R/derive_annual_results_inshore.R
In strathclyde-marine-resource-modelling/StrathE2E2: End-to-end marine food web model
#
# derive_annual_results_inshore
#
#' derive set of results for inshore only and write to files
#'
#' @param model model object
#' @param build model build object
#' @param output model output
#' @param aggregates aggregated model output
#'
#' @export
#
derive_annual_results_inshore <- function(model, build, output, aggregates) {
# Unpack:
setup <- elt(model, "setup")
identifier <- elt(setup, "model.ident")
resultsdir <- elt(setup, "resultsdir")
run <- elt(build, "run")
ndays <- elt(run, "ndays")
nyears <- elt(run, "nyears")
data <- elt(model, "data")
physical.parms <- elt(data, "physical.parameters")
# extract physical parameters:
so_depth <- elt(physical.parms, "so_depth")
d_depth <- elt(physical.parms, "d_depth")
si_depth <- elt(physical.parms, "si_depth")
x_depth_s1 <- elt(physical.parms, "x_depth_s1")
x_depth_s2 <- elt(physical.parms, "x_depth_s2")
x_depth_s3 <- elt(physical.parms, "x_depth_s3")
x_depth_d1 <- elt(physical.parms, "x_depth_d1")
x_depth_d2 <- elt(physical.parms, "x_depth_d2")
x_depth_d3 <- elt(physical.parms, "x_depth_d3")
x_area_s0 <- elt(physical.parms, "x_area_s0")
x_area_s1 <- elt(physical.parms, "x_area_s1")
x_area_s2 <- elt(physical.parms, "x_area_s2")
x_area_s3 <- elt(physical.parms, "x_area_s3")
x_area_d0 <- elt(physical.parms, "x_area_d0")
x_area_d1 <- elt(physical.parms, "x_area_d1")
x_area_d2 <- elt(physical.parms, "x_area_d2")
x_area_d3 <- elt(physical.parms, "x_area_d3")
x_poros_s1 <- elt(physical.parms, "x_poros_s1")
x_poros_s2 <- elt(physical.parms, "x_poros_s2")
x_poros_s3 <- elt(physical.parms, "x_poros_s3")
x_poros_d1 <- elt(physical.parms, "x_poros_d1")
x_poros_d2 <- elt(physical.parms, "x_poros_d2")
x_poros_d3 <- elt(physical.parms, "x_poros_d3")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
# extract output:
detritus_si <- elt(output, "detritus_si")
xR_detritus_s1 <- elt(output, "xR_detritus_s1")
xR_detritus_s2 <- elt(output, "xR_detritus_s2")
xR_detritus_s3 <- elt(output, "xR_detritus_s3")
discard_i <- elt(output, "discard_i")
kelpdebris <- elt(output, "kelpdebris")
ammonia_si <- elt(output, "ammonia_si")
nitrate_si <- elt(output, "nitrate_si")
kelpN <- elt(output, "kelpN")
phyt_si <- elt(output, "phyt_si")
herb_i <- elt(output, "herb_i")
carn_i <- elt(output, "carn_i")
benthslar_i <- elt(output, "benthslar_i")
benths_i <- elt(output, "benths_i")
benthclar_i <- elt(output, "benthclar_i")
benthc_i <- elt(output, "benthc_i")
fishplar_i <- elt(output, "fishplar_i")
fishp_i <- elt(output, "fishp_i")
fishm_i <- elt(output, "fishm_i")
fishdlar_i <- elt(output, "fishdlar_i")
fishd_i <- elt(output, "fishd_i")
bird_i <- elt(output, "bird_i")
seal_i <- elt(output, "seal_i")
ceta_i <- elt(output, "ceta_i")
fluxAMMinflow_i <- elt(output, "fluxAMMinflow_i")
fluxNITinflow_i <- elt(output, "fluxNITinflow_i")
fluxAMMoutflow_i <- elt(output, "fluxAMMoutflow_i")
fluxNIToutflow_i <- elt(output, "fluxNIToutflow_i")
fluxPHYTinflow_i <- elt(output, "fluxPHYTinflow_i")
fluxDETinflow_i <- elt(output, "fluxDETinflow_i")
fluxPHYToutflow_i <- elt(output, "fluxPHYToutflow_i")
fluxDEToutflow_i <- elt(output, "fluxDEToutflow_i")
atmosAMMinput_i <- elt(output, "atmosAMMinput_i")
atmosNITinput_i <- elt(output, "atmosNITinput_i")
rivAMMinflow <- elt(output, "rivAMMinflow")
rivNITinflow <- elt(output, "rivNITinflow")
rivPARTinflow <- elt(output, "rivPARTinflow")
fluxsedboundary_i <- elt(output, "fluxsedboundary_i")
fluxkelpdebris_beachexport <- elt(output, "fluxkelpdebris_beachexport")
netpprod_i <- elt(output, "netpprod_i")
nitrate_d <- elt(output, "nitrate_d")
PNP_i <- elt(output, "PNP_i")
fluxwcnit_phyt_i <- elt(output, "fluxwcnit_phyt_i")
fluxwcamm_phyt_i <- elt(output, "fluxwcamm_phyt_i")
fluxwcnit_kelp <- elt(output, "fluxwcnit_kelp")
fluxwcamm_kelp <- elt(output, "fluxwcamm_kelp")
kelpNprod_i <- elt(output, "kelpNprod_i")
phytgrossprod_i <- elt(output, "phytgrossprod_i")
herbgrossprod_i <- elt(output, "herbgrossprod_i")
carngrossprod_i <- elt(output, "carngrossprod_i")
pfishlargrossprod_i <- elt(output, "pfishlargrossprod_i")
dfishlargrossprod_i <- elt(output, "dfishlargrossprod_i")
pfishgrossprod_i <- elt(output, "pfishgrossprod_i")
mfishgrossprod_i <- elt(output, "mfishgrossprod_i")
dfishgrossprod_i <- elt(output, "dfishgrossprod_i")
benthslargrossprod_i <- elt(output, "benthslargrossprod_i")
benthclargrossprod_i <- elt(output, "benthclargrossprod_i")
benthsgrossprod_i <- elt(output, "benthsgrossprod_i")
benthcgrossprod_i <- elt(output, "benthcgrossprod_i")
birdgrossprod_i <- elt(output, "birdgrossprod_i")
sealgrossprod_i <- elt(output, "sealgrossprod_i")
cetagrossprod_i <- elt(output, "cetagrossprod_i")
herbnetprod_i <- elt(output, "herbnetprod_i")
carnnetprod_i <- elt(output, "carnnetprod_i")
pfishlarnetprod_i <- elt(output, "pfishlarnetprod_i")
dfishlarnetprod_i <- elt(output, "dfishlarnetprod_i")
pfishnetprod_i <- elt(output, "pfishnetprod_i")
mfishnetprod_i <- elt(output, "mfishnetprod_i")
dfishnetprod_i <- elt(output, "dfishnetprod_i")
benthslarnetprod_i <- elt(output, "benthslarnetprod_i")
benthclarnetprod_i <- elt(output, "benthclarnetprod_i")
benthsnetprod_i <- elt(output, "benthsnetprod_i")
benthcnetprod_i <- elt(output, "benthcnetprod_i")
birdnetprod_i <- elt(output, "birdnetprod_i")
sealnetprod_i <- elt(output, "sealnetprod_i")
cetanetprod_i <- elt(output, "cetanetprod_i")
fluxkelp_kelpdebris <- elt(output, "fluxkelp_kelpdebris")
fluxkelp_benthc <- elt(output, "fluxkelp_benthc")
fluxkelpdebris_benthc <- elt(output, "fluxkelpdebris_benthc")
landp_i <- elt(output, "landp_i")
landm_i <- elt(output, "landm_i")
landd_quota_i <- elt(output, "landd_quota_i")
landd_nonquota_i <- elt(output, "landd_nonquota_i")
landsb_i <- elt(output, "landsb_i")
landcb_i <- elt(output, "landcb_i")
landcz_i <- elt(output, "landcz_i")
landbd_i <- elt(output, "landbd_i")
landsl_i <- elt(output, "landsl_i")
landct_i <- elt(output, "landct_i")
landkp_i <- elt(output, "landkp_i")
discpel_i <- elt(output, "discpel_i")
discmig_i <- elt(output, "discmig_i")
discdem_quota_i <- elt(output, "discdem_quota_i")
discdem_nonquota_i <- elt(output, "discdem_nonquota_i")
discsb_i <- elt(output, "discsb_i")
disccb_i <- elt(output, "disccb_i")
disccz_i <- elt(output, "disccz_i")
discbd_i <- elt(output, "discbd_i")
discsl_i <- elt(output, "discsl_i")
discct_i <- elt(output, "discct_i")
disckp_i <- elt(output, "disckp_i")
offalpel_i <- elt(output, "offalpel_i")
offalmig_i <- elt(output, "offalmig_i")
offaldem_quota_i <- elt(output, "offaldem_quota_i")
offaldem_nonquota_i <- elt(output, "offaldem_nonquota_i")
offalsb_i <- elt(output, "offalsb_i")
offalcb_i <- elt(output, "offalcb_i")
offalcz_i <- elt(output, "offalcz_i")
offalbd_i <- elt(output, "offalbd_i")
offalsl_i <- elt(output, "offalsl_i")
offalct_i <- elt(output, "offalct_i")
offalkp_i <- elt(output, "offalkp_i")
# extract aggregates:
x_detritus_i <- elt(aggregates, "x_detritus_i")
corpse_i <- elt(aggregates, "corpse_i")
x_ammonia_i <- elt(aggregates, "x_ammonia_i")
x_nitrate_i <- elt(aggregates, "x_nitrate_i")
totalN_i <- elt(aggregates, "totalN_i")
DIN_NET_flux_o_i <- elt(aggregates, "DIN_NET_flux_o_i")
PART_NET_flux_o_i <- elt(aggregates, "PART_NET_flux_o_i")
NET_activemigpelfish_o_i<- elt(aggregates, "NET_activemigpelfish_o_i")
NET_activemigmigfish_o_i<- elt(aggregates, "NET_activemigmigfish_o_i")
NET_activemigdemfish_o_i<- elt(aggregates, "NET_activemigdemfish_o_i")
NET_activemigbird_o_i <- elt(aggregates, "NET_activemigbird_o_i")
NET_activemigseal_o_i <- elt(aggregates, "NET_activemigseal_o_i")
NET_activemigceta_o_i <- elt(aggregates, "NET_activemigceta_o_i")
landd_i <- elt(aggregates, "landd_i")
discdem_i <- elt(aggregates, "discdem_i")
offaldem_i <- elt(aggregates, "offaldem_i")
#Derive a load of stuff from the output and write to a file
#Extract annual average biomass in the final year for the OFFSHORE model domain
aamass_s_detritus<-mean(detritus_si[((nyears-1)*360+1):ndays])
#aamass_d_detritus<-mean(detritus_d[((nyears-1)*360+1):ndays])
aamass_d_detritus<-NA
aamass_x_detritus<-mean(x_detritus_i[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamass_xR_detritus<-mean(xR_detritus_s1[((nyears-1)*360+1):ndays]
+ xR_detritus_s2[((nyears-1)*360+1):ndays]
+ xR_detritus_s3[((nyears-1)*360+1):ndays])
aamass_discard<-mean(discard_i[((nyears-1)*360+1):ndays])
aamass_corpse<-mean(corpse_i[((nyears-1)*360+1):ndays])
aamass_kelpdebris<-mean(kelpdebris[((nyears-1)*360+1):ndays])
#aamass_kelpdebris<-NA
aamass_s_ammonia<-mean(ammonia_si[((nyears-1)*360+1):ndays])
#aamass_d_ammonia<-mean(ammonia_d[((nyears-1)*360+1):ndays])
aamass_d_ammonia<-NA
aamass_x_ammonia<-mean(x_ammonia_i[((nyears-1)*360+1):ndays])
aamass_s_nitrate<-mean(nitrate_si[((nyears-1)*360+1):ndays])
#aamass_d_nitrate<-mean(nitrate_d[((nyears-1)*360+1):ndays])
aamass_d_nitrate<-NA
aamass_x_nitrate<-mean(x_nitrate_i[((nyears-1)*360+1):ndays])
aamass_kelpN<-mean(kelpN[((nyears-1)*360+1):ndays])
#aamass_kelpN<-NA
aamass_s_phyt<-mean(phyt_si[((nyears-1)*360+1):ndays])
#aamass_d_phyt<-mean(phyt_d[((nyears-1)*360+1):ndays])
aamass_d_phyt<-NA
aamass_herb<-mean(herb_i[((nyears-1)*360+1):ndays])
aamass_carn<-mean(carn_i[((nyears-1)*360+1):ndays])
aamass_benthslar<-mean(benthslar_i[((nyears-1)*360+1):ndays])
aamass_benths<-mean(benths_i[((nyears-1)*360+1):ndays])
aamass_benthclar<-mean(benthclar_i[((nyears-1)*360+1):ndays])
aamass_benthc<-mean(benthc_i[((nyears-1)*360+1):ndays])
aamass_fishplar<-mean(fishplar_i[((nyears-1)*360+1):ndays])
aamass_fishp<-mean(fishp_i[((nyears-1)*360+1):ndays])
aamass_fishm<-mean(fishm_i[((nyears-1)*360+1):ndays])
aamass_fishdlar<-mean(fishdlar_i[((nyears-1)*360+1):ndays])
aamass_fishd<-mean(fishd_i[((nyears-1)*360+1):ndays])
aamass_bird<-mean(bird_i[((nyears-1)*360+1):ndays])
aamass_seal<-mean(seal_i[((nyears-1)*360+1):ndays])
aamass_ceta<-mean(ceta_i[((nyears-1)*360+1):ndays])
aamass_totalN<-mean(totalN_i[((nyears-1)*360+1):ndays])
#.........................................
