard[,10],inshore_gear_group_prop_discard[,10])
#colnames(gear_group_prop_discard_out)<-c("offshore_pelagic","inshore_pelagic",
# "offshore_demersal","inshore_demersal",
# "offshore_migratory","inshore_migratory",
# "offshore_filtben","inshore_filtben",
# "offshore_carnben","inshore_carnben",
# "offshore_carnzoo","inshore_carnzoo",
# "offshore_bird","inshore_bird",
# "offshore_seal","inshore_seal",
# "offshore_ceta","inshore_ceta",
# "offshore_kelp","inshore_kelp")
fleet_model_output <- list(
fleet_vector = fleet_vector,
offshore_gear_group_prop_effort = offshore_gear_group_prop_effort,
inshore_gear_group_prop_effort = inshore_gear_group_prop_effort,
offshore_gear_to_region_discard_rate_ratio = offshore_gear_to_region_discard_rate_ratio,
inshore_gear_to_region_discard_rate_ratio = inshore_gear_to_region_discard_rate_ratio
)
gear_group_props <- store_fleet_model_output(fleet_model_output, nyears)
# concat the lists:
fishing_fleet_model_output <- c(
fleet_model_output,
gear_group_props
)
fishing_fleet_model_output
}
strathclyde-marine-resource-modelling/StrathE2E2 documentation built on June 21, 2019, 2:43 a.m.
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#
# fishing_fleet_model.R
#
#' defines the fishing fleet model
#'
#' returns fishing fleet model
#'
#' @param model model object
#' @param build model build object
#'
#' @return fishing fleet model
#'
#' @export
#
fishing_fleet_model <- function(model, build) {
# Unpack:
data <- elt(model, "data")
initial.state <- elt(data, "initial.state")
fleet.model <- elt(data, "fleet.model")
physical.parameters <- elt(data, "physical.parameters")
habitat_areas <- elt(physical.parameters, "habitat_areas")
gear_activity <- elt(fleet.model, "gear_activity")
gear_group_rel_power <- elt(fleet.model, "gear_group_rel_power")
gear_group_discard <- elt(fleet.model, "gear_group_discard")
gear_group_gutting <- elt(fleet.model, "gear_group_gutting")
gear_ploughing_rate <- elt(fleet.model, "gear_ploughing_rate")
gear_habitat_activity <- elt(fleet.model, "gear_habitat_activity")
HRscale_vector <- elt(fleet.model, "HRscale_vector")
HRscale_vector_muliplier <- elt(fleet.model, "HRscale_vector_multiplier")
gear_mult <- elt(fleet.model, "gear_mult")
quota_nonquota_parms_vector <- elt(fleet.model, "quota_nonquota_parms_vector")
DFsize_SWITCH <- elt(fleet.model, "DFsize_SWITCH")
DFdiscard_SWITCH <- elt(fleet.model, "DFdiscard_SWITCH")
plough_depth_vector <- elt(fleet.model, "plough_depth_vector")
BSmort_gear <- elt(fleet.model, "BSmort_gear")
BCmort_gear <- elt(fleet.model, "BCmort_gear")
offal_prop_live_weight <- elt(fleet.model, "offal_prop_live_weight")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
Last_January <- 0
RESETS <- 0
xstart <- initial.state
out <- 0
HRscale_vector <- HRscale_vector*HRscale_vector_muliplier
## ------- Fishing fleet parameters -------- ##
#INPUTS REQUIRED FROM THE FLEET CONFIGURATION PROGRAMME
#gear_activity
#gear_group_rel_power
#gear_group_discard
#gear_group_gutting
#gear_ploughing_rate
#gear_habitat_activity
#HRscale_vector
#gear_mult
#quota_nonquota_parms_vector
#plough_depth_vector
#BSmort_gear, BCmort_gear
#offal_prop_live_weight
#INPUT REQUIRED FROM THE PHYSICAL CONFIGURATION PROGRAMME
#habitat_areas
#INPUT REQUIRED FROM THE MAIN MODEL MANAGEMENT SCRIPT
#RESETS, Last_January, xstart, out
#OUTPUTS FROM THE FLEET MODEL
#Vector of parameters needed fof the ecology model
#matrix of the proportional distribution of group effort across gears
#matrix of, for each group, the ratio of gear discard rate to the effort-weighted overall discard rate
# ------------------------------
# ------------------------------
# ------------------------------
#THIS BIT IS A PLACE-HOLDER FOR FUTURE DEVELOPMENT INVOLVING MANAGEMENT DECISION RULES
#Grab the 1 January value of any state variables eg. dfish from either the start conditions or the last 1 january row of the model output to date
#Illustrated here with the value of dfish
if(RESETS==0) {
current_dfish<-xstart["fishd"]
} else {
current_dfish<-out$fishd[which(out[,1]==Last_January)]
}
# ------------------------------
################################################## ///
# THE FISHING FLEET MODEL ///
################################################## ///
#Apply the group fishing multiplers - - these are activity scaling factors used to generate scenarios of fishing activity
# The scaling factors are applied across groups of gears which mainly target the same resource groups in the model
gear_activity_mult<-gear_activity * gear_mult
#Activity density - units s/m2/d
#-------------------------------------------------------------
#Divide the activity density between inshore and offshore subregions
#To preserve the activity density units of s/m2/d in each subregion we need to divide by the areas
#4 habitats inshore to account for kelp forests
inshore_gear_activity_mult <- (gear_activity_mult*rowSums(gear_habitat_activity[,1:4]))/sum(habitat_areas[1:4])
offshore_gear_activity_mult <- (gear_activity_mult*rowSums(gear_habitat_activity[,5:8]))/sum(habitat_areas[5:8])
#gear_habitat_activity has rows = gears columns = habitats, cells = proportion of activity by each gear in habitat, rowsums=1
#Units still s/m2/d
#-------------------------------------------------------------
#Derive the effort density for each gear ( = activity density * power)
#Units of group rel power = mMN/sec; rows = gears columns = groups.
