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R/assemble_flow_matrix_from_model_annual_output.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
assemble_flow_matrix_from_model_annual_output
#
# assemble_flow_matrix_from_model_annual_output.R
#
#' process the whole domain annual flux results held in the dataframe annual_flux_results
#' to produce a flow-matrix defining all of the annual integrated mass fluxes been every pair of
#' prey and predator guilds in the food web, alf the geochemical flows, and all of the boundary flows
#'
#' The code then uses the NetIndices R package which relies on the flow-matrix data as input
#' to derive a suite of network indices as outputs These are saved as a standard csv file
#'
#' @param model model object
#' @param build model build object
#' @param output model output
#' @param aggregates aggregated model output
#'
#' @importFrom NetIndices TrophInd AscInd PathInd GenInd EffInd
#'
#' @return list comprising flow matrices and NetIndices results
#'
#' @noRd
#
# ------------------------------------------------------------------------------
assemble_flow_matrix_from_model_annual_output <- function(model, build, output, aggregates) {
setup <- elt(model, "setup")
model.path <- elt(setup, "model.path")
identifier <- elt(setup, "model.ident")
resultsdir <- elt(setup, "resultsdir")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
# extract output:
fluxsedamm_wcamm <- elt(output, "fluxsedamm_wcamm")
fluxwcdet_wcamm <- elt(output, "fluxwcdet_wcamm")
fluxomni_wcamm <- elt(output, "fluxomni_wcamm")
fluxcarn_wcamm <- elt(output, "fluxcarn_wcamm")
fluxpfishlar_wcamm <- elt(output, "fluxpfishlar_wcamm")
fluxdfishlar_wcamm <- elt(output, "fluxdfishlar_wcamm")
fluxpfish_wcamm <- elt(output, "fluxpfish_wcamm")
fluxmfish_wcamm <- elt(output, "fluxmfish_wcamm")
fluxdfish_wcamm <- elt(output, "fluxdfish_wcamm")
fluxbenthslar_wcamm <- elt(output, "fluxbenthslar_wcamm")
fluxbenthclar_wcamm <- elt(output, "fluxbenthclar_wcamm")
fluxbenths_wcamm <- elt(output, "fluxbenths_wcamm")
fluxbenthc_wcamm <- elt(output, "fluxbenthc_wcamm")
fluxbird_wcamm <- elt(output, "fluxbird_wcamm")
fluxseal_wcamm <- elt(output, "fluxseal_wcamm")
fluxceta_wcamm <- elt(output, "fluxceta_wcamm")
fluxxdet_sedamm <- elt(output, "fluxxdet_sedamm")
fluxxRdet_sedamm <- elt(output, "fluxxRdet_sedamm")
fluxwcamm_wcnit <- elt(output, "fluxwcamm_wcnit")
fluxsednit_wcnit <- elt(output, "fluxsednit_wcnit")
fluxsedamm_sednit <- elt(output, "fluxsedamm_sednit")
fluxxdet_wcdet <- elt(output, "fluxxdet_wcdet")
fluxcorp_wcdet <- elt(output, "fluxcorp_wcdet")
fluxkelpdebris_wcdet <- elt(output, "fluxkelpdebris_wcdet")
fluxphyt_wcdet <- elt(output, "fluxphyt_wcdet")
fluxomni_wcdet <- elt(output, "fluxomni_wcdet")
fluxcarn_wcdet <- elt(output, "fluxcarn_wcdet")
fluxpfishlar_wcdet <- elt(output, "fluxpfishlar_wcdet")
fluxdfishlar_wcdet <- elt(output, "fluxdfishlar_wcdet")
fluxpfish_wcdet <- elt(output, "fluxpfish_wcdet")
fluxmfish_wcdet <- elt(output, "fluxmfish_wcdet")
fluxdfish_wcdet <- elt(output, "fluxdfish_wcdet")
fluxbenthslar_wcdet <- elt(output, "fluxbenthslar_wcdet")
fluxbenthclar_wcdet <- elt(output, "fluxbenthclar_wcdet")
fluxbenths_wcdet <- elt(output, "fluxbenths_wcdet")
fluxbenthc_wcdet <- elt(output, "fluxbenthc_wcdet")
fluxbird_wcdet <- elt(output, "fluxbird_wcdet")
fluxseal_wcdet <- elt(output, "fluxseal_wcdet")
fluxceta_wcdet <- elt(output, "fluxceta_wcdet")
fluxwcdet_xdet <- elt(output, "fluxwcdet_xdet")
fluxcorp_xdet <- elt(output, "fluxcorp_xdet")
fluxbenths_xdet <- elt(output, "fluxbenths_xdet")
fluxbenthc_xdet <- elt(output, "fluxbenthc_xdet")
fluxxdet_xRdet <- elt(output, "fluxxdet_xRdet")
fluxcorp_xRdet <- elt(output, "fluxcorp_xRdet")
fluxkelpdebris_xRdet <- elt(output, "fluxkelpdebris_xRdet")
fluxdisc_corp <- elt(output, "fluxdisc_corp")
fluxpfish_corp <- elt(output, "fluxpfish_corp")
fluxmfish_corp <- elt(output, "fluxmfish_corp")
fluxdfish_corp <- elt(output, "fluxdfish_corp")
fluxbenths_corp <- elt(output, "fluxbenths_corp")
fluxbenthc_corp <- elt(output, "fluxbenthc_corp")
fluxbird_corp <- elt(output, "fluxbird_corp")
fluxseal_corp <- elt(output, "fluxseal_corp")
fluxkelp_kelpdebris <- elt(output, "fluxkelp_kelpdebris")
fluxwcamm_kelp <- elt(output, "fluxwcamm_kelp")
fluxwcnit_kelp <- elt(output, "fluxwcnit_kelp")
fluxwcdet_omni <- elt(output, "fluxwcdet_omni")
fluxphyt_omni <- elt(output, "fluxphyt_omni")
fluxbenthslar_omni <- elt(output, "fluxbenthslar_omni")
fluxbenthclar_omni <- elt(output, "fluxbenthclar_omni")
fluxomni_carn <- elt(output, "fluxomni_carn")
fluxpfishlar_carn <- elt(output, "fluxpfishlar_carn")
fluxdfishlar_carn <- elt(output, "fluxdfishlar_carn")
fluxbenthslar_carn <- elt(output, "fluxbenthslar_carn")
fluxbenthclar_carn <- elt(output, "fluxbenthclar_carn")
fluxomni_pfishlar <- elt(output, "fluxomni_pfishlar")
fluxbenthslar_pfishlar <- elt(output, "fluxbenthslar_pfishlar")
fluxbenthclar_pfishlar <- elt(output, "fluxbenthclar_pfishlar")
Pfish_spawn <- elt(output, "Pfish_spawn")
fluxomni_dfishlar <- elt(output, "fluxomni_dfishlar")
fluxbenthslar_dfishlar <- elt(output, "fluxbenthslar_dfishlar")
fluxbenthclar_dfishlar <- elt(output, "fluxbenthclar_dfishlar")
Dfish_spawn <- elt(output, "Dfish_spawn")
fluxomni_pfish <- elt(output, "fluxomni_pfish")
fluxcarn_pfish <- elt(output, "fluxcarn_pfish")
fluxpfishlar_pfish <- elt(output, "fluxpfishlar_pfish")
Pfish_recruit <- elt(output, "Pfish_recruit")
fluxdfishlar_pfish <- elt(output, "fluxdfishlar_pfish")
fluxbenthslar_pfish <- elt(output, "fluxbenthslar_pfish")
fluxbenthclar_pfish <- elt(output, "fluxbenthclar_pfish")
fluxomni_mfish <- elt(output, "fluxomni_mfish")
fluxcarn_mfish <- elt(output, "fluxcarn_mfish")
fluxpfishlar_mfish <- elt(output, "fluxpfishlar_mfish")
fluxdfishlar_mfish <- elt(output, "fluxdfishlar_mfish")
fluxbenthslar_mfish <- elt(output, "fluxbenthslar_mfish")
fluxbenthclar_mfish <- elt(output, "fluxbenthclar_mfish")
fluxcorp_dfish <- elt(output, "fluxcorp_dfish")
fluxdisc_dfish <- elt(output, "fluxdisc_dfish")
fluxcarn_dfish <- elt(output, "fluxcarn_dfish")
fluxpfishlar_dfish <- elt(output, "fluxpfishlar_dfish")
fluxdfishlar_dfish <- elt(output, "fluxdfishlar_dfish")
Dfish_recruit <- elt(output, "Dfish_recruit")
fluxpfish_dfish <- elt(output, "fluxpfish_dfish")
fluxmfish_dfish <- elt(output, "fluxmfish_dfish")
fluxdfish_dfish <- elt(output, "fluxdfish_dfish")
fluxbenths_dfish <- elt(output, "fluxbenths_dfish")
fluxbenthc_dfish <- elt(output, "fluxbenthc_dfish")
fluxwcdet_benthslar <- elt(output, "fluxwcdet_benthslar")
fluxphyt_benthslar <- elt(output, "fluxphyt_benthslar")
Bs_spawn <- elt(output, "Bs_spawn")
fluxwcdet_benthclar <- elt(output, "fluxwcdet_benthclar")
fluxphyt_benthclar <- elt(output, "fluxphyt_benthclar")
Bc_spawn <- elt(output, "Bc_spawn")
fluxwcdet_benths <- elt(output, "fluxwcdet_benths")
fluxxdet_benths <- elt(output, "fluxxdet_benths")
fluxxRdet_benths <- elt(output, "fluxxRdet_benths")
fluxphyt_benths <- elt(output, "fluxphyt_benths")
Bs_recruit <- elt(output, "Bs_recruit")
fluxcorp_benthc <- elt(output, "fluxcorp_benthc")
fluxkelpdebris_benthc <- elt(output, "fluxkelpdebris_benthc")
fluxkelp_benthc <- elt(output, "fluxkelp_benthc")
fluxbenths_benthc <- elt(output, "fluxbenths_benthc")
Bc_recruit <- elt(output, "Bc_recruit")
fluxcorp_bird <- elt(output, "fluxcorp_bird")
fluxdisc_bird <- elt(output, "fluxdisc_bird")
fluxcarn_bird <- elt(output, "fluxcarn_bird")
fluxpfish_bird <- elt(output, "fluxpfish_bird")
fluxmfish_bird <- elt(output, "fluxmfish_bird")
fluxdfish_bird <- elt(output, "fluxdfish_bird")
fluxbenths_bird <- elt(output, "fluxbenths_bird")
fluxbenthc_bird <- elt(output, "fluxbenthc_bird")
fluxcorp_seal <- elt(output, "fluxcorp_seal")
fluxdisc_seal <- elt(output, "fluxdisc_seal")
fluxcarn_seal <- elt(output, "fluxcarn_seal")
fluxpfish_seal <- elt(output, "fluxpfish_seal")
fluxmfish_seal <- elt(output, "fluxmfish_seal")
fluxdfish_seal <- elt(output, "fluxdfish_seal")
fluxbenths_seal <- elt(output, "fluxbenths_seal")
fluxbenthc_seal <- elt(output, "fluxbenthc_seal")
fluxbird_seal <- elt(output, "fluxbird_seal")
fluxdisc_ceta <- elt(output, "fluxdisc_ceta")
fluxomni_ceta <- elt(output, "fluxomni_ceta")
fluxcarn_ceta <- elt(output, "fluxcarn_ceta")
fluxpfish_ceta <- elt(output, "fluxpfish_ceta")
fluxmfish_ceta <- elt(output, "fluxmfish_ceta")
fluxdfish_ceta <- elt(output, "fluxdfish_ceta")
fluxbenths_ceta <- elt(output, "fluxbenths_ceta")
fluxbenthc_ceta <- elt(output, "fluxbenthc_ceta")
fluxbird_ceta <- elt(output, "fluxbird_ceta")
fluxseal_ceta <- elt(output, "fluxseal_ceta")
fluxkelpdebris_beachexport <- elt(output, "fluxkelpdebris_beachexport")
mfish_emigration <- elt(output, "mfish_emigration")
fluxAMMoutflow_o <- elt(output, "fluxAMMoutflow_o")
fluxAMMoutflow_i <- elt(output, "fluxAMMoutflow_i")
fluxNIToutflow_o <- elt(output, "fluxNIToutflow_o")
fluxNIToutflow_i <- elt(output, "fluxNIToutflow_i")
fluxDEToutflow_o <- elt(output, "fluxDEToutflow_o")
fluxDEToutflow_i <- elt(output, "fluxDEToutflow_i")
fluxsedboundary_o <- elt(output, "fluxsedboundary_o")
fluxsedboundary_i <- elt(output, "fluxsedboundary_i")
fluxPHYToutflow_o <- elt(output, "fluxPHYToutflow_o")
fluxPHYToutflow_i <- elt(output, "fluxPHYToutflow_i")
mfish_imigration <- elt(output, "mfish_imigration")
fluxAMMinflow_i <- elt(output, "fluxAMMinflow_i")
fluxAMMinflow_o <- elt(output, "fluxAMMinflow_o")
rivAMMinflow <- elt(output, "rivAMMinflow")
atmosAMMinput_i <- elt(output, "atmosAMMinput_i")
atmosAMMinput_o <- elt(output, "atmosAMMinput_o")
fluxNITinflow_i <- elt(output, "fluxNITinflow_i")
fluxNITinflow_o <- elt(output, "fluxNITinflow_o")
rivNITinflow <- elt(output, "rivNITinflow")
atmosNITinput_i <- elt(output, "atmosNITinput_i")
atmosNITinput_o <- elt(output, "atmosNITinput_o")
fluxDETinflow_i <- elt(output, "fluxDETinflow_i")
fluxDETinflow_o <- elt(output, "fluxDETinflow_o")
rivPARTinflow <- elt(output, "rivPARTinflow")
fluxPHYTinflow_i <- elt(output, "fluxPHYTinflow_i")
fluxPHYTinflow_o <- elt(output, "fluxPHYTinflow_o")
disckp_i <- elt(output, "disckp_i") # Fix
offalkp_i <- elt(output, "offalkp_i") # Fix
landkp_i <- elt(output, "landkp_i") # Fix
# extract aggregates:
disccz <- elt(aggregates, "disccz")
offalcz <- elt(aggregates, "offalcz")
discpel <- elt(aggregates, "discpel")
offalpel <- elt(aggregates, "offalpel")
discmig <- elt(aggregates, "discmig")
offalmig <- elt(aggregates, "offalmig")
discdem <- elt(aggregates, "discdem")
offaldem <- elt(aggregates, "offaldem")
discsb <- elt(aggregates, "discsb")
offalsb <- elt(aggregates, "offalsb")
disccb <- elt(aggregates, "disccb")
offalcb <- elt(aggregates, "offalcb")
offalbd <- elt(aggregates, "offalbd")
offalsl <- elt(aggregates, "offalsl")
offalct <- elt(aggregates, "offalct")
fluxwcamm_phyt <- elt(aggregates, "fluxwcamm_phyt")
fluxwcnit_phyt <- elt(aggregates, "fluxwcnit_phyt")
landcz <- elt(aggregates, "landcz")
landp <- elt(aggregates, "landp")
landm <- elt(aggregates, "landm")
landd <- elt(aggregates, "landd")
landsb <- elt(aggregates, "landsb")
landcb <- elt(aggregates, "landcb")
landbd <- elt(aggregates, "landbd")
landsl <- elt(aggregates, "landsl")
landct <- elt(aggregates, "landct")
wcdenitrif <- elt(aggregates, "wcdenitrif")
seddenitrif <- elt(aggregates, "seddenitrif")
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Parameters which have been established by the simulated annealing scheme are