mass_results<-data.frame(rep(0,55))
mass_results[1,1]<-aamass_s_detritus
mass_results[2,1]<-aamass_d_detritus
mass_results[3,1]<-aamass_x_detritus
mass_results[4,1]<-aamass_xR_detritus
mass_results[5,1]<-aamass_discard
mass_results[6,1]<-aamass_corpse
mass_results[7,1]<-aamass_kelpdebris
mass_results[8,1]<-aamass_s_ammonia
mass_results[9,1]<-aamass_d_ammonia
mass_results[10,1]<-aamass_x_ammonia
mass_results[11,1]<-aamass_s_nitrate
mass_results[12,1]<-aamass_d_nitrate
mass_results[13,1]<-aamass_x_nitrate
mass_results[14,1]<-aamass_kelpN
mass_results[15,1]<-aamass_s_phyt
mass_results[16,1]<-aamass_d_phyt
mass_results[17,1]<-aamass_herb
mass_results[18,1]<-aamass_carn
mass_results[19,1]<-aamass_benthslar
mass_results[20,1]<-aamass_benths
mass_results[21,1]<-aamass_benthclar
mass_results[22,1]<-aamass_benthc
mass_results[23,1]<-aamass_fishplar
mass_results[24,1]<-aamass_fishp
mass_results[25,1]<-aamass_fishm
mass_results[26,1]<-aamass_fishdlar
mass_results[27,1]<-aamass_fishd
mass_results[28,1]<-aamass_bird
mass_results[29,1]<-aamass_seal
mass_results[30,1]<-aamass_ceta
mass_results[31,1]<-aamass_totalN
mass_results[32,1]<-x_shallowprop
mass_results[33,1]<-si_depth
mass_results[34,1]<-so_depth
mass_results[35,1]<-d_depth
mass_results[36,1]<-x_area_s0
mass_results[37,1]<-x_area_s1
mass_results[38,1]<-x_area_s2
mass_results[39,1]<-x_area_s3
mass_results[40,1]<-x_area_d0
mass_results[41,1]<-x_area_d1
mass_results[42,1]<-x_area_d2
mass_results[43,1]<-x_area_d3
mass_results[44,1]<-x_depth_s1
mass_results[45,1]<-x_depth_s2
mass_results[46,1]<-x_depth_s3
mass_results[47,1]<-x_depth_d1
mass_results[48,1]<-x_depth_d2
mass_results[49,1]<-x_depth_d3
mass_results[50,1]<-x_poros_s1
mass_results[51,1]<-x_poros_s2
mass_results[52,1]<-x_poros_s3
mass_results[53,1]<-x_poros_d1
mass_results[54,1]<-x_poros_d2
mass_results[55,1]<-x_poros_d3
mass_results[,2]<-"mMN_in_the_whole model_domain_(1m2)"
mass_results[c(32,36:43,50:55),2]<-"dimensionless"
mass_results[c(33:35,44:49),2]<-"m"
mass_results[,3]<-c(
"Surface_layer_detritus",
"Deep_layer_detritus",
"Sediment_labile_plus_refractory_detritus",
"Sediment_refractory_detritus",
"Fishery_discards",
"Corpses",
"Kelp_debris",
"Surface_layer_ammonia",
"Deep_layer_ammonia",
"Sediment_porewater_ammonia",
"Surface_layer_nitrate",
"Deep_layer_nitrate",
"Sediment_porewater_nitrate",
"Kelp_nitrogen",
"Surface_layer_phytoplankton",
"Deep_layer_phytoplankton",
"Omnivorous_zooplankton",
"Carnivorous_zooplankton",
"Benthos_susp/dep_feeders_larvae",
"Benthos_susp/dep_feeders",
"Benthos_carn/scav_feeders_larvae",
"Benthos_carn/scav_feeders",
"Planktivorous_fish_larvae",
"Planktivorous_fish",
"Migratory_fish",
"Demersal_fish_larvae",
"Demersal_fish",
"Bird",
"Seals",
"Cetaceans",
"Total_nitrogen_mass",
"Area_proportion_of_inshore_zone",
"Thickness_of_inshore_surface_layer",
"Thickness_of_offshore_surface_layer",
"Thickness_of_offshore_deep_layer",
"Area_proportion_inshore_rock",
"Area_proportion_inshore_sediment_s1",
"Area_proportion_inshore_sediment_s2",
"Area_proportion_inshore_sediment_s3",
"Area_proportion_offshore_rock",
"Area_proportion_offshore_sediment_d1",
"Area_proportion_offshore_sediment_d2",
"Area_proportion_offshore_sediment_d3",
"Thickness_of_inshore_sediment_layer_s1",
"Thickness_of_inshore_sediment_layer_s2",
"Thickness_of_inshore_sediment_layer_s3",
"Thickness_of_offshore_sediment_layer_d1",
"Thickness_of_offshore_sediment_layer_d2",
"Thickness_of_offshore_sediment_layer_d3",
"Porosity_of_inshore_sediment_layer_s1",
"Porosity_of_inshore_sediment_layer_s2",
"Porosity_of_inshore_sediment_layer_s3",
"Porosity_of_offshore_sediment_layer_d1",
"Porosity_of_offshore_sediment_layer_d2",
"Porosity_of_offshore_sediment_layer_d3")
colnames(mass_results)<-c("Model_annual_mean","Units","Description")
mass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_anav_biomass", identifier)
writecsv(mass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#copy the mass_results dataframe as a template for the annual maximum data
maxmass_results<-mass_results
maxmass_results[1:31,1]<-0
aamaxmass_s_detritus<-max(detritus_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_detritus<-max(detritus_d[((nyears-1)*360+1):ndays])
aamaxmass_d_detritus<-NA
aamaxmass_x_detritus<-max(x_detritus_i[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamaxmass_xR_detritus<-max(xR_detritus_s1[((nyears-1)*360+1):ndays]
+ xR_detritus_s2[((nyears-1)*360+1):ndays]
+ xR_detritus_s3[((nyears-1)*360+1):ndays])
aamaxmass_discard<-max(discard_i[((nyears-1)*360+1):ndays])
aamaxmass_corpse<-max(corpse_i[((nyears-1)*360+1):ndays])
aamaxmass_kelpdebris<-max(kelpdebris[((nyears-1)*360+1):ndays])
#aamaxmass_kelpdebris<-NA
aamaxmass_s_ammonia<-max(ammonia_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_ammonia<-max(ammonia_d[((nyears-1)*360+1):ndays])
aamaxmass_d_ammonia<-NA
aamaxmass_x_ammonia<-max(x_ammonia_i[((nyears-1)*360+1):ndays])
aamaxmass_s_nitrate<-max(nitrate_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_nitrate<-max(nitrate_d[((nyears-1)*360+1):ndays])
aamaxmass_d_nitrate<-NA
aamaxmass_x_nitrate<-max(x_nitrate_i[((nyears-1)*360+1):ndays])
aamaxmass_kelpN<-max(kelpN[((nyears-1)*360+1):ndays])
#aamaxmass_kelpN<-NA
aamaxmass_s_phyt<-max(phyt_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_phyt<-max(phyt_d[((nyears-1)*360+1):ndays])
aamaxmass_d_phyt<-NA
aamaxmass_herb<-max(herb_i[((nyears-1)*360+1):ndays])
aamaxmass_carn<-max(carn_i[((nyears-1)*360+1):ndays])
aamaxmass_benthslar<-max(benthslar_i[((nyears-1)*360+1):ndays])
aamaxmass_benths<-max(benths_i[((nyears-1)*360+1):ndays])
aamaxmass_benthclar<-max(benthclar_i[((nyears-1)*360+1):ndays])
aamaxmass_benthc<-max(benthc_i[((nyears-1)*360+1):ndays])
aamaxmass_fishplar<-max(fishplar_i[((nyears-1)*360+1):ndays])
aamaxmass_fishp<-max(fishp_i[((nyears-1)*360+1):ndays])
aamaxmass_fishm<-max(fishm_i[((nyears-1)*360+1):ndays])
aamaxmass_fishdlar<-max(fishdlar_i[((nyears-1)*360+1):ndays])
aamaxmass_fishd<-max(fishd_i[((nyears-1)*360+1):ndays])
aamaxmass_bird<-max(bird_i[((nyears-1)*360+1):ndays])
aamaxmass_seal<-max(seal_i[((nyears-1)*360+1):ndays])
aamaxmass_ceta<-max(ceta_i[((nyears-1)*360+1):ndays])
aamaxmass_totalN<-max(totalN_i[((nyears-1)*360+1):ndays])
#..........................................