gear_group_effort <- gear_activity_mult*gear_group_rel_power
# columns are : pelagic, demersal, migratory, filtben, carnben, carnzoo, bird, seal, ceta, kelp; rows are gears
# comparison between gears (down the columns) is meaningful. Comparison between groups (along rows) is not
group_effort<-colSums(gear_group_effort)
#Units of effort density = mMN/m2/d (for stock abundance during a calibration period when harvest ratio is known)
#Repeat for inshore and offshore
inshore_gear_group_effort <- inshore_gear_activity_mult*gear_group_rel_power
# columns are : pelagic, demersal, migratory, filtben, carnben, carnzoo, bird, seal, ceta, kelp
inshore_group_effort<-colSums(inshore_gear_group_effort)
#Units of effort density = mMN/m2/d
offshore_gear_group_effort <- offshore_gear_activity_mult*gear_group_rel_power
# columns are : pelagic, demersal, migratory, filtben, carnben, carnzoo, bird, seal, ceta, kelp (though kelp not meaningful offshore)
offshore_group_effort<-colSums(offshore_gear_group_effort)
#Units of effort density = mMN/m2/d
#-------------------------------------------------------------
#Derive the proportional distribution of effort density for each group across gears
#needed for disaggregating the simulated total landings and discards after the model run
#rows = gears, columns = groups, colsums = 1
gear_group_prop_effort<-gear_group_effort
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj]>0){
gear_group_prop_effort[,jj]<-gear_group_prop_effort[,jj]/group_effort[jj]
} else {
gear_group_prop_effort[,jj]<-0}
}
#Repeat for inshore and offshore
inshore_gear_group_prop_effort<-inshore_gear_group_effort
for(jj in 1:ncol(inshore_gear_group_effort)){
if(inshore_group_effort[jj]>0){
inshore_gear_group_prop_effort[,jj]<-inshore_gear_group_prop_effort[,jj]/inshore_group_effort[jj]
} else {
inshore_gear_group_prop_effort[,jj]<-0}
}
offshore_gear_group_prop_effort<-offshore_gear_group_effort
for(jj in 1:ncol(offshore_gear_group_effort)){
if(offshore_group_effort[jj]>0){
offshore_gear_group_prop_effort[,jj]<-offshore_gear_group_prop_effort[,jj]/offshore_group_effort[jj]
} else {
offshore_gear_group_prop_effort[,jj]<-0}
}
#-------------------------------------------------------------
#Derive the harvest ratios on each resource group ( = total effort * HRscaling)
Fx_daily<-group_effort * HRscale_vector
#Repeat for inshore and offshore
inshore_Fx_daily <- inshore_group_effort * HRscale_vector
offshore_Fx_daily<- offshore_group_effort * HRscale_vector
#-------------------------------------------------------------
#Calculate the gear effort-weighted overall discard rate of each resource group
gear_group_effort_times_discard<-gear_group_effort * gear_group_discard
gear_group_effortdiscard<-0*gear_group_effort_times_discard
for(jj in 1:ncol(gear_group_effort_times_discard)){
if(group_effort[jj]>0){
gear_group_effortdiscard[,jj]<-gear_group_effort_times_discard[,jj]/group_effort[jj]
} else {
gear_group_effortdiscard[,jj]<-0}
}
group_discard<-colSums(gear_group_effortdiscard)
#Repeat for inshore and offshore
inshore_gear_group_effort_times_discard<-inshore_gear_group_effort * gear_group_discard
inshore_gear_group_effortdiscard<-0*inshore_gear_group_effort_times_discard
for(jj in 1:ncol(inshore_gear_group_effort_times_discard)){
if(inshore_group_effort[jj]>0){
inshore_gear_group_effortdiscard[,jj]<-inshore_gear_group_effort_times_discard[,jj]/inshore_group_effort[jj]
} else {
inshore_gear_group_effortdiscard[,jj]<-0}
}
inshore_group_discard<-colSums(inshore_gear_group_effortdiscard)
offshore_gear_group_effort_times_discard<-offshore_gear_group_effort * gear_group_discard
offshore_gear_group_effortdiscard<-0*offshore_gear_group_effort_times_discard
for(jj in 1:ncol(offshore_gear_group_effort_times_discard)){
if(offshore_group_effort[jj]>0){
offshore_gear_group_effortdiscard[,jj]<-offshore_gear_group_effort_times_discard[,jj]/offshore_group_effort[jj]
} else {
offshore_gear_group_effortdiscard[,jj]<-0}
}
offshore_group_discard<-colSums(offshore_gear_group_effortdiscard)
#-------------------------------------------------------------
#Calculate the gear effort-weighted overall gutting-at-sea rate of each resource group
gear_group_effort_times_gutting<-gear_group_effort * gear_group_gutting
gear_group_effortgutting<-0*gear_group_effort_times_gutting
for(jj in 1:ncol(gear_group_effort_times_gutting)){
if(group_effort[jj]>0){
gear_group_effortgutting[,jj]<-gear_group_effort_times_gutting[,jj]/group_effort[jj]
} else {