# loaded from a csv file which is made from the last line of the 'accepted parameters'
# file produced by the annealing programme.
#
# A variety of other parameters which are not optimized by simulated annealing are
# hard-wired in this subroutine
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Read in the template for the flowmatrix
flowmatrix_template <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FOOD_WEB_FLOW_MATRIX, row.names=1) # special
#Now we need to trawl through the model output dataframe and integrate each o fthe flux terms over the final year and drop
#into the flow matrix template. For some elements of the matrix we have to aggregate a few individual fluxes, for example
#feeding and recruitment to adult fish groups, so it all has to be done carefully.
#names(flowmatrix_template)
# [1] "wcammonia" "sedammonia" "wcnitrate" "sednitrate"
# [5] "wcdetritus" "seddetritus" "seddetritusR" "corpses"
# [9] "discards" "phyt" "omnivzoo" "carnzoo"
#[13] "pfishlar" "dfishlar" "pfish" "mfish"
#[17] "dfish" "benthslar" "benthclar" "benths"
#[21] "benthc" "birdmam" "landings" "denitrification"
#[25] "emigration" "exports" "imigration" "imports"
#Its very importnat that the rownames = colnames
#The fluxes in matrix are from row elements to column elements
outrowstart<-((nyears-1)*360+1)
outrowend <-ndays
#-------------------------------
#Fluxes to water column ammonia
#From sediment ammonia
fluxvec<-fluxsedamm_wcamm
sourcename<-"sedammonia"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
#SPECIAL CASE
#If this flux is negative then it needs to go into a different cell
if(flux<0) {
destname<-"sedammonia"
sourcename <-"wcammonia"
}
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From wc detritus
fluxvec<-fluxwcdet_wcamm
sourcename<-"wcdetritus"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From omnivorous zooplankton
fluxvec<-fluxomni_wcamm
sourcename<-"omnivzoo"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_wcamm
sourcename<-"carnzoo"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_wcamm
sourcename<-"pfishlar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_wcamm
sourcename<-"dfishlar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_wcamm
sourcename<-"pfish"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_wcamm
sourcename<-"mfish"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_wcamm
sourcename<-"dfish"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_wcamm
sourcename<-"benthslar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_wcamm
sourcename<-"benthclar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_wcamm
sourcename<-"benths"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
## NOTE this correct - excretion by settled benthos gos direct to the water column not to porewaters
#From c/s benthos
fluxvec<-fluxbenthc_wcamm
sourcename<-"benthc"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
## NOTE this correct - excretion by settled benthos gos direct to the water column not to porewaters
#From birds
fluxvec<-fluxbird_wcamm
sourcename<-"bird"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-fluxseal_wcamm
sourcename<-"seal"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-fluxceta_wcamm
sourcename<-"ceta"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment porewater ammonia
#From sediment detritus
fluxvec<-fluxxdet_sedamm
sourcename<-"seddetritus"
destname <-"sedammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment refratory detritus
fluxvec<-fluxxRdet_sedamm
sourcename<-"seddetritusR"
destname <-"sedammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to water column nitrate
#From water column ammonia
fluxvec<-fluxwcamm_wcnit
sourcename<-"wcammonia"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment porewater nitrate
fluxvec<-fluxsednit_wcnit
sourcename<-"sednitrate"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
#SPECIAL CASE
#If this flux is negative then it needs to go into a different cell
if(flux<0) {
flux <- (-1*flux)
destname<-"sednitrate"
sourcename <-"wcnitrate"
}
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment porewater nitrate
#From sediment porewater ammonia
fluxvec<-fluxsedamm_sednit
sourcename<-"sedammonia"
destname <-"sednitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to water column detritus
#From sediment detritus (resuspension)
fluxvec<-fluxxdet_wcdet
sourcename<-"seddetritus"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From corpses (only over rocky habitats)
fluxvec<-fluxcorp_wcdet
sourcename<-"corpses"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp debris (only over inshore rocky habitats)
fluxvec<-fluxkelpdebris_wcdet
sourcename<-"kelpdebris"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_wcdet
sourcename<-"phyt"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From omnivorous zooplankton
fluxvec<-fluxomni_wcdet
sourcename<-"omnivzoo"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_wcdet
sourcename<-"carnzoo"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_wcdet
sourcename<-"pfishlar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_wcdet
sourcename<-"dfishlar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_wcdet
sourcename<-"pfish"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_wcdet
sourcename<-"mfish"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_wcdet
sourcename<-"dfish"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_wcdet
sourcename<-"benthslar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_wcdet
sourcename<-"benthclar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos (only over rocky habitats)
fluxvec<-fluxbenths_wcdet
sourcename<-"benths"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos (only over rocky habitats)
fluxvec<-fluxbenthc_wcdet
sourcename<-"benthc"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-fluxbird_wcdet
sourcename<-"bird"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-fluxseal_wcdet
sourcename<-"seal"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-fluxceta_wcdet
sourcename<-"ceta"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment detritus
#From water column detritus (sedimentation)
fluxvec<-fluxwcdet_xdet
sourcename<-"wcdetritus"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From corpses (over sand and mud)
fluxvec<-fluxcorp_xdet
sourcename<-"corpses"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos (over sand and mud)
fluxvec<-fluxbenths_xdet
sourcename<-"benths"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos (over sand and mud)
fluxvec<-fluxbenthc_xdet
sourcename<-"benthc"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment refractory detritus
#From sediment detritus
fluxvec<-fluxxdet_xRdet
sourcename<-"seddetritus"
destname <-"seddetritusR"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From corpses
fluxvec<-fluxcorp_xRdet
sourcename<-"corpses"
destname <-"seddetritusR"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelpdebris
fluxvec<-fluxkelpdebris_xRdet
sourcename<-"kelpdebris"
destname <-"seddetritusR"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to corpses
#From discards
fluxvec<-fluxdisc_corp
sourcename<-"discards"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_corp
sourcename<-"pfish"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_corp
sourcename<-"mfish"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_corp
sourcename<-"dfish"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_corp
sourcename<-"benths"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_corp
sourcename<-"benthc"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds (includes discards of by-catch)
fluxvec<-fluxbird_corp
sourcename<-"bird"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals (includes discards of by-catch)
fluxvec<-fluxseal_corp
sourcename<-"seal"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans (includes discards of by-catch)
fluxvec<-fluxseal_corp
sourcename<-"ceta"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to discards (includes fluxes of offal from processing at sea)
#From carnivorous zooplankton
fluxvec<-disccz + offalcz
sourcename<-"carnzoo"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-discpel + offalpel
sourcename<-"pfish"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-discmig + offalmig
sourcename<-"mfish"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-discdem + offaldem
sourcename<-"dfish"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-discsb + offalsb
sourcename<-"benths"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-disccb + offalcb
sourcename<-"benthc"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds & mammals - discards included within the model as a flux to corpses, but offal from processing at sea goes to discards
#From birds
fluxvec<-offalbd
sourcename<-"bird"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-offalsl
sourcename<-"seal"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-offalct
sourcename<-"ceta"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to kelp debris (includes destruction y waves plus discards and fluxes of kelp offal from processing at sea)
#From kelp
fluxvec<-fluxkelp_kelpdebris + disckp_i + offalkp_i
sourcename<-"kelp"
destname <-"kelpdebris"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to phytoplankton
#From water column ammonia
fluxvec<-fluxwcamm_phyt
sourcename<-"wcammonia"
destname <-"phyt"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From water column nitrate
fluxvec<-fluxwcnit_phyt
sourcename<-"wcnitrate"
destname <-"phyt"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to kelp
#From water column ammonia
fluxvec<-fluxwcamm_kelp
sourcename<-"wcammonia"
destname <-"kelp"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From water column nitrate
fluxvec<-fluxwcnit_kelp
sourcename<-"wcnitrate"
destname <-"kelp"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to omnivorous zooplankton
#From water column detritus
fluxvec<-fluxwcdet_omni
sourcename<-"wcdetritus"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_omni
sourcename<-"phyt"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_omni
sourcename<-"benthslar"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_omni
sourcename<-"benthclar"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to carnivorous zooplankton
#From omnivorous zooplankton
fluxvec<-fluxomni_carn
sourcename<-"omnivzoo"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_carn
sourcename<-"pfishlar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_carn
sourcename<-"dfishlar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_carn
sourcename<-"benthslar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_carn
sourcename<-"benthclar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to pelagic fish larvae
#From omnivorous zooplankton
fluxvec<-fluxomni_pfishlar
sourcename<-"omnivzoo"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_pfishlar
sourcename<-"benthslar"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_pfishlar
sourcename<-"benthclar"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from adult pelagic fish
fluxvec<-Pfish_spawn
sourcename<-"pfish"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to demersal fish larvae
#From omnivorous zooplankton
fluxvec<-fluxomni_dfishlar
sourcename<-"omnivzoo"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_dfishlar
sourcename<-"benthslar"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_dfishlar
sourcename<-"benthclar"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from adult demersal fish
fluxvec<-Dfish_spawn
sourcename<-"dfish"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to pelagic fish