maxmass_results[1,1]<-aamaxmass_s_detritus
maxmass_results[2,1]<-aamaxmass_d_detritus
maxmass_results[3,1]<-aamaxmass_x_detritus
maxmass_results[4,1]<-aamaxmass_xR_detritus
maxmass_results[5,1]<-aamaxmass_discard
maxmass_results[6,1]<-aamaxmass_corpse
maxmass_results[7,1]<-aamaxmass_kelpdebris
maxmass_results[8,1]<-aamaxmass_s_ammonia
maxmass_results[9,1]<-aamaxmass_d_ammonia
maxmass_results[10,1]<-aamaxmass_x_ammonia
maxmass_results[11,1]<-aamaxmass_s_nitrate
maxmass_results[12,1]<-aamaxmass_d_nitrate
maxmass_results[13,1]<-aamaxmass_x_nitrate
maxmass_results[14,1]<-aamaxmass_kelpN
maxmass_results[15,1]<-aamaxmass_s_phyt
maxmass_results[16,1]<-aamaxmass_d_phyt
maxmass_results[17,1]<-aamaxmass_herb
maxmass_results[18,1]<-aamaxmass_carn
maxmass_results[19,1]<-aamaxmass_benthslar
maxmass_results[20,1]<-aamaxmass_benths
maxmass_results[21,1]<-aamaxmass_benthclar
maxmass_results[22,1]<-aamaxmass_benthc
maxmass_results[23,1]<-aamaxmass_fishplar
maxmass_results[24,1]<-aamaxmass_fishp
maxmass_results[25,1]<-aamaxmass_fishm
maxmass_results[26,1]<-aamaxmass_fishdlar
maxmass_results[27,1]<-aamaxmass_fishd
maxmass_results[28,1]<-aamaxmass_bird
maxmass_results[29,1]<-aamaxmass_seal
maxmass_results[30,1]<-aamaxmass_ceta
maxmass_results[31,1]<-aamaxmass_totalN
colnames(maxmass_results)<-c("Model_annual_maximum","Units","Description")
maxmass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_maximum_biomass", identifier)
writecsv(maxmass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#copy the mass_results dataframe as a template for the annual minimum data
minmass_results<-mass_results
minmass_results[1:31,1]<-0
aaminmass_s_detritus<-min(detritus_si[((nyears-1)*360+1):ndays])
#aaminmass_d_detritus<-min(detritus_d[((nyears-1)*360+1):ndays])
aaminmass_d_detritus<-NA
aaminmass_x_detritus<-min(x_detritus_i[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aaminmass_xR_detritus<-min(xR_detritus_s1[((nyears-1)*360+1):ndays]
+ xR_detritus_s2[((nyears-1)*360+1):ndays]
+ xR_detritus_s3[((nyears-1)*360+1):ndays])
aaminmass_discard<-min(discard_i[((nyears-1)*360+1):ndays])
aaminmass_corpse<-min(corpse_i[((nyears-1)*360+1):ndays])
aaminmass_kelpdebris<-min(kelpdebris[((nyears-1)*360+1):ndays])
#aaminmass_kelpdebris<-NA
aaminmass_s_ammonia<-min(ammonia_si[((nyears-1)*360+1):ndays])
#aaminmass_d_ammonia<-min(ammonia_d[((nyears-1)*360+1):ndays])
aaminmass_d_ammonia<-NA
aaminmass_x_ammonia<-min(x_ammonia_i[((nyears-1)*360+1):ndays])
aaminmass_s_nitrate<-min(nitrate_si[((nyears-1)*360+1):ndays])
#aaminmass_d_nitrate<-min(nitrate_d[((nyears-1)*360+1):ndays])
aaminmass_d_nitrate<-NA
aaminmass_x_nitrate<-min(x_nitrate_i[((nyears-1)*360+1):ndays])
aaminmass_kelpN<-min(kelpN[((nyears-1)*360+1):ndays])
#aaminmass_kelpN<-NA
aaminmass_s_phyt<-min(phyt_si[((nyears-1)*360+1):ndays])
#aaminmass_d_phyt<-min(phyt_d[((nyears-1)*360+1):ndays])
aaminmass_d_phyt<-NA
aaminmass_herb<-min(herb_i[((nyears-1)*360+1):ndays])
aaminmass_carn<-min(carn_i[((nyears-1)*360+1):ndays])
aaminmass_benthslar<-min(benthslar_i[((nyears-1)*360+1):ndays])
aaminmass_benths<-min(benths_i[((nyears-1)*360+1):ndays])
aaminmass_benthclar<-min(benthclar_i[((nyears-1)*360+1):ndays])
aaminmass_benthc<-min(benthc_i[((nyears-1)*360+1):ndays])
aaminmass_fishplar<-min(fishplar_i[((nyears-1)*360+1):ndays])
aaminmass_fishp<-min(fishp_i[((nyears-1)*360+1):ndays])
aaminmass_fishm<-min(fishm_i[((nyears-1)*360+1):ndays])
aaminmass_fishdlar<-min(fishdlar_i[((nyears-1)*360+1):ndays])
aaminmass_fishd<-min(fishd_i[((nyears-1)*360+1):ndays])
aaminmass_bird<-min(bird_i[((nyears-1)*360+1):ndays])
aaminmass_seal<-min(seal_i[((nyears-1)*360+1):ndays])
aaminmass_ceta<-min(ceta_i[((nyears-1)*360+1):ndays])
aaminmass_totalN<-min(totalN_i[((nyears-1)*360+1):ndays])
#..........................................
minmass_results[1,1]<-aaminmass_s_detritus
minmass_results[2,1]<-aaminmass_d_detritus
minmass_results[3,1]<-aaminmass_x_detritus
minmass_results[4,1]<-aaminmass_xR_detritus
minmass_results[5,1]<-aaminmass_discard
minmass_results[6,1]<-aaminmass_corpse
minmass_results[7,1]<-aaminmass_kelpdebris
minmass_results[8,1]<-aaminmass_s_ammonia
minmass_results[9,1]<-aaminmass_d_ammonia
minmass_results[10,1]<-aaminmass_x_ammonia
minmass_results[11,1]<-aaminmass_s_nitrate
minmass_results[12,1]<-aaminmass_d_nitrate
minmass_results[13,1]<-aaminmass_x_nitrate
minmass_results[14,1]<-aaminmass_kelpN
minmass_results[15,1]<-aaminmass_s_phyt
minmass_results[16,1]<-aaminmass_d_phyt
minmass_results[17,1]<-aaminmass_herb
minmass_results[18,1]<-aaminmass_carn
minmass_results[19,1]<-aaminmass_benthslar
minmass_results[20,1]<-aaminmass_benths
minmass_results[21,1]<-aaminmass_benthclar
minmass_results[22,1]<-aaminmass_benthc
minmass_results[23,1]<-aaminmass_fishplar
minmass_results[24,1]<-aaminmass_fishp
minmass_results[25,1]<-aaminmass_fishm
minmass_results[26,1]<-aaminmass_fishdlar
minmass_results[27,1]<-aaminmass_fishd
minmass_results[28,1]<-aaminmass_bird
minmass_results[29,1]<-aaminmass_seal
minmass_results[30,1]<-aaminmass_ceta
minmass_results[31,1]<-aaminmass_totalN
colnames(minmass_results)<-c("Model_annual_minimum","Units","Description")
minmass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_minimum_biomass", identifier)
writecsv(minmass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#Extract all of the derived rate variables for the final year
#!!!!!!
DINinflow<-(fluxAMMinflow_i[ndays]-fluxAMMinflow_i[((nyears-1)*360+1)]) + (fluxNITinflow_i[ndays]-fluxNITinflow_i[((nyears-1)*360+1)])
DINoutflow<-(fluxAMMoutflow_i[ndays]-fluxAMMoutflow_i[((nyears-1)*360+1)]) + (fluxNIToutflow_i[ndays]-fluxNIToutflow_i[((nyears-1)*360+1)])
PARTinflow<-(fluxPHYTinflow_i[ndays]-fluxPHYTinflow_i[((nyears-1)*360+1)]) + (fluxDETinflow_i[ndays]-fluxDETinflow_i[((nyears-1)*360+1)])
PARToutflow<-(fluxPHYToutflow_i[ndays]-fluxPHYToutflow_i[((nyears-1)*360+1)]) + (fluxDEToutflow_i[ndays]-fluxDEToutflow_i[((nyears-1)*360+1)])
atmosphereDINinput<-(atmosAMMinput_i[ndays]-atmosAMMinput_i[((nyears-1)*360+1)]) + (atmosNITinput_i[ndays]-atmosNITinput_i[((nyears-1)*360+1)])
riverDINinflow<-(rivAMMinflow[ndays]-rivAMMinflow[((nyears-1)*360+1)]) + (rivNITinflow[ndays]-rivNITinflow[((nyears-1)*360+1)])
riverPARTinflow<-rivPARTinflow[ndays]-rivPARTinflow[((nyears-1)*360+1)]
#riverDINinflow<-0
#riverPARTinflow<-0
#!!!!!!
sumDINinflow<-(fluxAMMinflow_i[ndays-90]-fluxAMMinflow_i[((nyears-1)*360+1+89)]) + (fluxNITinflow_i[ndays-90]-fluxNITinflow_i[((nyears-1)*360+1+89)])
sumDINoutflow<-(fluxAMMoutflow_i[ndays-90]-fluxAMMoutflow_i[((nyears-1)*360+1+89)]) + (fluxNIToutflow_i[ndays-90]-fluxNIToutflow_i[((nyears-1)*360+1+89)])
sumPARTinflow<-(fluxPHYTinflow_i[ndays-90]-fluxPHYTinflow_i[((nyears-1)*360+1+89)]) + (fluxDETinflow_i[ndays-90]-fluxDETinflow_i[((nyears-1)*360+1+89)])
sumPARToutflow<-(fluxPHYToutflow_i[ndays-90]-fluxPHYToutflow_i[((nyears-1)*360+1+89)]) + (fluxDEToutflow_i[ndays-90]-fluxDEToutflow_i[((nyears-1)*360+1+89)])
sumriverDINinflow<-(rivAMMinflow[ndays-90]-rivAMMinflow[((nyears-1)*360+1+89)]) + (rivNITinflow[ndays-90]-rivNITinflow[((nyears-1)*360+1+89)])
sumatmosDINinput<-(atmosAMMinput_i[ndays-90]-atmosAMMinput_i[((nyears-1)*360+1+89)]) + (atmosNITinput_i[ndays-90]-atmosNITinput_i[((nyears-1)*360+1+89)])
#surfvertnitflux<-vertnitflux[ndays]-vertnitflux[((nyears-1)*360+1)]
surfvertnitflux<-NA
#surfhoriznitflux<-horiznitflux[ndays]-horiznitflux[((nyears-1)*360+1)]
surfhoriznitflux<-NA
#!!!!!!