gear_group_effortgutting[,jj]<-0}
}
group_gutting<-colSums(gear_group_effortgutting)
#Repeat for inshore and offshore
inshore_gear_group_effort_times_gutting<-inshore_gear_group_effort * gear_group_gutting
inshore_gear_group_effortgutting<-0*inshore_gear_group_effort_times_gutting
for(jj in 1:ncol(inshore_gear_group_effort_times_gutting)){
if(inshore_group_effort[jj]>0){
inshore_gear_group_effortgutting[,jj]<-inshore_gear_group_effort_times_gutting[,jj]/inshore_group_effort[jj]
} else {
inshore_gear_group_effortgutting[,jj]<-0}
}
inshore_group_gutting<-colSums(inshore_gear_group_effortgutting)
offshore_gear_group_effort_times_gutting<-offshore_gear_group_effort * gear_group_gutting
offshore_gear_group_effortgutting<-0*offshore_gear_group_effort_times_gutting
for(jj in 1:ncol(offshore_gear_group_effort_times_gutting)){
if(offshore_group_effort[jj]>0){
offshore_gear_group_effortgutting[,jj]<-offshore_gear_group_effort_times_gutting[,jj]/offshore_group_effort[jj]
} else {
offshore_gear_group_effortgutting[,jj]<-0}
}
offshore_group_gutting<-colSums(offshore_gear_group_effortgutting)
#-------------------------------------------------------------
#Calculate the proportional distribution of discard quantities across gears for each resource group
#Columns sum to 1 in the matrix gear_group_prop_discard
effort_time_discard_colsum <- colSums(gear_group_effort_times_discard)
gear_group_prop_discard<-0*gear_group_effort_times_discard
for(jj in 1:ncol(gear_group_prop_discard)){
if(effort_time_discard_colsum[jj]>0){
gear_group_prop_discard[,jj]<-gear_group_effort_times_discard[,jj]/effort_time_discard_colsum[jj]
} else {
gear_group_prop_discard[,jj]<-0}
}
#Just a bit of plotting for a reality check - compare propn distribution of effort and discards
#cc<-10
#plot(seq(1,12),gear_group_prop_discard[,cc],type="l",ylim=c(0,1))
#lines(rep(1:12),gear_group_prop_effort[,cc],type="p")
#Repeat for inshore and offshore
inshore_effort_time_discard_colsum <- colSums(inshore_gear_group_effort_times_discard)
inshore_gear_group_prop_discard<-0*inshore_gear_group_effort_times_discard
for(jj in 1:ncol(inshore_gear_group_prop_discard)){
if(inshore_effort_time_discard_colsum[jj]>0){
inshore_gear_group_prop_discard[,jj]<-inshore_gear_group_effort_times_discard[,jj]/inshore_effort_time_discard_colsum[jj]
} else {
inshore_gear_group_prop_discard[,jj]<-0}
}
offshore_effort_time_discard_colsum <- colSums(offshore_gear_group_effort_times_discard)
offshore_gear_group_prop_discard<-0*offshore_gear_group_effort_times_discard
for(jj in 1:ncol(offshore_gear_group_prop_discard)){
if(offshore_effort_time_discard_colsum[jj]>0){
offshore_gear_group_prop_discard[,jj]<-offshore_gear_group_effort_times_discard[,jj]/offshore_effort_time_discard_colsum[jj]
} else {
offshore_gear_group_prop_discard[,jj]<-0}
}
#-------------------------------------------------------------
#Generate matrices of the ratio of gear-discard rate to the regional effort weighted all-gear discard rate of each group
gear_to_region_discard_rate_ratio <- gear_group_discard
for(jj in 1:(ncol(gear_group_discard))) {
gear_to_region_discard_rate_ratio[,jj]<-0
}
for(jj in 1:ncol(gear_group_discard)){
if(group_discard[jj]>0){
gear_to_region_discard_rate_ratio[,jj] <- gear_group_discard[,jj] / group_discard[jj]
} else {
gear_to_region_discard_rate_ratio[,jj]<-0
}
}
#Inshore
inshore_gear_to_region_discard_rate_ratio <- gear_group_discard
for(jj in 1:(ncol(gear_group_discard))) {
inshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
for(jj in 1:ncol(gear_group_discard)){
if(inshore_group_discard[jj]>0){
inshore_gear_to_region_discard_rate_ratio[,jj] <- gear_group_discard[,jj] / inshore_group_discard[jj]
} else {
inshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
}
#Offshore
offshore_gear_to_region_discard_rate_ratio <- gear_group_discard
for(jj in 1:(ncol(gear_group_discard))) {
offshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
for(jj in 1:ncol(gear_group_discard)){
if(offshore_group_discard[jj]>0){
offshore_gear_to_region_discard_rate_ratio[,jj] <- gear_group_discard[,jj] / offshore_group_discard[jj]
} else {
offshore_gear_to_region_discard_rate_ratio[,jj]<-0
}
}
#-------------------------------------------------------------
#For each group get the proportion of effort in each habitat
group_effort_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity)))
for(jj in 2:(ncol(gear_group_effort))) {
group_effort_prop_habitat[,jj]<-0
}
names(group_effort_prop_habitat)<-names(gear_group_effort)