#From omnivorous zooplankton
fluxvec<-fluxomni_pfish
sourcename<-"omnivzoo"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_pfish
sourcename<-"carnzoo"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_pfish
#SPECIAL CASE
#Here we have to add on the recruitment flux from larvae to settled stage
fluxvec2<-Pfish_recruit
sourcename<-"pfishlar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From demersal fish larvae
fluxvec<-fluxdfishlar_pfish
sourcename<-"dfishlar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_pfish
sourcename<-"benthslar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_pfish
sourcename<-"benthclar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to migratory fish
#From omnivorous zooplankton
fluxvec<-fluxomni_mfish
sourcename<-"omnivzoo"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_mfish
sourcename<-"carnzoo"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_mfish
sourcename<-"pfishlar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_mfish
sourcename<-"dfishlar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_mfish
sourcename<-"benthslar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_mfish
sourcename<-"benthclar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to demersal fish
#From corpses
fluxvec<-fluxcorp_dfish
sourcename<-"corpses"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_dfish
sourcename<-"discards"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_dfish
sourcename<-"carnzoo"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_dfish
sourcename<-"pfishlar"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_dfish
#SPECIAL CASE
#Here we have to add on the recruitment flux from larvae to settled stage
fluxvec2<-Dfish_recruit
sourcename<-"dfishlar"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From pelagic fish
fluxvec<-fluxpfish_dfish
sourcename<-"pfish"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_dfish
sourcename<-"mfish"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_dfish
sourcename<-"dfish"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_dfish
sourcename<-"benths"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_dfish
sourcename<-"benthc"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to f/d benthos larvae
#From water column detritus
fluxvec<-fluxwcdet_benthslar
sourcename<-"wcdetritus"
destname <-"benthslar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_benthslar
sourcename<-"phyt"
destname <-"benthslar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from settled benthos
fluxvec<-Bs_spawn
sourcename<-"benths"
destname <-"benthslar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to c/s benthos larvae
#From water column detritus
fluxvec<-fluxwcdet_benthclar
sourcename<-"wcdetritus"
destname <-"benthclar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_benthclar
sourcename<-"phyt"
destname <-"benthclar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from settled benthos
fluxvec<-Bc_spawn
sourcename<-"benthc"
destname <-"benthclar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to f/d benthos
#From water column detritus
fluxvec<-fluxwcdet_benths
sourcename<-"wcdetritus"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment detritus
fluxvec<-fluxxdet_benths
sourcename<-"seddetritus"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment refractory detritus
fluxvec<-fluxxRdet_benths
sourcename<-"seddetritusR"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_benths
sourcename<-"phyt"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - recruitment flux from benthos larvae
fluxvec<-Bs_recruit
sourcename<-"benthslar"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to c/s benthos
#From corpses
fluxvec<-fluxcorp_benthc
sourcename<-"corpses"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp debris
fluxvec<-fluxkelpdebris_benthc
sourcename<-"kelpdebris"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp
fluxvec<-fluxkelp_benthc
sourcename<-"kelp"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_benthc
sourcename<-"benths"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - recruitment flux from benthos larvae
fluxvec<-Bc_recruit
sourcename<-"benthclar"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to birds
#From corpses
fluxvec<-fluxcorp_bird
sourcename<-"corpses"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_bird
sourcename<-"discards"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
# #From omnivorous zooplankton
# fluxvec<-fluxomni_bird
# sourcename<-"omnivzoo"
# destname <-"bird"
# flux<-fluxvec[outrowend]-fluxvec[outrowstart]
# flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_bird
sourcename<-"carnzoo"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_bird
sourcename<-"pfish"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_bird
sourcename<-"mfish"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_bird
sourcename<-"dfish"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_bird
sourcename<-"benths"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_bird
sourcename<-"benthc"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to seals
#From corpses
fluxvec<-fluxcorp_seal
sourcename<-"corpses"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_seal
sourcename<-"discards"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_seal
sourcename<-"carnzoo"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_seal
sourcename<-"pfish"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_seal
sourcename<-"mfish"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_seal
sourcename<-"dfish"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_seal
sourcename<-"benths"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_seal
sourcename<-"benthc"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-fluxbird_seal
sourcename<-"bird"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to cetaceans
# #From corpses
# fluxvec<-fluxcorp_ceta
# sourcename<-"corpses"
# destname <-"ceta"
# flux<-fluxvec[outrowend]-fluxvec[outrowstart]
# flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_ceta
sourcename<-"discards"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From omnivorous zooplankton
fluxvec<-fluxomni_ceta
sourcename<-"omnivzoo"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_ceta
sourcename<-"carnzoo"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_ceta
sourcename<-"pfish"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_ceta
sourcename<-"mfish"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_ceta
sourcename<-"dfish"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_ceta
sourcename<-"benths"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_ceta
sourcename<-"benthc"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-fluxbird_ceta
sourcename<-"bird"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-fluxseal_ceta
sourcename<-"seal"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to landings - THIS SHOULD BE THE PROCESSED LANDED WEIGHT ie LIVE WEIGHT MINUS OFFAL WEIGHT
#From carnivorous zooplankton
fluxvec<-landcz - offalcz
sourcename<-"carnzoo"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-landp - offalpel
sourcename<-"pfish"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-landm - offalmig
sourcename<-"mfish"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-landd - offaldem
sourcename<-"dfish"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-landsb - offalsb
sourcename<-"benths"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-landcb - offalcb
sourcename<-"benthc"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-landbd - offalbd
sourcename<-"bird"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-landsl - offalsl
sourcename<-"seal"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-landct - offalct
sourcename<-"ceta"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp
fluxvec<-landkp_i - offalkp_i
sourcename<-"kelp"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to beachcast
#From kelp debris
fluxvec<-fluxkelpdebris_beachexport
sourcename<-"kelpdebris"
destname <-"beachcast"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to nitrogen gas
#From water column nitrate
fluxvec<-wcdenitrif
sourcename<-"wcnitrate"
destname <-"atmosphere"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment porewater nitrate
fluxvec<-seddenitrif
sourcename<-"sednitrate"
destname <-"atmosphere"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to emigration
#From migratory fish
fluxvec<-mfish_emigration
sourcename<-"mfish"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to hydrodynamic exports and burial
#From water column ammonia
fluxvec<-fluxAMMoutflow_o
fluxvec2<-fluxAMMoutflow_i
sourcename<-"wcammonia"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From water column nitrate
fluxvec<-fluxNIToutflow_o
fluxvec2<-fluxNIToutflow_i
sourcename<-"wcnitrate"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From water column detritus
fluxvec<-fluxDEToutflow_o
fluxvec2<-fluxDEToutflow_i
sourcename<-"wcdetritus"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From sediment refractory detritus (burial)
fluxvec<-fluxsedboundary_o
fluxvec2<-fluxsedboundary_i
sourcename<-"seddetritusR"
destname <-"seabed"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
cflux<-flux+flux2
#SPECIAL CASE
#If the sum of these fluxes is -ve then it indicated burial so place it as an export
#If the sum of these fluxes is +ve then it indicated exhumation so place it as an import
if(cflux>0) {
destname <-"seddetritusR"
sourcename<-"seabed"
}
if(cflux<0) cflux <- (-1*cflux)
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- cflux
#From phytoplankton
fluxvec<-fluxPHYToutflow_o
fluxvec2<-fluxPHYToutflow_i
sourcename<-"phyt"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#----------------------------
#Imigration fluxes
#To migratory fish
fluxvec<-mfish_imigration
sourcename<-"ocean"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-----------------------------
#Hydrodynamic, river and atmosphere imports
#Ocean to water column ammonia
fluxvec <-fluxAMMinflow_i
fluxvec2<-fluxAMMinflow_o
sourcename<-"ocean"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Rivers to water column ammonia
fluxvec<-rivAMMinflow
sourcename<-"rivers"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#Atmosphere to water column ammonia
fluxvec<-atmosAMMinput_i
fluxvec2<-atmosAMMinput_o
sourcename<-"atmosphere"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Ocean to water column nitrate
fluxvec <-fluxNITinflow_i
fluxvec2<-fluxNITinflow_o
sourcename<-"ocean"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Rivers to water column nitrate
fluxvec<-rivNITinflow
sourcename<-"rivers"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#Atmosphere to water column nitrate
fluxvec<-atmosNITinput_i
fluxvec2<-atmosNITinput_o
sourcename<-"atmosphere"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Ocean to water column detritus
fluxvec <-fluxDETinflow_i
fluxvec2<-fluxDETinflow_o
sourcename<-"ocean"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Rivers to water column detritus
fluxvec<-rivPARTinflow
sourcename<-"rivers"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#To phytoplankton
fluxvec <-fluxPHYTinflow_i
fluxvec2<-fluxPHYTinflow_o
sourcename<-"ocean"
destname <-"phyt"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
flow_matrix_all_fluxes <- flowmatrix_template
#Save the new flow matrix to a file.