Flux_sedboundary <- (fluxsedboundary_i[ndays]-fluxsedboundary_i[((nyears-1)*360+1)])
kelp_beachcast<-((fluxkelpdebris_beachexport[ndays]-fluxkelpdebris_beachexport[((nyears-1)*360+1)]))
DIN_NET_flux_o_i <- DIN_NET_flux_o_i[ndays]-DIN_NET_flux_o_i[((nyears-1)*360+1)]
PART_NET_flux_o_i <- PART_NET_flux_o_i[ndays]-PART_NET_flux_o_i[((nyears-1)*360+1)]
NET_activemigpelfish_o_i <- NET_activemigpelfish_o_i[ndays]-NET_activemigpelfish_o_i[((nyears-1)*360+1)]
NET_activemigmigfish_o_i <- NET_activemigmigfish_o_i[ndays]-NET_activemigmigfish_o_i[((nyears-1)*360+1)]
NET_activemigdemfish_o_i <- NET_activemigdemfish_o_i[ndays]-NET_activemigdemfish_o_i[((nyears-1)*360+1)]
NET_activemigbird_o_i <- NET_activemigbird_o_i[ndays]-NET_activemigbird_o_i[((nyears-1)*360+1)]
NET_activemigseal_o_i <- NET_activemigseal_o_i[ndays]-NET_activemigseal_o_i[((nyears-1)*360+1)]
NET_activemigceta_o_i <- NET_activemigceta_o_i[ndays]-NET_activemigceta_o_i[((nyears-1)*360+1)]
#NET_mfish_ext_o <- NET_mfish_ext_o[ndays]-NET_mfish_ext_o[((nyears-1)*360+1)]
NET_mfish_ext_o<-NA
#Mfish_annual_imig <- mfish_imigration[ndays]-mfish_imigration[((nyears-1)*360+1)]
#Mfish_annual_emig <- mfish_emigration[ndays]-mfish_emigration[((nyears-1)*360+1)]
Mfish_annual_imig <- NA
Mfish_annual_emig <- NA
NETPrimaryP<-netpprod_i[ndays]-netpprod_i[((nyears-1)*360+1)]
MMP<-(max(nitrate_si[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays])) - (min(nitrate_si[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays]))
PNP<-PNP_i[ndays]-PNP_i[((nyears-1)*360+1)]
PhytNitUp<-fluxwcnit_phyt_i[ndays]-fluxwcnit_phyt_i[((nyears-1)*360+1)]
PhytAmmUp<-fluxwcamm_phyt_i[ndays]-fluxwcamm_phyt_i[((nyears-1)*360+1)]
NewP<-MMP+sumriverDINinflow+sumatmosDINinput+sumDINinflow-sumDINoutflow
fratio<-NewP/NETPrimaryP
Tfratio<-PhytNitUp/(PhytNitUp+PhytAmmUp)
KelpNitUp<-fluxwcnit_kelp[ndays]-fluxwcnit_kelp[((nyears-1)*360+1)]
KelpAmmUp<-fluxwcamm_kelp[ndays]-fluxwcamm_kelp[((nyears-1)*360+1)]
#KelpNitUp<-NA
#KelpAmmUp<-NA
KelpNprod <- kelpNprod_i[ndays] - kelpNprod_i[((nyears-1)*360+1)]
#KelpNprod <- NA
Phytgrossprod <- phytgrossprod_i[ndays] - phytgrossprod_i[((nyears-1)*360+1)]
Herbgrossprod <- herbgrossprod_i[ndays] - herbgrossprod_i[((nyears-1)*360+1)]
Carngrossprod <- carngrossprod_i[ndays] - carngrossprod_i[((nyears-1)*360+1)]
Fishplargrossprod <- pfishlargrossprod_i[ndays] - pfishlargrossprod_i[((nyears-1)*360+1)]
Fishdlargrossprod <- dfishlargrossprod_i[ndays] - dfishlargrossprod_i[((nyears-1)*360+1)]
Fishpgrossprod <- pfishgrossprod_i[ndays] - pfishgrossprod_i[((nyears-1)*360+1)]
Fishmgrossprod <- mfishgrossprod_i[ndays] - mfishgrossprod_i[((nyears-1)*360+1)]
Fishdgrossprod <- dfishgrossprod_i[ndays] - dfishgrossprod_i[((nyears-1)*360+1)]
Benthslargrossprod <- benthslargrossprod_i[ndays] - benthslargrossprod_i[((nyears-1)*360+1)]
Benthclargrossprod <- benthclargrossprod_i[ndays] - benthclargrossprod_i[((nyears-1)*360+1)]
Benthsgrossprod <- benthsgrossprod_i[ndays] - benthsgrossprod_i[((nyears-1)*360+1)]
Benthcgrossprod <- benthcgrossprod_i[ndays] - benthcgrossprod_i[((nyears-1)*360+1)]
Birdgrossprod <- birdgrossprod_i[ndays] - birdgrossprod_i[((nyears-1)*360+1)]
Sealgrossprod <- sealgrossprod_i[ndays] - sealgrossprod_i[((nyears-1)*360+1)]
Cetagrossprod <- cetagrossprod_i[ndays] - cetagrossprod_i[((nyears-1)*360+1)]
Herbnetprod <- herbnetprod_i[ndays] - herbnetprod_i[((nyears-1)*360+1)]
Carnnetprod <- carnnetprod_i[ndays] - carnnetprod_i[((nyears-1)*360+1)]
Fishplarnetprod <- pfishlarnetprod_i[ndays] - pfishlarnetprod_i[((nyears-1)*360+1)]
Fishdlarnetprod <- dfishlarnetprod_i[ndays] - dfishlarnetprod_i[((nyears-1)*360+1)]
Fishpnetprod <- pfishnetprod_i[ndays] - pfishnetprod_i[((nyears-1)*360+1)]
Fishmnetprod <- mfishnetprod_i[ndays] - mfishnetprod_i[((nyears-1)*360+1)]
Fishdnetprod <- dfishnetprod_i[ndays] - dfishnetprod_i[((nyears-1)*360+1)]
Benthslarnetprod <- benthslarnetprod_i[ndays] - benthslarnetprod_i[((nyears-1)*360+1)]
Benthclarnetprod <- benthclarnetprod_i[ndays] - benthclarnetprod_i[((nyears-1)*360+1)]
Benthsnetprod <- benthsnetprod_i[ndays] - benthsnetprod_i[((nyears-1)*360+1)]
Benthcnetprod <- benthcnetprod_i[ndays] - benthcnetprod_i[((nyears-1)*360+1)]
Birdnetprod <- birdnetprod_i[ndays] - birdnetprod_i[((nyears-1)*360+1)]
Sealnetprod <- sealnetprod_i[ndays] - sealnetprod_i[((nyears-1)*360+1)]
Cetanetprod <- cetanetprod_i[ndays] - cetanetprod_i[((nyears-1)*360+1)]
#WCdetritusprod <- fluxcorp_wcdet[ndays] - fluxcorp_wcdet[((nyears-1)*360+1)] +
# +fluxkelpdebris_wcdet[ndays] - fluxkelpdebris_wcdet[((nyears-1)*360+1)] +
# +fluxphyt_wcdet[ndays] - fluxphyt_wcdet[((nyears-1)*360+1)] +
# +fluxherb_wcdet[ndays] - fluxherb_wcdet[((nyears-1)*360+1)] +
# +fluxcarn_wcdet[ndays] - fluxcarn_wcdet[((nyears-1)*360+1)] +
# +fluxpfishlar_wcdet[ndays] - fluxpfishlar_wcdet[((nyears-1)*360+1)] +
# +fluxdfishlar_wcdet[ndays] - fluxdfishlar_wcdet[((nyears-1)*360+1)] +
# +fluxpfish_wcdet[ndays] - fluxpfish_wcdet[((nyears-1)*360+1)] +
# +fluxmfish_wcdet[ndays] - fluxmfish_wcdet[((nyears-1)*360+1)] +
# +fluxdfish_wcdet[ndays] - fluxdfish_wcdet[((nyears-1)*360+1)] +
# +fluxbenthslar_wcdet[ndays] - fluxbenthslar_wcdet[((nyears-1)*360+1)] +
# +fluxbenthclar_wcdet[ndays] - fluxbenthclar_wcdet[((nyears-1)*360+1)] +
# +fluxbenths_wcdet[ndays] - fluxbenths_wcdet[((nyears-1)*360+1)] +
# +fluxbenthc_wcdet[ndays] - fluxbenthc_wcdet[((nyears-1)*360+1)] +
# +fluxbird_wcdet[ndays] - fluxbird_wcdet[((nyears-1)*360+1)] +
# +fluxseal_wcdet[ndays] - fluxseal_wcdet[((nyears-1)*360+1)] +
# +fluxceta_wcdet[ndays] - fluxceta_wcdet[((nyears-1)*360+1)]
WCdetritusprod <- NA
#SEDdetritusprod <- fluxcorp_xdet[ndays] - fluxcorp_xdet[((nyears-1)*360+1)] +
# +fluxbenths_xdet[ndays] - fluxbenths_xdet[((nyears-1)*360+1)] +
# +fluxbenthc_xdet[ndays] - fluxbenthc_xdet[((nyears-1)*360+1)]
SEDdetritusprod <- NA
Kelpdebrisprod <- fluxkelp_kelpdebris[ndays] - fluxkelp_kelpdebris[((nyears-1)*360+1)]
#Kelpdebrisprod <- NA
#Corpseprod <- fluxdisc_corp[ndays] - fluxdisc_corp[((nyears-1)*360+1)] +
# +fluxpfish_corp[ndays] - fluxpfish_corp[((nyears-1)*360+1)] +
# +fluxmfish_corp[ndays] - fluxmfish_corp[((nyears-1)*360+1)] +
# +fluxdfish_corp[ndays] - fluxdfish_corp[((nyears-1)*360+1)] +
# +fluxbenths_corp[ndays] - fluxbenths_corp[((nyears-1)*360+1)] +
# +fluxbenthc_corp[ndays] - fluxbenthc_corp[((nyears-1)*360+1)] +
# +fluxbird_corp[ndays] - fluxbird_corp[((nyears-1)*360+1)] +
# +fluxseal_corp[ndays] - fluxseal_corp[((nyears-1)*360+1)] +
# +fluxceta_corp[ndays] - fluxceta_corp[((nyears-1)*360+1)]
Corpseprod <- NA
#Fluxpartwc_sed <- fluxwcdet_xdet[ndays] - fluxwcdet_xdet[((nyears-1)*360+1)] +
# +fluxdisc_corp[ndays] - fluxdisc_corp[((nyears-1)*360+1)] +
# +fluxpfish_corp[ndays] - fluxpfish_corp[((nyears-1)*360+1)] +
# +fluxmfish_corp[ndays] - fluxmfish_corp[((nyears-1)*360+1)] +
# +fluxdfish_corp[ndays] - fluxdfish_corp[((nyears-1)*360+1)] +
# +fluxbird_corp[ndays] - fluxbird_corp[((nyears-1)*360+1)] +
# +fluxphyt_benths[ndays] - fluxphyt_benths[((nyears-1)*360+1)]+
# +fluxwcdet_benths[ndays] - fluxwcdet_benths[((nyears-1)*360+1)]
##Includes the water column feeding flux of benthos
Fluxpartwc_sed <- NA
#Fluxdisc_corp <- fluxdisc_corp[ndays] - fluxdisc_corp[((nyears-1)*360+1)]
Fluxdisc_corp <- NA
#Pelagammprod <- fluxherb_wcamm[ndays] - fluxherb_wcamm[((nyears-1)*360+1)] +
# +fluxcarn_wcamm[ndays] - fluxcarn_wcamm[((nyears-1)*360+1)] +
# +fluxpfishlar_wcamm[ndays] - fluxpfishlar_wcamm[((nyears-1)*360+1)] +
# +fluxdfishlar_wcamm[ndays] - fluxdfishlar_wcamm[((nyears-1)*360+1)] +
# +fluxpfish_wcamm[ndays] - fluxpfish_wcamm[((nyears-1)*360+1)] +
# +fluxmfish_wcamm[ndays] - fluxmfish_wcamm[((nyears-1)*360+1)] +
# +fluxdfish_wcamm[ndays] - fluxdfish_wcamm[((nyears-1)*360+1)] +
# +fluxbenthslar_wcamm[ndays] - fluxbenthslar_wcamm[((nyears-1)*360+1)] +
# +fluxbenthclar_wcamm[ndays] - fluxbenthclar_wcamm[((nyears-1)*360+1)] +
# +fluxbird_wcamm[ndays] - fluxbird_wcamm[((nyears-1)*360+1)] +
# +fluxseal_wcamm[ndays] - fluxseal_wcamm[((nyears-1)*360+1)] +
# +fluxceta_wcamm[ndays] - fluxceta_wcamm[((nyears-1)*360+1)]
##Excludes mineralisation of detritus
Pelagammprod <- NA
#Benthammprod <- fluxbenths_wcamm[ndays] - fluxbenths_wcamm[((nyears-1)*360+1)]+
# +fluxbenthc_wcamm[ndays] - fluxbenthc_wcamm[((nyears-1)*360+1)]
##Excludes mineralisation of detritus
Benthammprod <- NA
#WCmineralisation <- fluxwcdet_wcamm[ndays] - fluxwcdet_wcamm[((nyears-1)*360+1)]
WCmineralisation <- NA
#SEDmineralisation <- fluxxdet_sedamm[ndays] - fluxxdet_sedamm[((nyears-1)*360+1)]+
# +fluxxRdet_sedamm[ndays] - fluxxRdet_sedamm[((nyears-1)*360+1)]
SEDmineralisation <- NA
#WCnitrification <- fluxwcamm_wcnit[ndays] - fluxwcamm_wcnit[((nyears-1)*360+1)]
WCnitrification <- NA
#SEDnitrification <- fluxsedamm_sednit[ndays] - fluxsedamm_sednit[((nyears-1)*360+1)]