rownames(group_effort_prop_habitat)<-names(gear_habitat_activity)
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj]>0){
group_effort_prop_habitat[,jj]<-(colSums(gear_group_effort[,jj]*gear_habitat_activity)) / group_effort[jj]
} else {
group_effort_prop_habitat[,jj]<-0}
}
#Extract separate matrices for inshore (4 rows) and offshore (4 rows), in which the columns still sum to 1 - ie its
#the proportionm distribution of effort across habitats WITHIN inshore and offshore zones
inshore_group_effort_prop_habitat <- (group_effort_prop_habitat[1:4,])
offshore_group_effort_prop_habitat <- (group_effort_prop_habitat[5:8,])
for(jj in 1:4){
inshore_group_effort_prop_habitat[jj,] <- inshore_group_effort_prop_habitat[jj,]/(colSums(group_effort_prop_habitat[1:4,]))
}
for(jj in 1:4){
offshore_group_effort_prop_habitat[jj,] <- offshore_group_effort_prop_habitat[jj,]/(colSums(group_effort_prop_habitat[5:8,]))
}
#-------------------------------------------------------------
#For each group get the proportion of total quantity discarded over each habitat
#In the matrix group_discard_prop_habitat rows=habitats columns = groups, so colsums = 1
group_discard_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity)))
for(jj in 2:(ncol(gear_group_effort))) {
group_discard_prop_habitat[,jj]<-0
}
names(group_discard_prop_habitat)<-names(gear_group_effort)
rownames(group_discard_prop_habitat)<-names(gear_habitat_activity)
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj] & group_discard[jj] >0){
group_discard_prop_habitat[,jj]<-(colSums(gear_group_effortdiscard[,jj]*gear_habitat_activity)) / group_discard[jj]
} else {
group_discard_prop_habitat[,jj]<-0}
}
#Extract separate matrices for inshore (4 row) and offshore (4 row), in which the columns still sum to 1 - ie its
#the proportional distribution of discard quantity across habitats WITHIN inshore and offshore zones
inshore_group_discard_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,1:4])))
for(jj in 2:(ncol(inshore_gear_group_effort))) {
inshore_group_discard_prop_habitat[,jj]<-0
}
names(inshore_group_discard_prop_habitat)<-names(inshore_gear_group_effort)
rownames(inshore_group_discard_prop_habitat)<-names(gear_habitat_activity[1:4])
for(jj in 1:ncol(inshore_gear_group_effort)){
if(inshore_group_effort[jj] & inshore_group_discard[jj] >0){
inshore_group_discard_prop_habitat[,jj]<-(colSums(inshore_gear_group_effortdiscard[,jj]*gear_habitat_activity[,1:4]/rowSums(gear_habitat_activity[,1:4],na.rm=TRUE),na.rm=TRUE)) / inshore_group_discard[jj]
} else {
inshore_group_discard_prop_habitat[,jj]<-0}
}
offshore_group_discard_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,5:8])))
for(jj in 2:(ncol(offshore_gear_group_effort))) {
offshore_group_discard_prop_habitat[,jj]<-0
}
names(offshore_group_discard_prop_habitat)<-names(offshore_gear_group_effort)
rownames(offshore_group_discard_prop_habitat)<-names(gear_habitat_activity[5:8])
for(jj in 1:ncol(offshore_gear_group_effort)){
if(offshore_group_effort[jj] & offshore_group_discard[jj] >0){
offshore_group_discard_prop_habitat[,jj]<-(colSums(offshore_gear_group_effortdiscard[,jj]*gear_habitat_activity[,5:8]/rowSums(gear_habitat_activity[,5:8],na.rm=TRUE),na.rm=TRUE)) / offshore_group_discard[jj]
} else {
offshore_group_discard_prop_habitat[,jj]<-0}
}
#-------------------------------------------------------------
#For each group get the proportion of total quantity of offal produced over each habitat
#In the matrix group_gutting_prop_habitat rows=habitats columns = groups, so colsums = 1
group_gutting_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity)))
for(jj in 2:(ncol(gear_group_effort))) {
group_gutting_prop_habitat[,jj]<-0
}
names(group_gutting_prop_habitat)<-names(gear_group_effort)
rownames(group_gutting_prop_habitat)<-names(gear_habitat_activity)
for(jj in 1:ncol(gear_group_effort)){
if(group_effort[jj] & group_gutting[jj] >0){
group_gutting_prop_habitat[,jj]<-(colSums(gear_group_effortgutting[,jj]*gear_habitat_activity)) / group_gutting[jj]
} else {
group_gutting_prop_habitat[,jj]<-0}
}
#Extract separate matrices for inshore (4 row) and offshore (4 row), in which the columns still sum to 1 - ie its
#the proportional distribution of gutting quantity across habitats WITHIN inshore and offshore zones
inshore_group_gutting_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,1:4])))
for(jj in 2:(ncol(inshore_gear_group_effort))) {
inshore_group_gutting_prop_habitat[,jj]<-0
}