filename = csvname(resultsdir, "flow_matrix_all_fluxes", identifier)
writecsv(flowmatrix_template, filename, header=TRUE)
#--------------------------------------------------------------------------------------------------------
#FOR SOME INDICES WE NEED TO REMOVE FROM THE FLOW MATRIX THE FLUXES DUE TO SPAWNING AND RECRUITMENT
#MAKE A COPY OF THE FLOWMATRIX
flowmatrix_no_sp_rec<-flowmatrix_template
outrowstart<-((nyears-1)*360+1)
outrowend <-ndays
#Remove recruitment of pelagic fish
sourcename<-"pfishlar"
destname <-"pfish"
fluxvec<-fluxpfishlar_pfish
rflux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <-
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] - rflux
#Remove recruitment of demersal fish
sourcename<-"dfishlar"
destname <-"dfish"
fluxvec<-fluxdfishlar_dfish
rflux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <-
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] - rflux
#Remove recruitment of f/d benthos
sourcename<-"benthslar"
destname <-"benths"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove recruitment of c/s benthos
sourcename<-"benthclar"
destname <-"benthc"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawning of pelagic fish
sourcename<-"pfish"
destname <-"pfishlar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawning of demersal fish
sourcename<-"dfish"
destname <-"dfishlar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawninmg of f/d benthos
sourcename<-"benths"
destname <-"benthslar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawning of c/s benthos
sourcename<-"benthc"
destname <-"benthclar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Save the new flow matrix to a file.
filename = csvname(resultsdir, "flow_matrix_excl_spawn_recruit", identifier)
writecsv(flowmatrix_no_sp_rec, filename, header=TRUE)
#--------------------------------------------------------------------------------------------------------
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Derive a load of network indices
#library(NetIndices)
#............................................................................
#Check if discards are present or not - if not we have to treat these as an inport and export
Disc_sum<-sum(flowmatrix_template$discards)
zerocheck<-which(colSums(flowmatrix_template)[1:(ncol(flowmatrix_template)-6)]==0)
zerolist<-colnames(flowmatrix_template)[zerocheck]
#............................................................................
#Trophic index calculation
TrophicIndexResults<-TrophInd(flowmatrix_no_sp_rec, Import = c("ocean","rivers","atmosphere","seabed"),
Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"),
Dead=c("wcammonia","sedammonia","wcnitrate","sednitrate","wcdetritus","seddetritus","seddetritusR","corpses","kelpdebris","discards"))
#Output -- TL = Trophic level, OI = Omnivory index
#............................................................................
if(Disc_sum>0) AscendencyIndexResults<-AscInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(Disc_sum==0) AscendencyIndexResults<-AscInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#asc the ascendency of the network, a measure of growth and development.
#overh the overhead of the network.
#cap the development capacity of the network, an upper bound on ascendency.
#ACratio the ratio of ascendency and capacity.
#............................................................................
#For dependency analysis we need to reduce the flowmatrix to the living components
#flowmatrix_for_dependency<-flowmatrix_template[8:26,8:27]
#Dependency(flowmatrix_for_dependency, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#Produces a matrix of the dependency of component i (row) on component j (column)
#............................................................................
if(length(zerolist)>0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c(zerolist,"ocean","rivers","atmosphere","seabed"),Export = c(zerolist,"ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(length(zerolist)==0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#if(Disc_sum>0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#if(Disc_sum==0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#TSTC total system cycled throughflow.
#TSTS non-cycled throughflow.
#FCI Finn's cycling index (1980).
#FCIb revised Finn's cycling index, sensu Allesina and Ulanowicz, 2004.
#APL average pathlength, also known as Network Aggradation (Sum of APLc and APLs in Latham 2006).
#............................................................................
if(Disc_sum>0) GeneralIndexResults<-GenInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(Disc_sum==0) GeneralIndexResults<-GenInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#N number of compartments, excluding the externals.
#T.. total System Throughput.
#TST total System Throughflow.
#Lint number of Internal links.
#Ltot total number of links.
#LD link Density
#C connectance (internal).
#Tijbar average Link Weight.
#TSTbar average Compartment Throughflow .
#Cbar compartmentalization, [0,1], the degree of connectedness of subsystems within a network.
#............................................................................
# if(length(zerolist)>0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c(zerolist,"ocean","rivers","atmosphere","seabed"),Export = c(zerolist,"ocean","rivers","atmosphere","seabed","landings","beachcast"))
# if(length(zerolist)==0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
# TEMPORARILY DISABLED
#if(Disc_sum>0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#if(Disc_sum==0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#NAG Network aggradation = average path length.
#HP Homogenization index.
#BC Synergism.
#ID Dominance of Indirect effects.
#MN Mean of non-dimensional flow-matrix (N).
#MG Mean of direct flow-matrix (G).
#CVN Coefficient of variation of non-dimensional flow-matrix (N).
#CVG Coefficient of variation of direct flow-matrix (G).
#U Only if Full == TRUE: The Utility non-dimensional matrix.
#N1 Only if Full == TRUE: The Integral non-dimensional Flow Matrix.
#G Only if Full == TRUE: The Normalized direct flow (or transitive closure) matrix.
#............................................................................
if(Disc_sum>0) EffectivenessIndexResults<-EffInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(Disc_sum==0) EffectivenessIndexResults<-EffInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#CZ Effective connectance
#FZ Effective Flows
#NZ Effective nodes
#RZ Effective roles
#............................................................................
#TrophicIndexResults
#AscendencyIndexResults
#PathwayIndexResults
#GeneralIndexResults
#EnvironmentIndexResults
#EffectivenessIndexResults
#Build all these indices together into a structure
#Need to store 47+number of rows in the trophic index results rows of data
for(ii in 1:(nrow(TrophicIndexResults))){
if(ii==1) trophicnames<-paste(rownames(TrophicIndexResults)[ii],"_trophiclevel",sep="")
if(ii>1) trophicnames<-c(trophicnames,paste(rownames(TrophicIndexResults)[ii],"_trophiclevel",sep=""))
}
for(ii in 1:(nrow(TrophicIndexResults))){
trophicnames<-c(trophicnames,paste(rownames(TrophicIndexResults)[ii],"_omnivoryindex",sep=""))
}
NetworkIndexResults<-data.frame(rep(NA,(47+(2*(nrow(TrophicIndexResults))))))
names(NetworkIndexResults)<-"NetworkData"
row.names(NetworkIndexResults)<-c(
trophicnames,
#Ascendency Indices
"Ascendency_total",
"Ascendency_internal",
"Ascendency_import",
"Ascendency_external",
"Ascendency_dissipation",
"Overhead_total",
"Overhead_internal",
"Overhead_import",
"Overhead_external",
"Overhead_dissipation",
"Capacity_total",
"Capacity_internal",
"Capacity_import",
"Capacity_external",
"Capacity_dissipation",
"ACratio_total",
"ACratio_internal",
"ACratio_import",
"ACratio_external",
"ACratio_dissipation",
#Pathway Indices
"Total_system_cycled_thoughflow_TSTC",
"Non_cycled_throughflow_TSTS",
"Finns_cycling_index_FCI",
"Revised_Finns_cycling_index_FCIb",
"Average_path_length",
#Generaal Indices
"Number_of_compartments_N",
"Total_system_throughput_T",
"Total_system_throughflow_TST",
"Number_of_internal_links_Lint",
"Total_number_of_links_Ltot",
"Link_density_LD",
"Connectance_C",
"Average_link_weight_Tijbar",
"Average_compartment_thoughflow_TSTbar",
"Compartmentalization_Cbar",
#Environment Indices
"Network_aggradation_NAG",
"Homogenization_index_HP",
"Synergism_BC",
"Dominance_of_indirect_effects_ID",
"Mean_of_non_dimension_flowmatrix_MN",
"Mean_of_direct_flowmatrix_MG",
"CV_of_non_dimension_flowmatrix_MN",
"CV_of_direct_flowmatrix_MG",
#Effectiveness Indices
"Effective_connectance_CZ",
"Effective_flows_FZ",
"Effective_nodes_NZ",
"Effective_roles_RZ")
NetworkIndexResults[1:(nrow(TrophicIndexResults)),1] <- TrophicIndexResults[,1]
NetworkIndexResults[(1+(nrow(TrophicIndexResults))):(2*(nrow(TrophicIndexResults))),1] <- TrophicIndexResults[,2]
lastfilled<-(2*(nrow(TrophicIndexResults)))
for(jj in 1:4){
NetworkIndexResults[(lastfilled+1+((jj-1)*5)):(lastfilled+5+((jj-1)*5)),1] <- AscendencyIndexResults[,jj]
}
lastfilled<-lastfilled+5+((4-1)*5)
NetworkIndexResults[(lastfilled+1):(lastfilled+5),1] <- t(as.data.frame(PathwayIndexResults))
lastfilled<-lastfilled+5
NetworkIndexResults[(lastfilled+1):(lastfilled+10),1] <- t(as.data.frame(GeneralIndexResults))
lastfilled<-lastfilled+10
#NetworkIndexResults[(lastfilled+1):(lastfilled+8),1] <- t(as.data.frame(EnvironmentIndexResults))
NetworkIndexResults[(lastfilled+1):(lastfilled+8),1] <- NA # OPTION WHERE THE ENVIND ROUTINE IS DISABLED
lastfilled<-lastfilled+8
NetworkIndexResults[(lastfilled+1):(lastfilled+4),1] <- t(as.data.frame(EffectivenessIndexResults))
lastfilled<-lastfilled+4
#Save the new flow matrix to a file.