SEDnitrification <- NA
#WCdenitrification <- wcdenitrif[ndays] - wcdenitrif[((nyears-1)*360+1)]
WCdenitrification <- NA
#SEDdenitrification <- seddenitrif[ndays] - seddenitrif[((nyears-1)*360+1)]
SEDdenitrification <- NA
#SEDWCammflux <- fluxsedamm_wcamm[ndays] - fluxsedamm_wcamm[((nyears-1)*360+1)]+
# +fluxbenths_wcamm[ndays] - fluxbenths_wcamm[((nyears-1)*360+1)]+
# +fluxbenthc_wcamm[ndays] - fluxbenthc_wcamm[((nyears-1)*360+1)]
##Includes excretion by benthos
SEDWCammflux <- NA
#SEDWCnitflux <- fluxsednit_wcnit[ndays] - fluxsednit_wcnit[((nyears-1)*360+1)]
SEDWCnitflux <- NA
#Fluxdet_herb <- fluxwcdet_herb[ndays] - fluxwcdet_herb[((nyears-1)*360+1)]
#Fluxphyt_herb <- fluxphyt_herb[ndays] - fluxphyt_herb[((nyears-1)*360+1)]
#Fluxbenthslar_herb <- fluxbenthslar_herb[ndays] - fluxbenthslar_herb[((nyears-1)*360+1)]
#Fluxbenthclar_herb <- fluxbenthclar_herb[ndays] - fluxbenthclar_herb[((nyears-1)*360+1)]
Fluxdet_herb <- NA
Fluxphyt_herb <- NA
Fluxbenthslar_herb <- NA
Fluxbenthclar_herb <- NA
#Fluxherb_carn <- fluxherb_carn[ndays] - fluxherb_carn[((nyears-1)*360+1)]
#Fluxpfishlar_carn <- fluxpfishlar_carn[ndays] - fluxpfishlar_carn[((nyears-1)*360+1)]
#Fluxdfishlar_carn <- fluxdfishlar_carn[ndays] - fluxdfishlar_carn[((nyears-1)*360+1)]
#Fluxbenthslar_carn <- fluxbenthslar_carn[ndays] - fluxbenthslar_carn[((nyears-1)*360+1)]
#Fluxbenthclar_carn <- fluxbenthclar_carn[ndays] - fluxbenthclar_carn[((nyears-1)*360+1)]
Fluxherb_carn <- NA
Fluxpfishlar_carn <- NA
Fluxdfishlar_carn <- NA
Fluxbenthslar_carn <- NA
Fluxbenthclar_carn <- NA
#Fluxherb_pfishlar <- fluxherb_pfishlar[ndays] - fluxherb_pfishlar[((nyears-1)*360+1)]
#Fluxbenthslar_pfishlar <- fluxbenthslar_pfishlar[ndays] - fluxbenthslar_pfishlar[((nyears-1)*360+1)]
#Fluxbenthclar_pfishlar <- fluxbenthclar_pfishlar[ndays] - fluxbenthclar_pfishlar[((nyears-1)*360+1)]
Fluxherb_pfishlar <- NA
Fluxbenthslar_pfishlar <- NA
Fluxbenthclar_pfishlar <- NA
#Fluxherb_dfishlar <- fluxherb_dfishlar[ndays] - fluxherb_dfishlar[((nyears-1)*360+1)]
#Fluxbenthslar_dfishlar <- fluxbenthslar_dfishlar[ndays] - fluxbenthslar_dfishlar[((nyears-1)*360+1)]
#Fluxbenthclar_dfishlar <- fluxbenthclar_dfishlar[ndays] - fluxbenthclar_dfishlar[((nyears-1)*360+1)]
Fluxherb_dfishlar <- NA
Fluxbenthslar_dfishlar <- NA
Fluxbenthclar_dfishlar <- NA
#Fluxherb_pfish <- fluxherb_pfish[ndays] - fluxherb_pfish[((nyears-1)*360+1)]
#Fluxcarn_pfish <- fluxcarn_pfish[ndays] - fluxcarn_pfish[((nyears-1)*360+1)]
#Fluxpfishlar_pfish <- fluxpfishlar_pfish[ndays] - fluxpfishlar_pfish[((nyears-1)*360+1)]
#Fluxdfishlar_pfish <- fluxdfishlar_pfish[ndays] - fluxdfishlar_pfish[((nyears-1)*360+1)]
#Fluxbenthslar_pfish <- fluxbenthslar_pfish[ndays] - fluxbenthslar_pfish[((nyears-1)*360+1)]
#Fluxbenthclar_pfish <- fluxbenthclar_pfish[ndays] - fluxbenthclar_pfish[((nyears-1)*360+1)]
Fluxherb_pfish <- NA
Fluxcarn_pfish <- NA
Fluxpfishlar_pfish <- NA
Fluxdfishlar_pfish <- NA
Fluxbenthslar_pfish <- NA
Fluxbenthclar_pfish <- NA
#Fluxherb_mfish <- fluxherb_mfish[ndays] - fluxherb_mfish[((nyears-1)*360+1)]
#Fluxcarn_mfish <- fluxcarn_mfish[ndays] - fluxcarn_mfish[((nyears-1)*360+1)]
#Fluxpfishlar_mfish <- fluxpfishlar_mfish[ndays] - fluxpfishlar_mfish[((nyears-1)*360+1)]
#Fluxdfishlar_mfish <- fluxdfishlar_mfish[ndays] - fluxdfishlar_mfish[((nyears-1)*360+1)]
#Fluxbenthslar_mfish <- fluxbenthslar_mfish[ndays] - fluxbenthslar_mfish[((nyears-1)*360+1)]
#Fluxbenthclar_mfish <- fluxbenthclar_mfish[ndays] - fluxbenthclar_mfish[((nyears-1)*360+1)]
Fluxherb_mfish <- NA
Fluxcarn_mfish <- NA
Fluxpfishlar_mfish <- NA
Fluxdfishlar_mfish <- NA
Fluxbenthslar_mfish <- NA
Fluxbenthclar_mfish <- NA
#Fluxcorp_dfish <- fluxcorp_dfish[ndays] - fluxcorp_dfish[((nyears-1)*360+1)]
#Fluxdisc_dfish <- fluxdisc_dfish[ndays] - fluxdisc_dfish[((nyears-1)*360+1)]
#Fluxcarn_dfish <- fluxcarn_dfish[ndays] - fluxcarn_dfish[((nyears-1)*360+1)]
#Fluxpfishlar_dfish <- fluxpfishlar_dfish[ndays] - fluxpfishlar_dfish[((nyears-1)*360+1)]
#Fluxdfishlar_dfish <- fluxdfishlar_dfish[ndays] - fluxdfishlar_dfish[((nyears-1)*360+1)]
#Fluxpfish_dfish <- fluxpfish_dfish[ndays] - fluxpfish_dfish[((nyears-1)*360+1)]
#Fluxmfish_dfish <- fluxmfish_dfish[ndays] - fluxmfish_dfish[((nyears-1)*360+1)]
#Fluxdfish_dfish <- fluxdfish_dfish[ndays] - fluxdfish_dfish[((nyears-1)*360+1)]
#Fluxbenths_dfish <- fluxbenths_dfish[ndays] - fluxbenths_dfish[((nyears-1)*360+1)]
#Fluxbenthc_dfish <- fluxbenthc_dfish[ndays] - fluxbenthc_dfish[((nyears-1)*360+1)]
Fluxcorp_dfish <- NA
Fluxdisc_dfish <- NA
Fluxcarn_dfish <- NA
Fluxpfishlar_dfish <- NA
Fluxdfishlar_dfish <- NA
Fluxpfish_dfish <- NA
Fluxmfish_dfish <- NA
Fluxdfish_dfish <- NA
Fluxbenths_dfish <- NA
Fluxbenthc_dfish <- NA
#Fluxdet_benthslar <- fluxwcdet_benthslar[ndays] - fluxwcdet_benthslar[((nyears-1)*360+1)]
#Fluxphyt_benthslar <- fluxphyt_benthslar[ndays] - fluxphyt_benthslar[((nyears-1)*360+1)]
Fluxdet_benthslar <- NA
Fluxphyt_benthslar <- NA
#Fluxdet_benthclar <- fluxwcdet_benthclar[ndays] - fluxwcdet_benthclar[((nyears-1)*360+1)]
#Fluxphyt_benthclar <- fluxphyt_benthclar[ndays] - fluxphyt_benthclar[((nyears-1)*360+1)]
Fluxdet_benthclar <- NA
Fluxphyt_benthclar <- NA
#Fluxdet_benths <- fluxwcdet_benths[ndays] - fluxwcdet_benths[((nyears-1)*360+1)]
#Fluxseddet_benths <- fluxxdet_benths[ndays] - fluxxdet_benths[((nyears-1)*360+1)] +
#Fluxphyt_benths <- fluxphyt_benths[ndays] - fluxphyt_benths[((nyears-1)*360+1)]
Fluxdet_benths <- NA
Fluxseddet_benths <- NA
Fluxphyt_benths <- NA
Fluxkelp_benthc <- fluxkelp_benthc[ndays] - fluxkelp_benthc[((nyears-1)*360+1)]
Fluxkelpdebris_benthc <- fluxkelpdebris_benthc[ndays] - fluxkelpdebris_benthc[((nyears-1)*360+1)]
#Fluxkelp_benthc <- NA
#Fluxkelpdebris_benthc <- NA
#Fluxcorp_benthc <- fluxcorp_benthc[ndays] - fluxcorp_benthc[((nyears-1)*360+1)]
#Fluxbenths_benthc <- fluxbenths_benthc[ndays] - fluxbenths_benthc[((nyears-1)*360+1)]
Fluxcorp_benthc <- NA
Fluxbenths_benthc <- NA
#Fluxcorp_bird <- fluxcorp_bird[ndays] - fluxcorp_bird[((nyears-1)*360+1)]
#Fluxdisc_bird <- fluxdisc_bird[ndays] - fluxdisc_bird[((nyears-1)*360+1)]
##Fluxherb_bird <- fluxherb_bird[ndays] - fluxherb_bird[((nyears-1)*360+1)]
#Fluxcarn_bird <- fluxcarn_bird[ndays] - fluxcarn_bird[((nyears-1)*360+1)]
#Fluxpfish_bird <- fluxpfish_bird[ndays] - fluxpfish_bird[((nyears-1)*360+1)]
#Fluxmfish_bird <- fluxmfish_bird[ndays] - fluxmfish_bird[((nyears-1)*360+1)]
#Fluxdfish_bird <- fluxdfish_bird[ndays] - fluxdfish_bird[((nyears-1)*360+1)]
#Fluxbenths_bird <- fluxbenths_bird[ndays] - fluxbenths_bird[((nyears-1)*360+1)]
#Fluxbenthc_bird <- fluxbenthc_bird[ndays] - fluxbenthc_bird[((nyears-1)*360+1)]
Fluxcorp_bird <- NA
Fluxdisc_bird <- NA
#Fluxherb_bird <- NA
Fluxcarn_bird <- NA
Fluxpfish_bird <- NA
Fluxmfish_bird <- NA
Fluxdfish_bird <- NA
Fluxbenths_bird <- NA
Fluxbenthc_bird <- NA
#Fluxcorp_seal <- fluxcorp_seal[ndays] - fluxcorp_seal[((nyears-1)*360+1)]
#Fluxdisc_seal <- fluxdisc_seal[ndays] - fluxdisc_seal[((nyears-1)*360+1)]
#Fluxcarn_seal <- fluxcarn_seal[ndays] - fluxcarn_seal[((nyears-1)*360+1)]
#Fluxpfish_seal <- fluxpfish_seal[ndays] - fluxpfish_seal[((nyears-1)*360+1)]
#Fluxmfish_seal <- fluxmfish_seal[ndays] - fluxmfish_seal[((nyears-1)*360+1)]
#Fluxdfish_seal <- fluxdfish_seal[ndays] - fluxdfish_seal[((nyears-1)*360+1)]
#Fluxbenths_seal <- fluxbenths_seal[ndays] - fluxbenths_seal[((nyears-1)*360+1)]
#Fluxbenthc_seal <- fluxbenthc_seal[ndays] - fluxbenthc_seal[((nyears-1)*360+1)]
#Fluxbird_seal <- fluxbird_seal[ndays] - fluxbird_seal[((nyears-1)*360+1)]
Fluxcorp_seal <- NA
Fluxdisc_seal <- NA
Fluxcarn_seal <- NA
Fluxpfish_seal <- NA
Fluxmfish_seal <- NA
Fluxdfish_seal <- NA
Fluxbenths_seal <- NA
Fluxbenthc_seal <- NA
Fluxbird_seal <- NA
#Fluxdisc_ceta <- fluxdisc_ceta[ndays] - fluxdisc_ceta[((nyears-1)*360+1)]
#Fluxherb_ceta <- fluxherb_ceta[ndays] - fluxherb_ceta[((nyears-1)*360+1)]
#Fluxcarn_ceta <- fluxcarn_ceta[ndays] - fluxcarn_ceta[((nyears-1)*360+1)]
#Fluxpfish_ceta <- fluxpfish_ceta[ndays] - fluxpfish_ceta[((nyears-1)*360+1)]
#Fluxmfish_ceta <- fluxmfish_ceta[ndays] - fluxmfish_ceta[((nyears-1)*360+1)]
#Fluxdfish_ceta <- fluxdfish_ceta[ndays] - fluxdfish_ceta[((nyears-1)*360+1)]
#Fluxbenths_ceta <- fluxbenths_ceta[ndays] - fluxbenths_ceta[((nyears-1)*360+1)]
#Fluxbenthc_ceta <- fluxbenthc_ceta[ndays] - fluxbenthc_ceta[((nyears-1)*360+1)]
#Fluxbird_ceta <- fluxbird_ceta[ndays] - fluxbird_ceta[((nyears-1)*360+1)]
#Fluxseal_ceta <- fluxseal_ceta[ndays] - fluxseal_ceta[((nyears-1)*360+1)]
Fluxdisc_ceta <- NA
Fluxherb_ceta <- NA
Fluxcarn_ceta <- NA
Fluxpfish_ceta <- NA
Fluxmfish_ceta <- NA
Fluxdfish_ceta <- NA
Fluxbenths_ceta <- NA
Fluxbenthc_ceta <- NA
Fluxbird_ceta <- NA
Fluxseal_ceta <- NA
HTLP<- Herbnetprod +
+ Carnnetprod +
+ Benthsnetprod +
+ Benthcnetprod +
+ Benthslarnetprod +
+ Benthclarnetprod +