names(inshore_group_gutting_prop_habitat)<-names(inshore_gear_group_effort)
rownames(inshore_group_gutting_prop_habitat)<-names(gear_habitat_activity[1:4])
for(jj in 1:ncol(inshore_gear_group_effort)){
if(inshore_group_effort[jj] & inshore_group_gutting[jj] >0){
inshore_group_gutting_prop_habitat[,jj]<-(colSums(inshore_gear_group_effortgutting[,jj]*gear_habitat_activity[,1:4]/rowSums(gear_habitat_activity[,1:4],na.rm=TRUE),na.rm=TRUE)) / inshore_group_gutting[jj]
} else {
inshore_group_gutting_prop_habitat[,jj]<-0}
}
offshore_group_gutting_prop_habitat<-data.frame(rep(0,ncol(gear_habitat_activity[,5:8])))
for(jj in 2:(ncol(offshore_gear_group_effort))) {
offshore_group_gutting_prop_habitat[,jj]<-0
}
names(offshore_group_gutting_prop_habitat)<-names(offshore_gear_group_effort)
rownames(offshore_group_gutting_prop_habitat)<-names(gear_habitat_activity[5:8])
for(jj in 1:ncol(offshore_gear_group_effort)){
if(offshore_group_effort[jj] & offshore_group_gutting[jj] >0){
offshore_group_gutting_prop_habitat[,jj]<-(colSums(offshore_gear_group_effortgutting[,jj]*gear_habitat_activity[,5:8]/rowSums(gear_habitat_activity[,5:8],na.rm=TRUE),na.rm=TRUE)) / offshore_group_gutting[jj]
} else {
offshore_group_gutting_prop_habitat[,jj]<-0}
}
#-------------------------------------------------------------
#Calculate the daily ploughing rate in each habitat (proportion of habitat area per day)
#To preserve the activity density units of s/m2/d in each subregion we need to divide by the areas
plough_daily_habitat<-rep(0,ncol(gear_habitat_activity))
for(jj in 1:ncol(gear_habitat_activity)){
if(habitat_areas[jj]>0){
plough_daily_habitat[jj]<-(sum(gear_activity_mult * gear_habitat_activity[,jj] * gear_ploughing_rate)) / habitat_areas[jj]
} else {
plough_daily_habitat[jj]<-0}
}
#-------------------------------------------------------------
# Calculate the mortality of benthos due to damage by passage of the trawl gear
# This is given by the area-weighted mortality per trawl pass x the proportion of total seabed area ploughed per day
bensdamage <- BSmort_gear * sum(plough_daily_habitat * habitat_areas)
bencdamage <- BCmort_gear * sum(plough_daily_habitat * habitat_areas)
#Inshore and offshore
inshore_bensdamage <- BSmort_gear * (sum(plough_daily_habitat[1:4] * habitat_areas[1:4]))/sum(habitat_areas[1:4])
offshore_bensdamage <- BSmort_gear * (sum(plough_daily_habitat[5:8] * habitat_areas[5:8]))/sum(habitat_areas[5:8])
inshore_bencdamage <- BCmort_gear * (sum(plough_daily_habitat[1:4] * habitat_areas[1:4]))/sum(habitat_areas[1:4])
offshore_bencdamage <- BCmort_gear * (sum(plough_daily_habitat[5:8] * habitat_areas[5:8]))/sum(habitat_areas[5:8])
#-------------------------------------------------------------
################################
#STUFF THAT NEEDS TO BE OUTPUT FROM THE ROUTINE AND PASSED TO THE ECOLOGY MODEL
#NEED TO COMPILE COMPOSITE VECTORS OF THE INSHORE AND OFFSHORE HARVEST RATES FOR FISH AND BENTHOS
#Compile a vector of daily harvest ratios - inshore and offshore rates for each group except birtds&mammals
Fx_daily_out<-c(inshore_Fx_daily["pelagic"],offshore_Fx_daily["pelagic"],
inshore_Fx_daily["demersal"],offshore_Fx_daily["demersal"],
inshore_Fx_daily["migratory"],offshore_Fx_daily["migratory"],
inshore_Fx_daily["filtben"],offshore_Fx_daily["filtben"],
inshore_Fx_daily["carnben"],offshore_Fx_daily["carnben"],
inshore_Fx_daily["carnzoo"],offshore_Fx_daily["carnzoo"],
inshore_Fx_daily["bird"],offshore_Fx_daily["bird"],
inshore_Fx_daily["seal"],offshore_Fx_daily["seal"],
inshore_Fx_daily["ceta"],offshore_Fx_daily["ceta"],
inshore_Fx_daily["kelp"],offshore_Fx_daily["kelp"])
#Compile a vector of discard rates - inshore and offshore rates for all group except birtds&mammals, plus whole region for demersal
group_discard_out<-c(inshore_group_discard["pelagic"],offshore_group_discard["pelagic"],
inshore_group_discard["demersal"],offshore_group_discard["demersal"],group_discard["demersal"],
inshore_group_discard["migratory"],offshore_group_discard["migratory"],
inshore_group_discard["filtben"],offshore_group_discard["filtben"],
inshore_group_discard["carnben"],offshore_group_discard["carnben"],
inshore_group_discard["carnzoo"],offshore_group_discard["carnzoo"],
inshore_group_discard["bird"],offshore_group_discard["bird"],
inshore_group_discard["seal"],offshore_group_discard["seal"],
inshore_group_discard["ceta"],offshore_group_discard["ceta"],
inshore_group_discard["kelp"],offshore_group_discard["kelp"])