filename = csvname(resultsdir, "Network_indices_output", identifier)
writecsv(NetworkIndexResults, filename, header=TRUE)
list(
flow_matrix_all_fluxes = flow_matrix_all_fluxes,
flow_matrix_excl_spawn_recruit = flowmatrix_no_sp_rec,
NetworkIndexResults = NetworkIndexResults
)
}
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Defines functions assemble_flow_matrix_from_model_annual_output
#
# assemble_flow_matrix_from_model_annual_output.R
#
#' process the whole domain annual flux results held in the dataframe annual_flux_results
#' to produce a flow-matrix defining all of the annual integrated mass fluxes been every pair of
#' prey and predator guilds in the food web, alf the geochemical flows, and all of the boundary flows
#'
#' The code then uses the NetIndices R package which relies on the flow-matrix data as input
#' to derive a suite of network indices as outputs These are saved as a standard csv file
#'
#' @param model model object
#' @param build model build object
#' @param output model output
#' @param aggregates aggregated model output
#'
#' @importFrom NetIndices TrophInd AscInd PathInd GenInd EffInd
#'
#' @return list comprising flow matrices and NetIndices results
#'
#' @noRd
#
# ------------------------------------------------------------------------------
assemble_flow_matrix_from_model_annual_output <- function(model, build, output, aggregates) {
setup <- elt(model, "setup")
model.path <- elt(setup, "model.path")
identifier <- elt(setup, "model.ident")
resultsdir <- elt(setup, "resultsdir")
run <- elt(build, "run")
nyears <- elt(run, "nyears")
ndays <- elt(run, "ndays")
# extract output:
fluxsedamm_wcamm <- elt(output, "fluxsedamm_wcamm")
fluxwcdet_wcamm <- elt(output, "fluxwcdet_wcamm")
fluxomni_wcamm <- elt(output, "fluxomni_wcamm")
fluxcarn_wcamm <- elt(output, "fluxcarn_wcamm")
fluxpfishlar_wcamm <- elt(output, "fluxpfishlar_wcamm")
fluxdfishlar_wcamm <- elt(output, "fluxdfishlar_wcamm")
fluxpfish_wcamm <- elt(output, "fluxpfish_wcamm")
fluxmfish_wcamm <- elt(output, "fluxmfish_wcamm")
fluxdfish_wcamm <- elt(output, "fluxdfish_wcamm")
fluxbenthslar_wcamm <- elt(output, "fluxbenthslar_wcamm")
fluxbenthclar_wcamm <- elt(output, "fluxbenthclar_wcamm")
fluxbenths_wcamm <- elt(output, "fluxbenths_wcamm")
fluxbenthc_wcamm <- elt(output, "fluxbenthc_wcamm")
fluxbird_wcamm <- elt(output, "fluxbird_wcamm")
fluxseal_wcamm <- elt(output, "fluxseal_wcamm")
fluxceta_wcamm <- elt(output, "fluxceta_wcamm")
fluxxdet_sedamm <- elt(output, "fluxxdet_sedamm")
fluxxRdet_sedamm <- elt(output, "fluxxRdet_sedamm")
fluxwcamm_wcnit <- elt(output, "fluxwcamm_wcnit")
fluxsednit_wcnit <- elt(output, "fluxsednit_wcnit")
fluxsedamm_sednit <- elt(output, "fluxsedamm_sednit")
fluxxdet_wcdet <- elt(output, "fluxxdet_wcdet")
fluxcorp_wcdet <- elt(output, "fluxcorp_wcdet")
fluxkelpdebris_wcdet <- elt(output, "fluxkelpdebris_wcdet")
fluxphyt_wcdet <- elt(output, "fluxphyt_wcdet")
fluxomni_wcdet <- elt(output, "fluxomni_wcdet")
fluxcarn_wcdet <- elt(output, "fluxcarn_wcdet")
fluxpfishlar_wcdet <- elt(output, "fluxpfishlar_wcdet")
fluxdfishlar_wcdet <- elt(output, "fluxdfishlar_wcdet")
fluxpfish_wcdet <- elt(output, "fluxpfish_wcdet")
fluxmfish_wcdet <- elt(output, "fluxmfish_wcdet")
fluxdfish_wcdet <- elt(output, "fluxdfish_wcdet")
fluxbenthslar_wcdet <- elt(output, "fluxbenthslar_wcdet")
fluxbenthclar_wcdet <- elt(output, "fluxbenthclar_wcdet")
fluxbenths_wcdet <- elt(output, "fluxbenths_wcdet")
fluxbenthc_wcdet <- elt(output, "fluxbenthc_wcdet")
fluxbird_wcdet <- elt(output, "fluxbird_wcdet")
fluxseal_wcdet <- elt(output, "fluxseal_wcdet")
fluxceta_wcdet <- elt(output, "fluxceta_wcdet")
fluxwcdet_xdet <- elt(output, "fluxwcdet_xdet")
fluxcorp_xdet <- elt(output, "fluxcorp_xdet")
fluxbenths_xdet <- elt(output, "fluxbenths_xdet")
fluxbenthc_xdet <- elt(output, "fluxbenthc_xdet")
fluxxdet_xRdet <- elt(output, "fluxxdet_xRdet")
fluxcorp_xRdet <- elt(output, "fluxcorp_xRdet")
fluxkelpdebris_xRdet <- elt(output, "fluxkelpdebris_xRdet")
fluxdisc_corp <- elt(output, "fluxdisc_corp")
fluxpfish_corp <- elt(output, "fluxpfish_corp")
fluxmfish_corp <- elt(output, "fluxmfish_corp")
fluxdfish_corp <- elt(output, "fluxdfish_corp")
fluxbenths_corp <- elt(output, "fluxbenths_corp")
fluxbenthc_corp <- elt(output, "fluxbenthc_corp")
fluxbird_corp <- elt(output, "fluxbird_corp")
fluxseal_corp <- elt(output, "fluxseal_corp")
fluxkelp_kelpdebris <- elt(output, "fluxkelp_kelpdebris")
fluxwcamm_kelp <- elt(output, "fluxwcamm_kelp")
fluxwcnit_kelp <- elt(output, "fluxwcnit_kelp")
fluxwcdet_omni <- elt(output, "fluxwcdet_omni")
fluxphyt_omni <- elt(output, "fluxphyt_omni")
fluxbenthslar_omni <- elt(output, "fluxbenthslar_omni")
fluxbenthclar_omni <- elt(output, "fluxbenthclar_omni")
fluxomni_carn <- elt(output, "fluxomni_carn")
fluxpfishlar_carn <- elt(output, "fluxpfishlar_carn")
fluxdfishlar_carn <- elt(output, "fluxdfishlar_carn")
fluxbenthslar_carn <- elt(output, "fluxbenthslar_carn")
fluxbenthclar_carn <- elt(output, "fluxbenthclar_carn")
fluxomni_pfishlar <- elt(output, "fluxomni_pfishlar")
fluxbenthslar_pfishlar <- elt(output, "fluxbenthslar_pfishlar")
fluxbenthclar_pfishlar <- elt(output, "fluxbenthclar_pfishlar")
Pfish_spawn <- elt(output, "Pfish_spawn")
fluxomni_dfishlar <- elt(output, "fluxomni_dfishlar")
fluxbenthslar_dfishlar <- elt(output, "fluxbenthslar_dfishlar")
fluxbenthclar_dfishlar <- elt(output, "fluxbenthclar_dfishlar")
Dfish_spawn <- elt(output, "Dfish_spawn")
fluxomni_pfish <- elt(output, "fluxomni_pfish")
fluxcarn_pfish <- elt(output, "fluxcarn_pfish")
fluxpfishlar_pfish <- elt(output, "fluxpfishlar_pfish")
Pfish_recruit <- elt(output, "Pfish_recruit")
fluxdfishlar_pfish <- elt(output, "fluxdfishlar_pfish")
fluxbenthslar_pfish <- elt(output, "fluxbenthslar_pfish")
fluxbenthclar_pfish <- elt(output, "fluxbenthclar_pfish")
fluxomni_mfish <- elt(output, "fluxomni_mfish")
fluxcarn_mfish <- elt(output, "fluxcarn_mfish")
fluxpfishlar_mfish <- elt(output, "fluxpfishlar_mfish")
fluxdfishlar_mfish <- elt(output, "fluxdfishlar_mfish")
fluxbenthslar_mfish <- elt(output, "fluxbenthslar_mfish")
fluxbenthclar_mfish <- elt(output, "fluxbenthclar_mfish")
fluxcorp_dfish <- elt(output, "fluxcorp_dfish")
fluxdisc_dfish <- elt(output, "fluxdisc_dfish")
fluxcarn_dfish <- elt(output, "fluxcarn_dfish")
fluxpfishlar_dfish <- elt(output, "fluxpfishlar_dfish")
fluxdfishlar_dfish <- elt(output, "fluxdfishlar_dfish")
Dfish_recruit <- elt(output, "Dfish_recruit")
fluxpfish_dfish <- elt(output, "fluxpfish_dfish")
fluxmfish_dfish <- elt(output, "fluxmfish_dfish")
fluxdfish_dfish <- elt(output, "fluxdfish_dfish")
fluxbenths_dfish <- elt(output, "fluxbenths_dfish")
fluxbenthc_dfish <- elt(output, "fluxbenthc_dfish")
fluxwcdet_benthslar <- elt(output, "fluxwcdet_benthslar")
fluxphyt_benthslar <- elt(output, "fluxphyt_benthslar")
Bs_spawn <- elt(output, "Bs_spawn")
fluxwcdet_benthclar <- elt(output, "fluxwcdet_benthclar")
fluxphyt_benthclar <- elt(output, "fluxphyt_benthclar")
Bc_spawn <- elt(output, "Bc_spawn")
fluxwcdet_benths <- elt(output, "fluxwcdet_benths")
fluxxdet_benths <- elt(output, "fluxxdet_benths")
fluxxRdet_benths <- elt(output, "fluxxRdet_benths")
fluxphyt_benths <- elt(output, "fluxphyt_benths")
Bs_recruit <- elt(output, "Bs_recruit")
fluxcorp_benthc <- elt(output, "fluxcorp_benthc")
fluxkelpdebris_benthc <- elt(output, "fluxkelpdebris_benthc")
fluxkelp_benthc <- elt(output, "fluxkelp_benthc")
fluxbenths_benthc <- elt(output, "fluxbenths_benthc")
Bc_recruit <- elt(output, "Bc_recruit")
fluxcorp_bird <- elt(output, "fluxcorp_bird")
fluxdisc_bird <- elt(output, "fluxdisc_bird")
fluxcarn_bird <- elt(output, "fluxcarn_bird")
fluxpfish_bird <- elt(output, "fluxpfish_bird")
fluxmfish_bird <- elt(output, "fluxmfish_bird")
fluxdfish_bird <- elt(output, "fluxdfish_bird")
fluxbenths_bird <- elt(output, "fluxbenths_bird")
fluxbenthc_bird <- elt(output, "fluxbenthc_bird")
fluxcorp_seal <- elt(output, "fluxcorp_seal")
fluxdisc_seal <- elt(output, "fluxdisc_seal")
fluxcarn_seal <- elt(output, "fluxcarn_seal")
fluxpfish_seal <- elt(output, "fluxpfish_seal")
fluxmfish_seal <- elt(output, "fluxmfish_seal")
fluxdfish_seal <- elt(output, "fluxdfish_seal")
fluxbenths_seal <- elt(output, "fluxbenths_seal")
fluxbenthc_seal <- elt(output, "fluxbenthc_seal")
fluxbird_seal <- elt(output, "fluxbird_seal")
fluxdisc_ceta <- elt(output, "fluxdisc_ceta")
fluxomni_ceta <- elt(output, "fluxomni_ceta")
fluxcarn_ceta <- elt(output, "fluxcarn_ceta")
fluxpfish_ceta <- elt(output, "fluxpfish_ceta")
fluxmfish_ceta <- elt(output, "fluxmfish_ceta")
fluxdfish_ceta <- elt(output, "fluxdfish_ceta")
fluxbenths_ceta <- elt(output, "fluxbenths_ceta")
fluxbenthc_ceta <- elt(output, "fluxbenthc_ceta")
fluxbird_ceta <- elt(output, "fluxbird_ceta")
fluxseal_ceta <- elt(output, "fluxseal_ceta")
fluxkelpdebris_beachexport <- elt(output, "fluxkelpdebris_beachexport")
mfish_emigration <- elt(output, "mfish_emigration")
fluxAMMoutflow_o <- elt(output, "fluxAMMoutflow_o")
fluxAMMoutflow_i <- elt(output, "fluxAMMoutflow_i")
fluxNIToutflow_o <- elt(output, "fluxNIToutflow_o")
fluxNIToutflow_i <- elt(output, "fluxNIToutflow_i")
fluxDEToutflow_o <- elt(output, "fluxDEToutflow_o")
fluxDEToutflow_i <- elt(output, "fluxDEToutflow_i")
fluxsedboundary_o <- elt(output, "fluxsedboundary_o")
fluxsedboundary_i <- elt(output, "fluxsedboundary_i")
fluxPHYToutflow_o <- elt(output, "fluxPHYToutflow_o")
fluxPHYToutflow_i <- elt(output, "fluxPHYToutflow_i")
mfish_imigration <- elt(output, "mfish_imigration")
fluxAMMinflow_i <- elt(output, "fluxAMMinflow_i")
fluxAMMinflow_o <- elt(output, "fluxAMMinflow_o")
rivAMMinflow <- elt(output, "rivAMMinflow")
atmosAMMinput_i <- elt(output, "atmosAMMinput_i")
atmosAMMinput_o <- elt(output, "atmosAMMinput_o")
fluxNITinflow_i <- elt(output, "fluxNITinflow_i")
fluxNITinflow_o <- elt(output, "fluxNITinflow_o")
rivNITinflow <- elt(output, "rivNITinflow")
atmosNITinput_i <- elt(output, "atmosNITinput_i")
atmosNITinput_o <- elt(output, "atmosNITinput_o")
fluxDETinflow_i <- elt(output, "fluxDETinflow_i")
fluxDETinflow_o <- elt(output, "fluxDETinflow_o")
rivPARTinflow <- elt(output, "rivPARTinflow")
fluxPHYTinflow_i <- elt(output, "fluxPHYTinflow_i")
fluxPHYTinflow_o <- elt(output, "fluxPHYTinflow_o")
disckp_i <- elt(output, "disckp_i") # Fix
offalkp_i <- elt(output, "offalkp_i") # Fix
landkp_i <- elt(output, "landkp_i") # Fix
# extract aggregates:
disccz <- elt(aggregates, "disccz")
offalcz <- elt(aggregates, "offalcz")
discpel <- elt(aggregates, "discpel")
offalpel <- elt(aggregates, "offalpel")
discmig <- elt(aggregates, "discmig")
offalmig <- elt(aggregates, "offalmig")
discdem <- elt(aggregates, "discdem")
offaldem <- elt(aggregates, "offaldem")
discsb <- elt(aggregates, "discsb")
offalsb <- elt(aggregates, "offalsb")
disccb <- elt(aggregates, "disccb")
offalcb <- elt(aggregates, "offalcb")
offalbd <- elt(aggregates, "offalbd")
offalsl <- elt(aggregates, "offalsl")
offalct <- elt(aggregates, "offalct")
fluxwcamm_phyt <- elt(aggregates, "fluxwcamm_phyt")
fluxwcnit_phyt <- elt(aggregates, "fluxwcnit_phyt")
landcz <- elt(aggregates, "landcz")
landp <- elt(aggregates, "landp")
landm <- elt(aggregates, "landm")
landd <- elt(aggregates, "landd")
landsb <- elt(aggregates, "landsb")
landcb <- elt(aggregates, "landcb")
landbd <- elt(aggregates, "landbd")
landsl <- elt(aggregates, "landsl")
landct <- elt(aggregates, "landct")
wcdenitrif <- elt(aggregates, "wcdenitrif")
seddenitrif <- elt(aggregates, "seddenitrif")
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Parameters which have been established by the simulated annealing scheme are
# loaded from a csv file which is made from the last line of the 'accepted parameters'
# file produced by the annealing programme.
#
# A variety of other parameters which are not optimized by simulated annealing are
# hard-wired in this subroutine
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Read in the template for the flowmatrix