+ Fishplarnetprod +
+ Fishdlarnetprod +
+ Fishpnetprod +
+ Fishmnetprod +
+ Fishdnetprod +
+ Birdnetprod +
+ Sealnetprod +
+ Cetanetprod
#export_from_2prod<- Fluxherb_carn +
# + Fluxherb_pfishlar +
# + Fluxherb_dfishlar +
# + Fluxherb_pfish +
# + Fluxherb_ceta +
# + Fluxbenths_dfish +
# + Fluxbenths_benthc +
# + Fluxbenths_bird +
# + Fluxbenths_seal +
# + Fluxbenths_ceta
export_from_2prod<- NA
#Pfish_annual_spawn <- Pfish_spawn[ndays]-Pfish_spawn[((nyears-1)*360+1)]
#Pfish_annual_recruit <- Pfish_recruit[ndays]-Pfish_recruit[((nyears-1)*360+1)]
#Dfish_annual_spawn <- Dfish_spawn[ndays]-Dfish_spawn[((nyears-1)*360+1)]
#Dfish_annual_recruit <- Dfish_recruit[ndays]-Dfish_recruit[((nyears-1)*360+1)]
Pfish_annual_spawn <- NA
Pfish_annual_recruit <- NA
Dfish_annual_spawn <- NA
Dfish_annual_recruit <- NA
#Benths_annual_spawn <- Bs_spawn[ndays]-Bs_spawn[((nyears-1)*360+1)]
#Benths_annual_recruit <- Bs_recruit[ndays]-Bs_recruit[((nyears-1)*360+1)]
#Benthc_annual_spawn <- Bc_spawn[ndays]-Bc_spawn[((nyears-1)*360+1)]
#Benthc_annual_recruit <- Bc_recruit[ndays]-Bc_recruit[((nyears-1)*360+1)]
Benths_annual_spawn <- NA
Benths_annual_recruit <- NA
Benthc_annual_spawn <- NA
Benthc_annual_recruit <- NA
FishpLand_livewt<-landp_i[ndays]-landp_i[((nyears-1)*360+1)]
FishmLand_livewt<-landm_i[ndays]-landm_i[((nyears-1)*360+1)]
FishdLand_livewt<-landd_i[ndays]-landd_i[((nyears-1)*360+1)]
Fishd_qLand_livewt<-landd_quota_i[ndays]-landd_quota_i[((nyears-1)*360+1)]
Fishd_nqLand_livewt<-landd_nonquota_i[ndays]-landd_nonquota_i[((nyears-1)*360+1)]
BenthsLand_livewt <- landsb_i[ndays]-landsb_i[((nyears-1)*360+1)]
BenthcLand_livewt <- landcb_i[ndays]-landcb_i[((nyears-1)*360+1)]
CarnzLand_livewt <- landcz_i[ndays]-landcz_i[((nyears-1)*360+1)]
BirdLand_livewt <- landbd_i[ndays]-landbd_i[((nyears-1)*360+1)]
SealLand_livewt <- landsl_i[ndays]-landsl_i[((nyears-1)*360+1)]
CetaLand_livewt <- landct_i[ndays]-landct_i[((nyears-1)*360+1)]
KelpLand_livewt <- landkp_i[ndays]-landkp_i[((nyears-1)*360+1)]
#KelpLand_livewt <- NA
FishpDiscard<-discpel_i[ndays]-discpel_i[((nyears-1)*360+1)]
FishmDiscard<-discmig_i[ndays]-discmig_i[((nyears-1)*360+1)]
FishdDiscard<-discdem_i[ndays]-discdem_i[((nyears-1)*360+1)]
Fishd_qDiscard<-discdem_quota_i[ndays]-discdem_quota_i[((nyears-1)*360+1)]
Fishd_nqDiscard<-discdem_nonquota_i[ndays]-discdem_nonquota_i[((nyears-1)*360+1)]
BenthsDiscard <- discsb_i[ndays]-discsb_i[((nyears-1)*360+1)]
BenthcDiscard <- disccb_i[ndays]-disccb_i[((nyears-1)*360+1)]
CarnzDiscard <- disccz_i[ndays]-disccz_i[((nyears-1)*360+1)]
BirdDiscard <- discbd_i[ndays]-discbd_i[((nyears-1)*360+1)]
SealDiscard <- discsl_i[ndays]-discsl_i[((nyears-1)*360+1)]
CetaDiscard <- discct_i[ndays]-discct_i[((nyears-1)*360+1)]
KelpDiscard <- disckp_i[ndays]-disckp_i[((nyears-1)*360+1)]
#KelpDiscard <- NA
FishpOffal<-offalpel_i[ndays]-offalpel_i[((nyears-1)*360+1)]
FishmOffal<-offalmig_i[ndays]-offalmig_i[((nyears-1)*360+1)]
FishdOffal<-offaldem_i[ndays]-offaldem_i[((nyears-1)*360+1)]
Fishd_qOffal<-offaldem_quota_i[ndays]-offaldem_quota_i[((nyears-1)*360+1)]
Fishd_nqOffal<-offaldem_nonquota_i[ndays]-offaldem_nonquota_i[((nyears-1)*360+1)]
BenthsOffal <- offalsb_i[ndays]-offalsb_i[((nyears-1)*360+1)]
BenthcOffal <- offalcb_i[ndays]-offalcb_i[((nyears-1)*360+1)]
CarnzOffal <- offalcz_i[ndays]-offalcz_i[((nyears-1)*360+1)]
BirdOffal <- offalbd_i[ndays]-offalbd_i[((nyears-1)*360+1)]
SealOffal <- offalsl_i[ndays]-offalsl_i[((nyears-1)*360+1)]
CetaOffal <- offalct_i[ndays]-offalct_i[((nyears-1)*360+1)]
KelpOffal <- offalkp_i[ndays]-offalkp_i[((nyears-1)*360+1)]
#KelpOffal <- NA
FishpLand_processedwt<- FishpLand_livewt - FishpOffal
FishmLand_processedwt<- FishmLand_livewt - FishmOffal
FishdLand_processedwt<- FishdLand_livewt - FishdOffal
Fishd_qLand_processedwt<- Fishd_qLand_livewt - Fishd_qOffal
Fishd_nqLand_processedwt<- Fishd_nqLand_livewt - Fishd_nqOffal
BenthsLand_processedwt <- BenthsLand_livewt - BenthsOffal
BenthcLand_processedwt <- BenthcLand_livewt - BenthcOffal
CarnzLand_processedwt <- CarnzLand_livewt - CarnzOffal
BirdLand_processedwt <- BirdLand_livewt - BirdOffal
SealLand_processedwt <- SealLand_livewt - SealOffal
CetaLand_processedwt <- CetaLand_livewt - CetaOffal
KelpLand_processedwt <- KelpLand_livewt - KelpOffal
#KelpLand_processedwt <- NA
annual_flux_results<-data.frame(rep(0,240))
#EXTRACT THE RESULTS INTO A DATA FRAME
#COLUMN 1 IS IN NITROGEN UNITS (mM N/m2/y)
#DERIVED ANNUAL VALUES IN UNITS OF mM N/m2 and fluxes in mMN/m2/y
annual_flux_results[1,1]<-DINinflow
annual_flux_results[2,1]<-DINoutflow
annual_flux_results[3,1]<-PARTinflow
annual_flux_results[4,1]<-PARToutflow
annual_flux_results[5,1]<-atmosphereDINinput
annual_flux_results[6,1]<-riverDINinflow
annual_flux_results[7,1]<-riverPARTinflow
annual_flux_results[8,1]<-sumDINinflow
annual_flux_results[9,1]<-sumDINoutflow
annual_flux_results[10,1]<-sumPARTinflow
annual_flux_results[11,1]<-sumPARToutflow
annual_flux_results[12,1]<-sumriverDINinflow
annual_flux_results[13,1]<-sumatmosDINinput
annual_flux_results[14,1]<-surfvertnitflux
annual_flux_results[15,1]<-surfhoriznitflux
annual_flux_results[16,1]<-Flux_sedboundary
annual_flux_results[17,1]<-kelp_beachcast
annual_flux_results[18,1]<-DIN_NET_flux_o_i
annual_flux_results[19,1]<-PART_NET_flux_o_i
annual_flux_results[20,1]<-NET_activemigpelfish_o_i
annual_flux_results[21,1]<-NET_activemigmigfish_o_i
annual_flux_results[22,1]<-NET_activemigdemfish_o_i
annual_flux_results[23,1]<-NET_activemigbird_o_i
annual_flux_results[24,1]<-NET_activemigseal_o_i
annual_flux_results[25,1]<-NET_activemigceta_o_i
annual_flux_results[26,1]<-NET_mfish_ext_o
annual_flux_results[27,1]<-Mfish_annual_imig
annual_flux_results[28,1]<-Mfish_annual_emig
annual_flux_results[29,1]<-NETPrimaryP
annual_flux_results[30,1]<-MMP
annual_flux_results[31,1]<-PNP
annual_flux_results[32,1]<-PhytNitUp
annual_flux_results[33,1]<-PhytAmmUp
annual_flux_results[34,1]<-NewP
annual_flux_results[35,1]<-fratio
annual_flux_results[36,1]<-Tfratio
annual_flux_results[37,1]<-KelpNitUp
annual_flux_results[38,1]<-KelpAmmUp
annual_flux_results[39,1]<-KelpNprod
annual_flux_results[40,1]<-Phytgrossprod
annual_flux_results[41,1]<-Herbgrossprod
annual_flux_results[42,1]<-Carngrossprod
annual_flux_results[43,1]<-Fishplargrossprod
annual_flux_results[44,1]<-Fishdlargrossprod
annual_flux_results[45,1]<-Fishpgrossprod
annual_flux_results[46,1]<-Fishmgrossprod
annual_flux_results[47,1]<-Fishdgrossprod
annual_flux_results[48,1]<-Benthslargrossprod
annual_flux_results[49,1]<-Benthclargrossprod
annual_flux_results[50,1]<-Benthsgrossprod
annual_flux_results[51,1]<-Benthcgrossprod
annual_flux_results[52,1]<-Birdgrossprod
annual_flux_results[53,1]<-Sealgrossprod
annual_flux_results[54,1]<-Cetagrossprod
annual_flux_results[55,1]<-Herbnetprod
annual_flux_results[56,1]<-Carnnetprod
annual_flux_results[57,1]<-Fishplarnetprod
annual_flux_results[58,1]<-Fishdlarnetprod
annual_flux_results[59,1]<-Fishpnetprod
annual_flux_results[60,1]<-Fishmnetprod
annual_flux_results[61,1]<-Fishdnetprod
annual_flux_results[62,1]<-Benthslarnetprod
annual_flux_results[63,1]<-Benthclarnetprod
annual_flux_results[64,1]<-Benthsnetprod
annual_flux_results[65,1]<-Benthcnetprod
annual_flux_results[66,1]<-Birdnetprod
annual_flux_results[67,1]<-Sealnetprod
annual_flux_results[68,1]<-Cetanetprod
annual_flux_results[69,1]<-WCdetritusprod
annual_flux_results[70,1]<-SEDdetritusprod
annual_flux_results[71,1]<-Corpseprod
annual_flux_results[72,1]<-Fluxpartwc_sed
annual_flux_results[73,1]<-Fluxdisc_corp
annual_flux_results[74,1]<-Pelagammprod
annual_flux_results[75,1]<-Benthammprod
annual_flux_results[76,1]<-WCmineralisation
annual_flux_results[77,1]<-SEDmineralisation
annual_flux_results[78,1]<-WCnitrification
annual_flux_results[79,1]<-SEDnitrification
annual_flux_results[80,1]<-WCdenitrification
annual_flux_results[81,1]<-SEDdenitrification
annual_flux_results[82,1]<-SEDWCammflux
annual_flux_results[83,1]<-SEDWCnitflux
annual_flux_results[84,1]<-Fluxdet_herb
annual_flux_results[85,1]<-Fluxphyt_herb
annual_flux_results[85,1]<-Fluxbenthslar_herb
annual_flux_results[87,1]<-Fluxbenthclar_herb
annual_flux_results[88,1]<-Fluxherb_carn
annual_flux_results[89,1]<-Fluxpfishlar_carn
annual_flux_results[90,1]<-Fluxdfishlar_carn
annual_flux_results[91,1]<-Fluxbenthslar_carn
annual_flux_results[92,1]<-Fluxbenthclar_carn
annual_flux_results[93,1]<-Fluxherb_pfishlar
annual_flux_results[94,1]<-Fluxbenthslar_pfishlar
annual_flux_results[95,1]<-Fluxbenthclar_pfishlar
annual_flux_results[96,1]<-Fluxherb_dfishlar
annual_flux_results[97,1]<-Fluxbenthslar_dfishlar
annual_flux_results[98,1]<-Fluxbenthclar_dfishlar
annual_flux_results[99,1]<-Fluxherb_pfish
annual_flux_results[100,1]<-Fluxcarn_pfish
annual_flux_results[101,1]<-Fluxpfishlar_pfish