#Compile a vector of gutting rates - inshore and offshore rates for all group except birtds&mammals, plus whole region for demersal
group_gutting_out<-c(inshore_group_gutting["pelagic"],offshore_group_gutting["pelagic"],
inshore_group_gutting["demersal"],offshore_group_gutting["demersal"],
inshore_group_gutting["migratory"],offshore_group_gutting["migratory"],
inshore_group_gutting["filtben"],offshore_group_gutting["filtben"],
inshore_group_gutting["carnben"],offshore_group_gutting["carnben"],
inshore_group_gutting["carnzoo"],offshore_group_gutting["carnzoo"],
inshore_group_gutting["bird"],offshore_group_gutting["bird"],
inshore_group_gutting["seal"],offshore_group_gutting["seal"],
inshore_group_gutting["ceta"],offshore_group_gutting["ceta"],
inshore_group_gutting["kelp"],offshore_group_gutting["kelp"])
#Compile a vector of proportions of discard quantity over each habitat WITHIN the inshore and offshore subregions
#except for birds and mamals where its the proportions across all habitats
discard_map<- c(
inshore_group_discard_prop_habitat[,1], # pelagic fish distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,1], # pelagic fish distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,2], # demersal fish distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,2], # demersal fish distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,3], # migratory fish distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,3], # migratory fish distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,4], # inshire filtben distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,4], # offshore filtben distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,5], # inshore carnben distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,5], # offshore carnben distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,6], # carnzoo distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,6], # carnzoo distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,7], # bird distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,7], # bird distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,8], # seal distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,8], # seal distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,9], # ceta distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,9], # ceta distribution of discard quantity across 4 offshore habitats
inshore_group_discard_prop_habitat[,10], # kelp distribution of discard quantity across 4 inshore habitats
offshore_group_discard_prop_habitat[,10]) # kelp distribution of discard quantity across 4 offshore habitats
#Compile a vector of proportions of discard quantity over each habitat WITHIN the inshore and offshore subregions
#except for birds and mamals where its the proportions across all habitats
gutting_map<- c(
inshore_group_gutting_prop_habitat[,1], # pelagic fish distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,1], # pelagic fish distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,2], # demersal fish distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,2], # demersal fish distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,3], # migratory fish distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,3], # migratory fish distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,4], # inshire filtben distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,4], # offshore filtben distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,5], # inshore carnben distribution of offal quantity across 4 inshore habitats
offshore_group_gutting_prop_habitat[,5], # offshore carnben distribution of offal quantity across 4 offshore habitats
inshore_group_gutting_prop_habitat[,6], # carnzoo distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,6], # carnzoo distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,7], # bird distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,7], # bird distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,8], # seal distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,8], # seal distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,9], # ceta distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,9], # ceta distribution of gutting offal across 4 offshore habitats
inshore_group_gutting_prop_habitat[,10], # kelp distribution of gutting offal across 4 inshore habitats
offshore_group_gutting_prop_habitat[,10]) # kelp distribution of gutting offal across 4 offshore habitats
#.........................