flowmatrix_template <- get.model.file(model.path, PARAMETERS_DIR, file.pattern=FOOD_WEB_FLOW_MATRIX, row.names=1) # special
#Now we need to trawl through the model output dataframe and integrate each o fthe flux terms over the final year and drop
#into the flow matrix template. For some elements of the matrix we have to aggregate a few individual fluxes, for example
#feeding and recruitment to adult fish groups, so it all has to be done carefully.
#names(flowmatrix_template)
# [1] "wcammonia" "sedammonia" "wcnitrate" "sednitrate"
# [5] "wcdetritus" "seddetritus" "seddetritusR" "corpses"
# [9] "discards" "phyt" "omnivzoo" "carnzoo"
#[13] "pfishlar" "dfishlar" "pfish" "mfish"
#[17] "dfish" "benthslar" "benthclar" "benths"
#[21] "benthc" "birdmam" "landings" "denitrification"
#[25] "emigration" "exports" "imigration" "imports"
#Its very importnat that the rownames = colnames
#The fluxes in matrix are from row elements to column elements
outrowstart<-((nyears-1)*360+1)
outrowend <-ndays
#-------------------------------
#Fluxes to water column ammonia
#From sediment ammonia
fluxvec<-fluxsedamm_wcamm
sourcename<-"sedammonia"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
#SPECIAL CASE
#If this flux is negative then it needs to go into a different cell
if(flux<0) {
destname<-"sedammonia"
sourcename <-"wcammonia"
}
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From wc detritus
fluxvec<-fluxwcdet_wcamm
sourcename<-"wcdetritus"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From omnivorous zooplankton
fluxvec<-fluxomni_wcamm
sourcename<-"omnivzoo"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_wcamm
sourcename<-"carnzoo"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_wcamm
sourcename<-"pfishlar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_wcamm
sourcename<-"dfishlar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_wcamm
sourcename<-"pfish"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_wcamm
sourcename<-"mfish"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_wcamm
sourcename<-"dfish"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_wcamm
sourcename<-"benthslar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_wcamm
sourcename<-"benthclar"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_wcamm
sourcename<-"benths"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
## NOTE this correct - excretion by settled benthos gos direct to the water column not to porewaters
#From c/s benthos
fluxvec<-fluxbenthc_wcamm
sourcename<-"benthc"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
## NOTE this correct - excretion by settled benthos gos direct to the water column not to porewaters
#From birds
fluxvec<-fluxbird_wcamm
sourcename<-"bird"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-fluxseal_wcamm
sourcename<-"seal"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-fluxceta_wcamm
sourcename<-"ceta"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment porewater ammonia
#From sediment detritus
fluxvec<-fluxxdet_sedamm
sourcename<-"seddetritus"
destname <-"sedammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment refratory detritus
fluxvec<-fluxxRdet_sedamm
sourcename<-"seddetritusR"
destname <-"sedammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to water column nitrate
#From water column ammonia
fluxvec<-fluxwcamm_wcnit
sourcename<-"wcammonia"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment porewater nitrate
fluxvec<-fluxsednit_wcnit
sourcename<-"sednitrate"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
#SPECIAL CASE
#If this flux is negative then it needs to go into a different cell
if(flux<0) {
flux <- (-1*flux)
destname<-"sednitrate"
sourcename <-"wcnitrate"
}
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment porewater nitrate
#From sediment porewater ammonia
fluxvec<-fluxsedamm_sednit
sourcename<-"sedammonia"
destname <-"sednitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to water column detritus
#From sediment detritus (resuspension)
fluxvec<-fluxxdet_wcdet
sourcename<-"seddetritus"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From corpses (only over rocky habitats)
fluxvec<-fluxcorp_wcdet
sourcename<-"corpses"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp debris (only over inshore rocky habitats)
fluxvec<-fluxkelpdebris_wcdet
sourcename<-"kelpdebris"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_wcdet
sourcename<-"phyt"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From omnivorous zooplankton
fluxvec<-fluxomni_wcdet
sourcename<-"omnivzoo"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_wcdet
sourcename<-"carnzoo"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_wcdet
sourcename<-"pfishlar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_wcdet
sourcename<-"dfishlar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_wcdet
sourcename<-"pfish"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_wcdet
sourcename<-"mfish"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_wcdet
sourcename<-"dfish"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_wcdet
sourcename<-"benthslar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_wcdet
sourcename<-"benthclar"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos (only over rocky habitats)
fluxvec<-fluxbenths_wcdet
sourcename<-"benths"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos (only over rocky habitats)
fluxvec<-fluxbenthc_wcdet
sourcename<-"benthc"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-fluxbird_wcdet
sourcename<-"bird"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-fluxseal_wcdet
sourcename<-"seal"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-fluxceta_wcdet
sourcename<-"ceta"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment detritus
#From water column detritus (sedimentation)
fluxvec<-fluxwcdet_xdet
sourcename<-"wcdetritus"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From corpses (over sand and mud)
fluxvec<-fluxcorp_xdet
sourcename<-"corpses"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos (over sand and mud)
fluxvec<-fluxbenths_xdet
sourcename<-"benths"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos (over sand and mud)
fluxvec<-fluxbenthc_xdet
sourcename<-"benthc"
destname <-"seddetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to sediment refractory detritus
#From sediment detritus
fluxvec<-fluxxdet_xRdet
sourcename<-"seddetritus"
destname <-"seddetritusR"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From corpses
fluxvec<-fluxcorp_xRdet
sourcename<-"corpses"
destname <-"seddetritusR"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelpdebris
fluxvec<-fluxkelpdebris_xRdet
sourcename<-"kelpdebris"
destname <-"seddetritusR"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to corpses
#From discards
fluxvec<-fluxdisc_corp
sourcename<-"discards"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_corp
sourcename<-"pfish"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_corp
sourcename<-"mfish"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_corp
sourcename<-"dfish"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_corp
sourcename<-"benths"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_corp
sourcename<-"benthc"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds (includes discards of by-catch)
fluxvec<-fluxbird_corp
sourcename<-"bird"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals (includes discards of by-catch)
fluxvec<-fluxseal_corp
sourcename<-"seal"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans (includes discards of by-catch)
fluxvec<-fluxseal_corp
sourcename<-"ceta"
destname <-"corpses"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to discards (includes fluxes of offal from processing at sea)
#From carnivorous zooplankton
fluxvec<-disccz + offalcz
sourcename<-"carnzoo"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-discpel + offalpel
sourcename<-"pfish"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-discmig + offalmig
sourcename<-"mfish"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-discdem + offaldem
sourcename<-"dfish"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-discsb + offalsb
sourcename<-"benths"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-disccb + offalcb
sourcename<-"benthc"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds & mammals - discards included within the model as a flux to corpses, but offal from processing at sea goes to discards
#From birds
fluxvec<-offalbd
sourcename<-"bird"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-offalsl
sourcename<-"seal"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-offalct
sourcename<-"ceta"
destname <-"discards"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to kelp debris (includes destruction y waves plus discards and fluxes of kelp offal from processing at sea)
#From kelp
fluxvec<-fluxkelp_kelpdebris + disckp_i + offalkp_i
sourcename<-"kelp"
destname <-"kelpdebris"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to phytoplankton
#From water column ammonia
fluxvec<-fluxwcamm_phyt
sourcename<-"wcammonia"
destname <-"phyt"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From water column nitrate
fluxvec<-fluxwcnit_phyt
sourcename<-"wcnitrate"
destname <-"phyt"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to kelp
#From water column ammonia
fluxvec<-fluxwcamm_kelp
sourcename<-"wcammonia"
destname <-"kelp"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From water column nitrate
fluxvec<-fluxwcnit_kelp
sourcename<-"wcnitrate"
destname <-"kelp"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to omnivorous zooplankton
#From water column detritus
fluxvec<-fluxwcdet_omni
sourcename<-"wcdetritus"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_omni
sourcename<-"phyt"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_omni
sourcename<-"benthslar"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_omni
sourcename<-"benthclar"
destname <-"omnivzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to carnivorous zooplankton
#From omnivorous zooplankton
fluxvec<-fluxomni_carn
sourcename<-"omnivzoo"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_carn
sourcename<-"pfishlar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_carn
sourcename<-"dfishlar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_carn
sourcename<-"benthslar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_carn
sourcename<-"benthclar"
destname <-"carnzoo"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to pelagic fish larvae
#From omnivorous zooplankton
fluxvec<-fluxomni_pfishlar
sourcename<-"omnivzoo"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_pfishlar
sourcename<-"benthslar"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_pfishlar
sourcename<-"benthclar"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from adult pelagic fish
fluxvec<-Pfish_spawn
sourcename<-"pfish"
destname <-"pfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to demersal fish larvae
#From omnivorous zooplankton
fluxvec<-fluxomni_dfishlar
sourcename<-"omnivzoo"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_dfishlar
sourcename<-"benthslar"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_dfishlar
sourcename<-"benthclar"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from adult demersal fish
fluxvec<-Dfish_spawn
sourcename<-"dfish"
destname <-"dfishlar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to pelagic fish
#From omnivorous zooplankton
fluxvec<-fluxomni_pfish
sourcename<-"omnivzoo"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_pfish
sourcename<-"carnzoo"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_pfish
#SPECIAL CASE
#Here we have to add on the recruitment flux from larvae to settled stage
fluxvec2<-Pfish_recruit
sourcename<-"pfishlar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From demersal fish larvae
fluxvec<-fluxdfishlar_pfish
sourcename<-"dfishlar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_pfish