annual_flux_results[102,1]<-Fluxdfishlar_pfish
annual_flux_results[103,1]<-Fluxbenthslar_pfish
annual_flux_results[104,1]<-Fluxbenthclar_pfish
annual_flux_results[105,1]<-Fluxherb_mfish
annual_flux_results[106,1]<-Fluxcarn_mfish
annual_flux_results[107,1]<-Fluxpfishlar_mfish
annual_flux_results[108,1]<-Fluxdfishlar_mfish
annual_flux_results[109,1]<-Fluxbenthslar_mfish
annual_flux_results[110,1]<-Fluxbenthclar_mfish
annual_flux_results[111,1]<-Fluxcorp_dfish
annual_flux_results[112,1]<-Fluxdisc_dfish
annual_flux_results[113,1]<-Fluxcarn_dfish
annual_flux_results[114,1]<-Fluxpfishlar_dfish
annual_flux_results[115,1]<-Fluxdfishlar_dfish
annual_flux_results[116,1]<-Fluxpfish_dfish
annual_flux_results[117,1]<-Fluxmfish_dfish
annual_flux_results[118,1]<-Fluxdfish_dfish
annual_flux_results[119,1]<-Fluxbenths_dfish
annual_flux_results[120,1]<-Fluxbenthc_dfish
annual_flux_results[121,1]<-Fluxdet_benthslar
annual_flux_results[122,1]<-Fluxphyt_benthslar
annual_flux_results[123,1]<-Fluxdet_benthclar
annual_flux_results[124,1]<-Fluxphyt_benthclar
annual_flux_results[125,1]<-Fluxdet_benths
annual_flux_results[126,1]<-Fluxseddet_benths
annual_flux_results[127,1]<-Fluxphyt_benths
annual_flux_results[128,1]<-Fluxkelpdebris_benthc
annual_flux_results[129,1]<-Fluxcorp_benthc
annual_flux_results[130,1]<-Fluxkelp_benthc
annual_flux_results[131,1]<-Fluxbenths_benthc
annual_flux_results[132,1]<-Fluxcorp_bird
annual_flux_results[133,1]<-Fluxdisc_bird
#annual_flux_results[xxx,1]<-Fluxherb_bird
annual_flux_results[134,1]<-Fluxcarn_bird
annual_flux_results[135,1]<-Fluxpfish_bird
annual_flux_results[136,1]<-Fluxmfish_bird
annual_flux_results[137,1]<-Fluxdfish_bird
annual_flux_results[138,1]<-Fluxbenths_bird
annual_flux_results[139,1]<-Fluxbenthc_bird
annual_flux_results[140,1]<-Fluxcorp_seal
annual_flux_results[141,1]<-Fluxdisc_seal
annual_flux_results[142,1]<-Fluxcarn_seal
annual_flux_results[143,1]<-Fluxpfish_seal
annual_flux_results[144,1]<-Fluxmfish_seal
annual_flux_results[145,1]<-Fluxdfish_seal
annual_flux_results[146,1]<-Fluxbenths_seal
annual_flux_results[147,1]<-Fluxbenthc_seal
annual_flux_results[148,1]<-Fluxbird_seal
annual_flux_results[149,1]<-Fluxdisc_ceta
annual_flux_results[150,1]<-Fluxherb_ceta
annual_flux_results[151,1]<-Fluxcarn_ceta
annual_flux_results[152,1]<-Fluxpfish_ceta
annual_flux_results[153,1]<-Fluxmfish_ceta
annual_flux_results[154,1]<-Fluxdfish_ceta
annual_flux_results[155,1]<-Fluxbenths_ceta
annual_flux_results[156,1]<-Fluxbenthc_ceta
annual_flux_results[157,1]<-Fluxbird_ceta
annual_flux_results[158,1]<-Fluxseal_ceta
annual_flux_results[159,1]<-HTLP
annual_flux_results[160,1]<-export_from_2prod
annual_flux_results[161,1]<-Pfish_annual_spawn
annual_flux_results[162,1]<-Pfish_annual_recruit
annual_flux_results[163,1]<-Dfish_annual_spawn
annual_flux_results[164,1]<-Dfish_annual_recruit
annual_flux_results[165,1]<-Benths_annual_spawn
annual_flux_results[166,1]<-Benths_annual_recruit
annual_flux_results[167,1]<-Benthc_annual_spawn
annual_flux_results[168,1]<-Benthc_annual_recruit
annual_flux_results[169,1]<-FishpLand_livewt
annual_flux_results[170,1]<-FishmLand_livewt
annual_flux_results[171,1]<-FishdLand_livewt
annual_flux_results[172,1]<-Fishd_qLand_livewt
annual_flux_results[173,1]<-Fishd_nqLand_livewt
annual_flux_results[174,1]<-BenthsLand_livewt
annual_flux_results[175,1]<-BenthcLand_livewt
annual_flux_results[176,1]<-CarnzLand_livewt
annual_flux_results[177,1]<-BirdLand_livewt
annual_flux_results[178,1]<-SealLand_livewt
annual_flux_results[179,1]<-CetaLand_livewt
annual_flux_results[180,1]<-KelpLand_livewt
annual_flux_results[181,1]<-FishpDiscard
annual_flux_results[182,1]<-FishmDiscard
annual_flux_results[183,1]<-FishdDiscard
annual_flux_results[184,1]<-Fishd_qDiscard
annual_flux_results[185,1]<-Fishd_nqDiscard
annual_flux_results[186,1]<-BenthsDiscard
annual_flux_results[187,1]<-BenthcDiscard
annual_flux_results[188,1]<-CarnzDiscard
annual_flux_results[189,1]<-BirdDiscard
annual_flux_results[190,1]<-SealDiscard
annual_flux_results[191,1]<-CetaDiscard
annual_flux_results[192,1]<-KelpDiscard
annual_flux_results[193,1]<-FishpOffal
annual_flux_results[194,1]<-FishmOffal
annual_flux_results[195,1]<-FishdOffal
annual_flux_results[196,1]<-Fishd_qOffal
annual_flux_results[197,1]<-Fishd_nqOffal
annual_flux_results[198,1]<-BenthsOffal
annual_flux_results[199,1]<-BenthcOffal
annual_flux_results[200,1]<-CarnzOffal
annual_flux_results[201,1]<-BirdOffal
annual_flux_results[202,1]<-SealOffal
annual_flux_results[203,1]<-CetaOffal
annual_flux_results[204,1]<-KelpOffal
annual_flux_results[205,1]<-FishpLand_processedwt
annual_flux_results[206,1]<-FishmLand_processedwt
annual_flux_results[207,1]<-FishdLand_processedwt
annual_flux_results[208,1]<-Fishd_qLand_processedwt
annual_flux_results[209,1]<-Fishd_nqLand_processedwt
annual_flux_results[210,1]<-BenthsLand_processedwt
annual_flux_results[211,1]<-BenthcLand_processedwt
annual_flux_results[212,1]<-CarnzLand_processedwt
annual_flux_results[213,1]<-BirdLand_processedwt
annual_flux_results[214,1]<-SealLand_processedwt
annual_flux_results[215,1]<-CetaLand_processedwt
annual_flux_results[216,1]<-KelpLand_processedwt
annual_flux_results[217,1]<-x_shallowprop
annual_flux_results[218,1]<-si_depth
annual_flux_results[219,1]<-so_depth
annual_flux_results[220,1]<-d_depth
annual_flux_results[221,1]<-x_area_s0
annual_flux_results[222,1]<-x_area_s1
annual_flux_results[223,1]<-x_area_s2
annual_flux_results[224,1]<-x_area_s3
annual_flux_results[225,1]<-x_area_d0
annual_flux_results[226,1]<-x_area_d1
annual_flux_results[227,1]<-x_area_d2
annual_flux_results[228,1]<-x_area_d3
annual_flux_results[229,1]<-x_depth_s1
annual_flux_results[230,1]<-x_depth_s2
annual_flux_results[231,1]<-x_depth_s3
annual_flux_results[232,1]<-x_depth_d1
annual_flux_results[233,1]<-x_depth_d2
annual_flux_results[234,1]<-x_depth_d3
annual_flux_results[235,1]<-x_poros_s1
annual_flux_results[236,1]<-x_poros_s2
annual_flux_results[237,1]<-x_poros_s3
annual_flux_results[238,1]<-x_poros_d1
annual_flux_results[239,1]<-x_poros_d2
annual_flux_results[240,1]<-x_poros_d3
annual_flux_results[,2]<-rep("mMN/whole_model_domain_(1m2)/y",240)
annual_flux_results[8:13,2]<-("mMN/whole_model_domain_(1m2)/summer_period_AMJJAS")
annual_flux_results[c(217,221:228,235:240),2]<-"dimensionless"
annual_flux_results[c(218:220,229:234),2]<-"m"
annual_flux_results[,3]<-c(
"DIN_inflow",
"DIN_outflow",
"Particulate_inflow",
"Particulate_outflow",
"Atmosphere_DIN_input",
"River_DIN_inflow",
"River_particulate_inflow",
"Summer_DIN_inflow",
"Summer_DIN_outflow",
"Summer_particulate_inflow",
"Summer_particulate_outflow",
"Summer_river_DIN_inflow",
"Summer_atmosphere_DIN_input",
"Vertical_nitrate_flux",
"Surface_horizontal_nitrate_flux",
"Net_import/export_flux_in_the_sediment",
"Beachcast_export_of_kelp_debris",
"DIN_Net_flux_offshore_to_inshore",
"Particulate_net_flux_offshore_to_inshore",
"Plank.fish_net_active_migration_offshore_to_inshore",
"Mig.fish_net_active_migration_offshore_to_inshore",
"Dem.fish_net_active_migration_offshore_to_inshore",
"Bird_net_active_migration_offshore_to_inshore",
"Seal_net_active_migration_offshore_to_inshore",
"Cetacean_net_active_migration_offshore_to_inshore",
"Mig.fish_net_migration_external_offshore",
"Mig.fish_annual_immigration",
"Mig.fish_annual_emigration",
"Phytoplankton_net_primary_production",
"Phytoplankton_new_production_(nitrate_drawdown)",
"Phytoplankton_new_production_(traditional)",
"Phytoplankton_new_production_(Heath&Beare)",
"Phytoplankton_nitrate_uptake",
"Phytoplankton_ammonia_uptake",
"Phytoplankton_fratio_(H&B/NetPP)",
"Phytoplankton_fratio_(traditional)",
"Kelp_nitrate_uptake",
"Kelp_ammonia_uptake",
"Kelp_gross_production",
"Phytoplankton_gross_production",
"Omniv.zooplankton_gross_production",
"Carniv.zooplankton_gross_production",
"Planktiv.fish_larvae_gross_production",
"Dem.fish_larvae_gross_production",
"Planktiv.fish_gross_production",
"Mig.fish_gross_production",
"Dem.fish_gross_production",
"Benthos_filt/dep_larvae_gross_production",
"Benthos_carn/scav_larvae_gross_production",
"Benthos_filt/dep_gross_production",
"Benthos_carn/scav_gross_production",
"Bird_gross_production",
"Seal_gross_production",
"Cetacean_gross_production",
"Omniv.zooplankton_net_production",
"Carniv.zooplankton_net_production",
"Planktiv.fish_larvae_net_production",
"Dem.fish_larvae_net_production",
"Planktiv.fish_net_production",
"Mig.fish_net_production",
"Dem.fish_net_production",
"Benthos_filt/dep_larvae_net_production",
"Benthos_carn/scav_larvae_net_production",
"Benthos_filt/dep_net_production",
"Benthos_carn/scav_net_production",
"Bird_net_production",
"Seal_net_production",
"Cetacean_net_production",
"Water_column_detritus_production",
"Sediment_detritus_production",
"Corpse_production",