#Compile all the above elements into a single vector that will be piped into the ecology model (6 more elements than the orignal version)
fleet_vector<-c(
Fx_daily_out,
quota_nonquota_parms_vector,
group_discard_out,
group_gutting_out,
DFsize_SWITCH,
DFdiscard_SWITCH,
discard_map,
gutting_map,
plough_daily_habitat,
inshore_bensdamage,
offshore_bensdamage,
inshore_bencdamage,
offshore_bencdamage,
offal_prop_live_weight,
plough_depth_vector
)
names(fleet_vector)<-c(
"F_inshore_pelagic","F_offshore_pelagic",
"F_inshore_demersal","F_offshore_demersal",
"F_inshore_migratory","F_offshore_migratory",
"F_inshore_filtben","F_offshore_filtben",
"F_inshore_carnben","F_offshore_carnben",
"F_inshore_carnzoo","F_offshore_carnzoo",
"F_inshore_bird","F_offshore_bird",
"F_inshore_seal","F_offshore_seal",
"F_inshore_ceta","F_offshore_ceta",
"F_inshore_kelp","F_offshore_kelp",
"QnQ_coef","QnQ_exp","NQus_coef","NQus_exp","QLus_coef","QLus_exp",
"D_inshore_pelagic","D_offshore_pelagic",
"D_inshore_demersal","D_offshore_demersal","D_demersal",
"D_inshore_migratory","D_offshore_migratory",
"D_inshore_filtben","D_offshore_filtben",
"D_inshore_carnben","D_offshore_carnben",
"D_inshore_carnzoo","D_offshore_carnzoo",
"D_inshore_bird","D_offshore_bird",
"D_inshore_seal","D_offshore_seal",
"D_inshore_ceta","D_offshore_ceta",
"D_inshore_kelp","D_offshore_kelp",
"G_inshore_pelagic","G_offshore_pelagic",
"G_inshore_demersal","G_offshore_demersal",
"G_inshore_migratory","G_offshore_migratory",
"G_inshore_filtben","G_offshore_filtben",
"G_inshore_carnben","G_offshore_carnben",
"G_inshore_carnzoo","G_offshore_carnzoo",
"G_inshore_bird","G_offshore_bird",
"G_inshore_seal","G_offshore_seal",
"G_inshore_ceta","G_offshore_ceta",
"G_inshore_kelp","G_offshore_kelp",
"Undersizeswitch",
"Discardswitch",
"PelpD_S0","PelpD_S1","PelpD_S2","PelpD_S3","PelpD_D0","PelpD_D1","PelpD_D2","PelpD_D3",
"DempD_S0","DempD_S1","DempD_S2","DempD_S3","DempD_D0","DempD_D1","DempD_D2","DempD_D3",
"MigpD_S0","MigpD_S1","MigpD_S2","MigpD_S3","MigpD_D0","MigpD_D1","MigpD_D2","MigpD_D3",
"IBfpD_S0","IBfpD_S1","IBfpD_S2","IBfpD_S3","OBfpD_D0","OBfpD_D1","OBfpD_D2","OBfpD_D3",
"IBcpD_S0","IBcpD_S1","IBcpD_S2","IBcpD_S3","OBcpD_D0","OBcpD_D1","OBcpD_D2","OBcpD_D3",
"CzopD_S0","CzopD_S1","CzopD_S2","CzopD_S3","CzopD_D0","CzopD_D1","CzopD_D2","CzopD_D3",
"BirpD_S0","BirpD_S1","BirpD_S2","BirpD_S3","BirpD_D0","BirpD_D1","BirpD_D2","BirpD_D3",
"SeapD_S0","SeapD_S1","SeapD_S2","SeapD_S3","SeapD_D0","SeapD_D1","SeapD_D2","SeapD_D3",
"CetpD_S0","CetpD_S1","CetpD_S2","CetpD_S3","CetpD_D0","CetpD_D1","CetpD_D2","CetpD_D3",
"KelpD_S0","KelpD_S1","KelpD_S2","KelpD_S3","KelpD_D0","KelpD_D1","KelpD_D2","KelpD_D3",
"PelpG_S0","PelpG_S1","PelpG_S2","PelpG_S3","PelpG_D0","PelpG_D1","PelpG_D2","PelpG_D3",
"DempG_S0","DempG_S1","DempG_S2","DempG_S3","DempG_D0","DempG_D1","DempG_D2","DempG_D3",
"MigpG_S0","MigpG_S1","MigpG_S2","MigpG_S3","MigpG_D0","MigpG_D1","MigpG_D2","MigpG_D3",
"IBfpG_S0","IBfpG_S1","IBfpG_S2","IBfpG_S3","OBfpG_D0","OBfpG_D1","OBfpG_D2","OBfpG_D3",
"IBcpG_S0","IBcpG_S1","IBcpG_S2","IBcpG_S3","OBcpG_D0","OBcpG_D1","OBcpG_D2","OBcpG_D3",
"CzopG_S0","CzopG_S1","CzopG_S2","CzopG_S3","CzopG_D0","CzopG_D1","CzopG_D2","CzopG_D3",
"BirpG_S0","BirpG_S1","BirpG_S2","BirpG_S3","BirpG_D0","BirpG_D1","BirpG_D2","BirpG_D3",
"SeapG_S0","SeapG_S1","SeapG_S2","SeapG_S3","SeapG_D0","SeapG_D1","SeapG_D2","SeapG_D3",
"CetpG_S0","CetpG_S1","CetpG_S2","CetpG_S3","CetpG_D0","CetpG_D1","CetpG_D2","CetpG_D3",
"KelpG_S0","KelpG_S1","KelpG_S2","KelpG_S3","KelpG_D0","KelpG_D1","KelpG_D2","KelpG_D3",