sourcename<-"benthslar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_pfish
sourcename<-"benthclar"
destname <-"pfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to migratory fish
#From omnivorous zooplankton
fluxvec<-fluxomni_mfish
sourcename<-"omnivzoo"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_mfish
sourcename<-"carnzoo"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_mfish
sourcename<-"pfishlar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_mfish
sourcename<-"dfishlar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos larvae
fluxvec<-fluxbenthslar_mfish
sourcename<-"benthslar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos larvae
fluxvec<-fluxbenthclar_mfish
sourcename<-"benthclar"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to demersal fish
#From corpses
fluxvec<-fluxcorp_dfish
sourcename<-"corpses"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_dfish
sourcename<-"discards"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_dfish
sourcename<-"carnzoo"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish larvae
fluxvec<-fluxpfishlar_dfish
sourcename<-"pfishlar"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish larvae
fluxvec<-fluxdfishlar_dfish
#SPECIAL CASE
#Here we have to add on the recruitment flux from larvae to settled stage
fluxvec2<-Dfish_recruit
sourcename<-"dfishlar"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From pelagic fish
fluxvec<-fluxpfish_dfish
sourcename<-"pfish"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_dfish
sourcename<-"mfish"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_dfish
sourcename<-"dfish"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_dfish
sourcename<-"benths"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_dfish
sourcename<-"benthc"
destname <-"dfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to f/d benthos larvae
#From water column detritus
fluxvec<-fluxwcdet_benthslar
sourcename<-"wcdetritus"
destname <-"benthslar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_benthslar
sourcename<-"phyt"
destname <-"benthslar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from settled benthos
fluxvec<-Bs_spawn
sourcename<-"benths"
destname <-"benthslar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to c/s benthos larvae
#From water column detritus
fluxvec<-fluxwcdet_benthclar
sourcename<-"wcdetritus"
destname <-"benthclar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_benthclar
sourcename<-"phyt"
destname <-"benthclar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - spawning flux from settled benthos
fluxvec<-Bc_spawn
sourcename<-"benthc"
destname <-"benthclar"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to f/d benthos
#From water column detritus
fluxvec<-fluxwcdet_benths
sourcename<-"wcdetritus"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment detritus
fluxvec<-fluxxdet_benths
sourcename<-"seddetritus"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment refractory detritus
fluxvec<-fluxxRdet_benths
sourcename<-"seddetritusR"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From phytoplankton
fluxvec<-fluxphyt_benths
sourcename<-"phyt"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - recruitment flux from benthos larvae
fluxvec<-Bs_recruit
sourcename<-"benthslar"
destname <-"benths"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to c/s benthos
#From corpses
fluxvec<-fluxcorp_benthc
sourcename<-"corpses"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp debris
fluxvec<-fluxkelpdebris_benthc
sourcename<-"kelpdebris"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp
fluxvec<-fluxkelp_benthc
sourcename<-"kelp"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_benthc
sourcename<-"benths"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#SPECIAL CASE - recruitment flux from benthos larvae
fluxvec<-Bc_recruit
sourcename<-"benthclar"
destname <-"benthc"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to birds
#From corpses
fluxvec<-fluxcorp_bird
sourcename<-"corpses"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_bird
sourcename<-"discards"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
# #From omnivorous zooplankton
# fluxvec<-fluxomni_bird
# sourcename<-"omnivzoo"
# destname <-"bird"
# flux<-fluxvec[outrowend]-fluxvec[outrowstart]
# flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_bird
sourcename<-"carnzoo"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_bird
sourcename<-"pfish"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_bird
sourcename<-"mfish"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_bird
sourcename<-"dfish"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_bird
sourcename<-"benths"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_bird
sourcename<-"benthc"
destname <-"bird"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to seals
#From corpses
fluxvec<-fluxcorp_seal
sourcename<-"corpses"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_seal
sourcename<-"discards"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_seal
sourcename<-"carnzoo"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_seal
sourcename<-"pfish"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_seal
sourcename<-"mfish"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_seal
sourcename<-"dfish"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_seal
sourcename<-"benths"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_seal
sourcename<-"benthc"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-fluxbird_seal
sourcename<-"bird"
destname <-"seal"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to cetaceans
# #From corpses
# fluxvec<-fluxcorp_ceta
# sourcename<-"corpses"
# destname <-"ceta"
# flux<-fluxvec[outrowend]-fluxvec[outrowstart]
# flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From discards
fluxvec<-fluxdisc_ceta
sourcename<-"discards"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From omnivorous zooplankton
fluxvec<-fluxomni_ceta
sourcename<-"omnivzoo"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From carnivorous zooplankton
fluxvec<-fluxcarn_ceta
sourcename<-"carnzoo"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-fluxpfish_ceta
sourcename<-"pfish"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-fluxmfish_ceta
sourcename<-"mfish"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-fluxdfish_ceta
sourcename<-"dfish"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-fluxbenths_ceta
sourcename<-"benths"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-fluxbenthc_ceta
sourcename<-"benthc"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-fluxbird_ceta
sourcename<-"bird"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-fluxseal_ceta
sourcename<-"seal"
destname <-"ceta"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-------------------------------
#Fluxes to landings - THIS SHOULD BE THE PROCESSED LANDED WEIGHT ie LIVE WEIGHT MINUS OFFAL WEIGHT
#From carnivorous zooplankton
fluxvec<-landcz - offalcz
sourcename<-"carnzoo"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From pelagic fish
fluxvec<-landp - offalpel
sourcename<-"pfish"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From migratory fish
fluxvec<-landm - offalmig
sourcename<-"mfish"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From demersal fish
fluxvec<-landd - offaldem
sourcename<-"dfish"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From f/d benthos
fluxvec<-landsb - offalsb
sourcename<-"benths"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From c/s benthos
fluxvec<-landcb - offalcb
sourcename<-"benthc"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From birds
fluxvec<-landbd - offalbd
sourcename<-"bird"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From seals
fluxvec<-landsl - offalsl
sourcename<-"seal"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From cetaceans
fluxvec<-landct - offalct
sourcename<-"ceta"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From kelp
fluxvec<-landkp_i - offalkp_i
sourcename<-"kelp"
destname <-"landings"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to beachcast
#From kelp debris
fluxvec<-fluxkelpdebris_beachexport
sourcename<-"kelpdebris"
destname <-"beachcast"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to nitrogen gas
#From water column nitrate
fluxvec<-wcdenitrif
sourcename<-"wcnitrate"
destname <-"atmosphere"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#From sediment porewater nitrate
fluxvec<-seddenitrif
sourcename<-"sednitrate"
destname <-"atmosphere"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to emigration
#From migratory fish
fluxvec<-mfish_emigration
sourcename<-"mfish"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#----------------------------
#Fluxes to hydrodynamic exports and burial
#From water column ammonia
fluxvec<-fluxAMMoutflow_o
fluxvec2<-fluxAMMoutflow_i
sourcename<-"wcammonia"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From water column nitrate
fluxvec<-fluxNIToutflow_o
fluxvec2<-fluxNIToutflow_i
sourcename<-"wcnitrate"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From water column detritus
fluxvec<-fluxDEToutflow_o
fluxvec2<-fluxDEToutflow_i
sourcename<-"wcdetritus"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#From sediment refractory detritus (burial)
fluxvec<-fluxsedboundary_o
fluxvec2<-fluxsedboundary_i
sourcename<-"seddetritusR"
destname <-"seabed"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
cflux<-flux+flux2
#SPECIAL CASE
#If the sum of these fluxes is -ve then it indicated burial so place it as an export
#If the sum of these fluxes is +ve then it indicated exhumation so place it as an import
if(cflux>0) {
destname <-"seddetritusR"
sourcename<-"seabed"
}
if(cflux<0) cflux <- (-1*cflux)
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- cflux
#From phytoplankton
fluxvec<-fluxPHYToutflow_o
fluxvec2<-fluxPHYToutflow_i
sourcename<-"phyt"
destname <-"ocean"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#----------------------------
#Imigration fluxes
#To migratory fish
fluxvec<-mfish_imigration
sourcename<-"ocean"
destname <-"mfish"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#-----------------------------
#Hydrodynamic, river and atmosphere imports
#Ocean to water column ammonia
fluxvec <-fluxAMMinflow_i
fluxvec2<-fluxAMMinflow_o
sourcename<-"ocean"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Rivers to water column ammonia
fluxvec<-rivAMMinflow
sourcename<-"rivers"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#Atmosphere to water column ammonia
fluxvec<-atmosAMMinput_i
fluxvec2<-atmosAMMinput_o
sourcename<-"atmosphere"
destname <-"wcammonia"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Ocean to water column nitrate
fluxvec <-fluxNITinflow_i
fluxvec2<-fluxNITinflow_o
sourcename<-"ocean"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Rivers to water column nitrate
fluxvec<-rivNITinflow
sourcename<-"rivers"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#Atmosphere to water column nitrate
fluxvec<-atmosNITinput_i
fluxvec2<-atmosNITinput_o
sourcename<-"atmosphere"
destname <-"wcnitrate"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Ocean to water column detritus
fluxvec <-fluxDETinflow_i
fluxvec2<-fluxDETinflow_o
sourcename<-"ocean"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
#Rivers to water column detritus
fluxvec<-rivPARTinflow
sourcename<-"rivers"
destname <-"wcdetritus"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux
#To phytoplankton
fluxvec <-fluxPHYTinflow_i
fluxvec2<-fluxPHYTinflow_o
sourcename<-"ocean"
destname <-"phyt"
flux<-fluxvec[outrowend]-fluxvec[outrowstart]
flux2<-fluxvec2[outrowend]-fluxvec2[outrowstart]
flowmatrix_template[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- flux+flux2
flow_matrix_all_fluxes <- flowmatrix_template
#Save the new flow matrix to a file.