"ploughdaily_S0","ploughdaily_S1","ploughdaily_S2","ploughdaily_S3","ploughdaily_D0","ploughdaily_D1","ploughdaily_D2","ploughdaily_D3",
"inshore_bensdamage","offshore_bensdamage",
"inshore_bencdamage","offshore_bencdamage",
"offal_prop_live_weight",
"ploughdepth_S0","ploughdepth_S1","ploughdepth_S2","ploughdepth_S3","ploughdepth_D0","ploughdepth_D1","ploughdepth_D2","ploughdepth_D3"
)
#STUFF THAT NEEDS TO BE SAVED FOR POST-PROCESSING OF THE ECOLOGY MODEL OUTPUT
#gear_group_prop_effort_out
#gear_group_prop_discard_out
#Compile the gear_group_prop_effort_out matrix
#gear_group_prop_effort_out<-cbind(
# offshore_gear_group_prop_effort[,1],inshore_gear_group_prop_effort[,1],
# offshore_gear_group_prop_effort[,2],inshore_gear_group_prop_effort[,2],
# offshore_gear_group_prop_effort[,3],inshore_gear_group_prop_effort[,2],
# offshore_gear_group_prop_effort[,4],inshore_gear_group_prop_effort[,4],
# offshore_gear_group_prop_effort[,5],inshore_gear_group_prop_effort[,5],
# offshore_gear_group_prop_effort[,6],inshore_gear_group_prop_effort[,6],
# offshore_gear_group_prop_effort[,7],inshore_gear_group_prop_effort[,7],
# offshore_gear_group_prop_effort[,8],inshore_gear_group_prop_effort[,8],
# offshore_gear_group_prop_effort[,9],inshore_gear_group_prop_effort[,9],
# offshore_gear_group_prop_effort[,10],inshore_gear_group_prop_effort[,10])
#colnames(gear_group_prop_effort_out)<-c("offshore_pelagic","inshore_pelagic",
# "offshore_demersal","inshore_demersal",
# "offshore_migratory","inshore_migratory",
# "offshore_filtben","inshore_filtben",
# "offshore_carnben","inshore_carnben",
# "offshore_carnzoo","inshore_carnzoo",
# "offshore_bird","inshore_bird",
# "offshore_seal","inshore_seal",
# "offshore_ceta","inshore_ceta",
# "offshore_kelp","inshore_kelp")
#Compile the gear_group_prop_discard_out matrix
#gear_group_prop_discard_out<-cbind(
# offshore_gear_group_prop_discard[,1],inshore_gear_group_prop_discard[,1],
# offshore_gear_group_prop_discard[,2],inshore_gear_group_prop_discard[,2],
# offshore_gear_group_prop_discard[,3],inshore_gear_group_prop_discard[,3],
# offshore_gear_group_prop_discard[,4],inshore_gear_group_prop_discard[,4],
# offshore_gear_group_prop_discard[,5],inshore_gear_group_prop_discard[,5],
# offshore_gear_group_prop_discard[,6],inshore_gear_group_prop_discard[,6],
# offshore_gear_group_prop_discard[,7],inshore_gear_group_prop_discard[,7],
# offshore_gear_group_prop_discard[,8],inshore_gear_group_prop_discard[,8],
# offshore_gear_group_prop_discard[,9],inshore_gear_group_prop_discard[,9],
# offshore_gear_group_prop_discard[,10],inshore_gear_group_prop_discard[,10])
#colnames(gear_group_prop_discard_out)<-c("offshore_pelagic","inshore_pelagic",
# "offshore_demersal","inshore_demersal",
# "offshore_migratory","inshore_migratory",
# "offshore_filtben","inshore_filtben",
# "offshore_carnben","inshore_carnben",
# "offshore_carnzoo","inshore_carnzoo",
# "offshore_bird","inshore_bird",
# "offshore_seal","inshore_seal",
# "offshore_ceta","inshore_ceta",
# "offshore_kelp","inshore_kelp")
fleet_model_output <- list(
fleet_vector = fleet_vector,
offshore_gear_group_prop_effort = offshore_gear_group_prop_effort,
inshore_gear_group_prop_effort = inshore_gear_group_prop_effort,
offshore_gear_to_region_discard_rate_ratio = offshore_gear_to_region_discard_rate_ratio,
inshore_gear_to_region_discard_rate_ratio = inshore_gear_to_region_discard_rate_ratio
)
gear_group_props <- store_fleet_model_output(fleet_model_output, nyears)
# concat the lists:
fishing_fleet_model_output <- c(
fleet_model_output,
gear_group_props
)
fishing_fleet_model_output
}
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