filename = csvname(resultsdir, "flow_matrix_all_fluxes", identifier)
writecsv(flowmatrix_template, filename, header=TRUE)
#--------------------------------------------------------------------------------------------------------
#FOR SOME INDICES WE NEED TO REMOVE FROM THE FLOW MATRIX THE FLUXES DUE TO SPAWNING AND RECRUITMENT
#MAKE A COPY OF THE FLOWMATRIX
flowmatrix_no_sp_rec<-flowmatrix_template
outrowstart<-((nyears-1)*360+1)
outrowend <-ndays
#Remove recruitment of pelagic fish
sourcename<-"pfishlar"
destname <-"pfish"
fluxvec<-fluxpfishlar_pfish
rflux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <-
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] - rflux
#Remove recruitment of demersal fish
sourcename<-"dfishlar"
destname <-"dfish"
fluxvec<-fluxdfishlar_dfish
rflux<-fluxvec[outrowend]-fluxvec[outrowstart]
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <-
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] - rflux
#Remove recruitment of f/d benthos
sourcename<-"benthslar"
destname <-"benths"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove recruitment of c/s benthos
sourcename<-"benthclar"
destname <-"benthc"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawning of pelagic fish
sourcename<-"pfish"
destname <-"pfishlar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawning of demersal fish
sourcename<-"dfish"
destname <-"dfishlar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawninmg of f/d benthos
sourcename<-"benths"
destname <-"benthslar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Remove spawning of c/s benthos
sourcename<-"benthc"
destname <-"benthclar"
flowmatrix_no_sp_rec[(which(colnames(flowmatrix_template)==sourcename)),(which(colnames(flowmatrix_template)==destname))] <- 0
#Save the new flow matrix to a file.
filename = csvname(resultsdir, "flow_matrix_excl_spawn_recruit", identifier)
writecsv(flowmatrix_no_sp_rec, filename, header=TRUE)
#--------------------------------------------------------------------------------------------------------
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Derive a load of network indices
#library(NetIndices)
#............................................................................
#Check if discards are present or not - if not we have to treat these as an inport and export
Disc_sum<-sum(flowmatrix_template$discards)
zerocheck<-which(colSums(flowmatrix_template)[1:(ncol(flowmatrix_template)-6)]==0)
zerolist<-colnames(flowmatrix_template)[zerocheck]
#............................................................................
#Trophic index calculation
TrophicIndexResults<-TrophInd(flowmatrix_no_sp_rec, Import = c("ocean","rivers","atmosphere","seabed"),
Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"),
Dead=c("wcammonia","sedammonia","wcnitrate","sednitrate","wcdetritus","seddetritus","seddetritusR","corpses","kelpdebris","discards"))
#Output -- TL = Trophic level, OI = Omnivory index
#............................................................................
if(Disc_sum>0) AscendencyIndexResults<-AscInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(Disc_sum==0) AscendencyIndexResults<-AscInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#asc the ascendency of the network, a measure of growth and development.
#overh the overhead of the network.
#cap the development capacity of the network, an upper bound on ascendency.
#ACratio the ratio of ascendency and capacity.
#............................................................................
#For dependency analysis we need to reduce the flowmatrix to the living components
#flowmatrix_for_dependency<-flowmatrix_template[8:26,8:27]
#Dependency(flowmatrix_for_dependency, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#Produces a matrix of the dependency of component i (row) on component j (column)
#............................................................................
if(length(zerolist)>0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c(zerolist,"ocean","rivers","atmosphere","seabed"),Export = c(zerolist,"ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(length(zerolist)==0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#if(Disc_sum>0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#if(Disc_sum==0) PathwayIndexResults<-PathInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#TSTC total system cycled throughflow.
#TSTS non-cycled throughflow.
#FCI Finn's cycling index (1980).
#FCIb revised Finn's cycling index, sensu Allesina and Ulanowicz, 2004.
#APL average pathlength, also known as Network Aggradation (Sum of APLc and APLs in Latham 2006).
#............................................................................
if(Disc_sum>0) GeneralIndexResults<-GenInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(Disc_sum==0) GeneralIndexResults<-GenInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#N number of compartments, excluding the externals.
#T.. total System Throughput.
#TST total System Throughflow.
#Lint number of Internal links.
#Ltot total number of links.
#LD link Density
#C connectance (internal).
#Tijbar average Link Weight.
#TSTbar average Compartment Throughflow .
#Cbar compartmentalization, [0,1], the degree of connectedness of subsystems within a network.
#............................................................................
# if(length(zerolist)>0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c(zerolist,"ocean","rivers","atmosphere","seabed"),Export = c(zerolist,"ocean","rivers","atmosphere","seabed","landings","beachcast"))
# if(length(zerolist)==0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
# TEMPORARILY DISABLED
#if(Disc_sum>0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
#if(Disc_sum==0) EnvironmentIndexResults<-EnvInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#NAG Network aggradation = average path length.
#HP Homogenization index.
#BC Synergism.
#ID Dominance of Indirect effects.
#MN Mean of non-dimensional flow-matrix (N).
#MG Mean of direct flow-matrix (G).
#CVN Coefficient of variation of non-dimensional flow-matrix (N).
#CVG Coefficient of variation of direct flow-matrix (G).
#U Only if Full == TRUE: The Utility non-dimensional matrix.
#N1 Only if Full == TRUE: The Integral non-dimensional Flow Matrix.
#G Only if Full == TRUE: The Normalized direct flow (or transitive closure) matrix.
#............................................................................
if(Disc_sum>0) EffectivenessIndexResults<-EffInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast"))
if(Disc_sum==0) EffectivenessIndexResults<-EffInd(flowmatrix_template, Import = c("ocean","rivers","atmosphere","seabed","discards"),Export = c("ocean","rivers","atmosphere","seabed","landings","beachcast","discards"))
#Outputs:
#CZ Effective connectance
#FZ Effective Flows
#NZ Effective nodes
#RZ Effective roles
#............................................................................
#TrophicIndexResults
#AscendencyIndexResults
#PathwayIndexResults
#GeneralIndexResults
#EnvironmentIndexResults
#EffectivenessIndexResults
#Build all these indices together into a structure
#Need to store 47+number of rows in the trophic index results rows of data
for(ii in 1:(nrow(TrophicIndexResults))){
if(ii==1) trophicnames<-paste(rownames(TrophicIndexResults)[ii],"_trophiclevel",sep="")
if(ii>1) trophicnames<-c(trophicnames,paste(rownames(TrophicIndexResults)[ii],"_trophiclevel",sep=""))
}
for(ii in 1:(nrow(TrophicIndexResults))){
trophicnames<-c(trophicnames,paste(rownames(TrophicIndexResults)[ii],"_omnivoryindex",sep=""))
}
NetworkIndexResults<-data.frame(rep(NA,(47+(2*(nrow(TrophicIndexResults))))))
names(NetworkIndexResults)<-"NetworkData"
row.names(NetworkIndexResults)<-c(
trophicnames,
#Ascendency Indices
"Ascendency_total",
"Ascendency_internal",
"Ascendency_import",
"Ascendency_external",
"Ascendency_dissipation",
"Overhead_total",
"Overhead_internal",
"Overhead_import",
"Overhead_external",
"Overhead_dissipation",
"Capacity_total",
"Capacity_internal",
"Capacity_import",
"Capacity_external",
"Capacity_dissipation",
"ACratio_total",
"ACratio_internal",
"ACratio_import",
"ACratio_external",
"ACratio_dissipation",
#Pathway Indices
"Total_system_cycled_thoughflow_TSTC",
"Non_cycled_throughflow_TSTS",
"Finns_cycling_index_FCI",
"Revised_Finns_cycling_index_FCIb",
"Average_path_length",
#Generaal Indices
"Number_of_compartments_N",
"Total_system_throughput_T",
"Total_system_throughflow_TST",
"Number_of_internal_links_Lint",
"Total_number_of_links_Ltot",
"Link_density_LD",
"Connectance_C",
"Average_link_weight_Tijbar",
"Average_compartment_thoughflow_TSTbar",
"Compartmentalization_Cbar",
#Environment Indices
"Network_aggradation_NAG",
"Homogenization_index_HP",
"Synergism_BC",
"Dominance_of_indirect_effects_ID",
"Mean_of_non_dimension_flowmatrix_MN",
"Mean_of_direct_flowmatrix_MG",
"CV_of_non_dimension_flowmatrix_MN",
"CV_of_direct_flowmatrix_MG",
#Effectiveness Indices
"Effective_connectance_CZ",
"Effective_flows_FZ",
"Effective_nodes_NZ",
"Effective_roles_RZ")
NetworkIndexResults[1:(nrow(TrophicIndexResults)),1] <- TrophicIndexResults[,1]
NetworkIndexResults[(1+(nrow(TrophicIndexResults))):(2*(nrow(TrophicIndexResults))),1] <- TrophicIndexResults[,2]
lastfilled<-(2*(nrow(TrophicIndexResults)))
for(jj in 1:4){
NetworkIndexResults[(lastfilled+1+((jj-1)*5)):(lastfilled+5+((jj-1)*5)),1] <- AscendencyIndexResults[,jj]
}
lastfilled<-lastfilled+5+((4-1)*5)
NetworkIndexResults[(lastfilled+1):(lastfilled+5),1] <- t(as.data.frame(PathwayIndexResults))
lastfilled<-lastfilled+5
NetworkIndexResults[(lastfilled+1):(lastfilled+10),1] <- t(as.data.frame(GeneralIndexResults))
lastfilled<-lastfilled+10
#NetworkIndexResults[(lastfilled+1):(lastfilled+8),1] <- t(as.data.frame(EnvironmentIndexResults))
NetworkIndexResults[(lastfilled+1):(lastfilled+8),1] <- NA # OPTION WHERE THE ENVIND ROUTINE IS DISABLED
lastfilled<-lastfilled+8
NetworkIndexResults[(lastfilled+1):(lastfilled+4),1] <- t(as.data.frame(EffectivenessIndexResults))
lastfilled<-lastfilled+4
#Save the new flow matrix to a file.
filename = csvname(resultsdir, "Network_indices_output", identifier)
writecsv(NetworkIndexResults, filename, header=TRUE)
list(
flow_matrix_all_fluxes = flow_matrix_all_fluxes,
flow_matrix_excl_spawn_recruit = flowmatrix_no_sp_rec,
NetworkIndexResults = NetworkIndexResults
)
}
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