"Flux_of_detritus_from_water_to_sediment",
"Flux_of_discards_to_corpses",
"Pelagic_fauna_ammonia_production",
"Benthic_fauna_ammonia_production",
"Water_column_detritus_mineralisation",
"Sediment_detritus_mineralisation",
"Water_column_nitrification",
"Sediment_nitrification",
"Water_column_denitrification",
"Sediment_denitrification",
"Sediment_to_water_ammonia_flux",
"Sediment_to_water_nitrate_flux",
"Flux_detritus_to_omniv.zooplankton",
"Flux_phytoplankton_to_omniv.zooplankton",
"Flux_benthosf/d.larvae_to_omniv.zooplankton",
"Flux_benthosc/s.larvae_to_omniv.zooplankton",
"Flux_omniv.zooplankton_to_carniv.zooplankton",
"Flux_plank.fish.larvae_to_carniv.zooplankton",
"Flux_dem.fish.larvae_to_carniv.zooplankton",
"Flux_benthosf/d.larvae_to_carniv.zooplankton",
"Flux_benthosc/s.larvae_to_carniv.zooplankton",
"Flux_omniv.zooplankton_to_plank.fish.larvae",
"Flux_benthosf/d.larvae_to_plank.fish.larvae",
"Flux_benthosc/s.larvae_to_plank.fish.larvae",
"Flux_omniv.zooplankton_to_dem.fish.larvae",
"Flux_benthosf/d.larvae_to_dem.fish.larvae",
"Flux_benthosc/s.larvae_to_dem.fish.larvae",
"Flux_omniv.zooplankton_to_plank.fish",
"Flux_carniv.zooplankton_to_plank.fish",
"Flux_plank.fish.larvae_to_plank.fish",
"Flux_dem.fish.larvae_to_plank.fish",
"Flux_benthosf/d.larvae_to_plank.fish",
"Flux_benthosc/s.larvae_to_plank.fish",
"Flux_omniv.zooplankton_to_mig.fish",
"Flux_carniv.zooplankton_to_mig.fish",
"Flux_plank.fish.larvae_to_mig.fish",
"Flux_dem.fish.larvae_to_mig.fish",
"Flux_benthosf/d.larvae_to_mig.fish",
"Flux_benthosc/s.larvae_to_mig.fish",
"Flux_corpses_to_dem.fish",
"Flux_discards_to_dem.fish",
"Flux_carniv.zooplankton_to_dem.fish",
"Flux_plank.fish.larvae_to_dem.fish",
"Flux_dem.fish.larvae_to_dem.fish",
"Flux_plank.fish_to_dem.fish",
"Flux_mig.fish_to_dem.fish",
"Flux_dem.fish_to_dem.fish",
"Flux_benthosf/d_to_dem.fish",
"Flux_benthosc/s_to_dem.fish",
"Flux_detritus_to_benthosf/d.larvae",
"Flux_phytoplankton_to_benthosf/d.larvae",
"Flux_detritus_to_benthosc/s.larvae",
"Flux_phytoplankton_to_benthosc/s.larvae",
"Flux_detritus_to_benthosf/d",
"Flux_sediment.detritus_to_benthosf/d",
"Flux_phytoplankton_to_benthosf/d",
"Flux_kelp.debris_to_benthosc/s",
"Flux_corpses_to_benthosc/s",
"Flux_kelp_to_benthosc/s",
"Flux_benthosf/d_to_benthosc/sc",
"Flux_corpses_to_birds",
"Flux_discards_to_birds",
#"Flux_ominiv.zooplankton_to_birds",
"Flux_carniv.zooplankton_to_birds",
"Flux_plank.fish_to_birds",
"Flux_mig.fish_to_birds",
"Flux_dem.fish_to_birds",
"Flux_benthosf/d_to_birds",
"Flux_benthosc/s_to_birds",
"Flux_corpses_to_seals",
"Flux_discards_to_seals",
"Flux_carniv.zooplankton_to_seals",
"Flux_plank.fish_to_seals",
"Flux_mig.fish_to_seals",
"Flux_dem.fish_to_seals",
"Flux_benthosf/d_to_seals",
"Flux_benthosc/s_to_seals",
"Flux_birds_to_seals",
"Flux_discards_to_cetaceans",
"Flux_ominiv.zooplankton_to_cetaceans",
"Flux_carniv.zooplankton_to_cetaceans",
"Flux_plank.fish_to_cetaceans",
"Flux_mig.fish_to_cetaceans",
"Flux_dem.fish_to_cetaceans",
"Flux_benthosf/d_to_cetaceans",
"Flux_benthosc/s_to_cetaceans",
"Flux_birds_to_cetaceans",
"Flux_seals_to_cetaceans",
"Net_production_of_all_secondary_and_higher_trophic_levels",
"Export_from_secondary_producers",
"Plank.fish_annual_spawning",
"Plank.fish_annual_recruitment",
"Dem.fish_annual_spawning",
"Dem.fish_annual_recruitment",
"Benthosf/d_annual_spawning",
"Benthosf/d_annual_recruitment",
"Benthosc/s_annual_spawning",
"Benthosc/sc_annual_recruitment",
"Plank.fish_landings_live_weight",
"Mig.fish_landings_live_weight",
"Dem.fish_landings_live_weight",
"Dem.fish_quota_limited_landings_live_weight",
"Dem.fish_non.quota_landings_live_weight",
"Benthosf/d_landings_live_weight",
"Benthosc/s_landings_live_weight",
"Carniv.zooplankton_landings_live_weight",
"Bird_landings_live_weight",
"Seal_landings_live_weight",
"Cetacean_landings_live_weight",
"Kelp_landings_live_weight",
"Plank.fish_discards",
"Mig.fish_discards",
"Dem.fish_discards",
"Dem.fish_quota_limited_discards",
"Dem.fish_non.quota_discards",
"Benthosf/d_discards",
"Benthosc/s_discards",
"Carniv.zooplankton_discards",
"Bird_discards",
"Seal_discards",
"Cetacean_discards",
"Kelp_discards",
"Plank.fish_offal",
"Mig.fish_offal",
"Dem.fish_offal",
"Dem.fish_quota_limited_offal",
"Dem.fish_non.quota_offal",
"Benthosf/d_offal",
"Benthosc/s_offal",
"Carniv.zooplankton_offal",
"Bird_offal",
"Seal_offal",
"Cetacean_offal",
"Kelp_offal",
"Plank.fish_landings_processed_weight",
"Mig.fish_landings_processed_weight",
"Dem.fish_landings_processed_weight",
"Dem.fish_quota_limited_landings_processed_weight",
"Dem.fish_non.quota_landings_processed_weight",
"Benthosf/d_landings_processed_weight",
"Benthosc/s_landings_processed_weight",
"Carniv.zooplankton_landings_processed_weight",
"Bird_landings_processed_weight",
"Seal_landings_processed_weight",
"Cetacean_landings_processed_weight",
"Kelp_landings_processed_weight",
"Area_proportion_of_inshore_zone",
"Thickness_of_inshore_surface_layer",
"Thickness_of_offshore_surface_layer",
"Thickness_of_offshore_deep_layer",
"Area_proportion_inshore_rock",
"Area_proportion_inshore_sediment_s1",
"Area_proportion_inshore_sediment_s2",
"Area_proportion_inshore_sediment_s3",
"Area_proportion_offshore_rock",
"Area_proportion_offshore_sediment_d1",
"Area_proportion_offshore_sediment_d2",
"Area_proportion_offshore_sediment_d3",
"Thickness_of_inshore_sediment_layer_s1",
"Thickness_of_inshore_sediment_layer_s2",
"Thickness_of_inshore_sediment_layer_s3",
"Thickness_of_offshore_sediment_layer_d1",
"Thickness_of_offshore_sediment_layer_d2",
"Thickness_of_offshore_sediment_layer_d3",
"Porosity_of_inshore_sediment_layer_s1",
"Porosity_of_inshore_sediment_layer_s2",
"Porosity_of_inshore_sediment_layer_s3",
"Porosity_of_offshore_sediment_layer_d1",
"Porosity_of_offshore_sediment_layer_d2",
"Porosity_of_offshore_sediment_layer_d3")
names(annual_flux_results)<-c("Model_annual_flux","Units","Description")
#annual_flux_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_annualresults", identifier)
writecsv(annual_flux_results, filename, row.names=FALSE)
list(
mass_results = mass_results,
maxmass_results = maxmass_results,
minmass_results = minmass_results,
annual_flux_results = annual_flux_results
)
}
strathclyde-marine-resource-modelling/StrathE2E2 documentation built on June 21, 2019, 2:43 a.m.
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#
# derive_annual_results_inshore
#
#' derive set of results for inshore only and write to files
#'
#' @param model model object
#' @param build model build object
#' @param output model output
#' @param aggregates aggregated model output
#'
#' @export
#
derive_annual_results_inshore <- function(model, build, output, aggregates) {
# Unpack:
setup <- elt(model, "setup")
identifier <- elt(setup, "model.ident")
resultsdir <- elt(setup, "resultsdir")
run <- elt(build, "run")
ndays <- elt(run, "ndays")
nyears <- elt(run, "nyears")
data <- elt(model, "data")
physical.parms <- elt(data, "physical.parameters")
# extract physical parameters:
so_depth <- elt(physical.parms, "so_depth")
d_depth <- elt(physical.parms, "d_depth")
si_depth <- elt(physical.parms, "si_depth")
x_depth_s1 <- elt(physical.parms, "x_depth_s1")
x_depth_s2 <- elt(physical.parms, "x_depth_s2")
x_depth_s3 <- elt(physical.parms, "x_depth_s3")
x_depth_d1 <- elt(physical.parms, "x_depth_d1")
x_depth_d2 <- elt(physical.parms, "x_depth_d2")
x_depth_d3 <- elt(physical.parms, "x_depth_d3")
x_area_s0 <- elt(physical.parms, "x_area_s0")
x_area_s1 <- elt(physical.parms, "x_area_s1")
x_area_s2 <- elt(physical.parms, "x_area_s2")
x_area_s3 <- elt(physical.parms, "x_area_s3")
x_area_d0 <- elt(physical.parms, "x_area_d0")
x_area_d1 <- elt(physical.parms, "x_area_d1")
x_area_d2 <- elt(physical.parms, "x_area_d2")
x_area_d3 <- elt(physical.parms, "x_area_d3")
x_poros_s1 <- elt(physical.parms, "x_poros_s1")
x_poros_s2 <- elt(physical.parms, "x_poros_s2")
x_poros_s3 <- elt(physical.parms, "x_poros_s3")
x_poros_d1 <- elt(physical.parms, "x_poros_d1")
x_poros_d2 <- elt(physical.parms, "x_poros_d2")
x_poros_d3 <- elt(physical.parms, "x_poros_d3")
x_shallowprop <- elt(physical.parms, "x_shallowprop")
# extract output:
detritus_si <- elt(output, "detritus_si")
xR_detritus_s1 <- elt(output, "xR_detritus_s1")
xR_detritus_s2 <- elt(output, "xR_detritus_s2")
xR_detritus_s3 <- elt(output, "xR_detritus_s3")
discard_i <- elt(output, "discard_i")
kelpdebris <- elt(output, "kelpdebris")
ammonia_si <- elt(output, "ammonia_si")
nitrate_si <- elt(output, "nitrate_si")
kelpN <- elt(output, "kelpN")
phyt_si <- elt(output, "phyt_si")
herb_i <- elt(output, "herb_i")
carn_i <- elt(output, "carn_i")
benthslar_i <- elt(output, "benthslar_i")
benths_i <- elt(output, "benths_i")
benthclar_i <- elt(output, "benthclar_i")
benthc_i <- elt(output, "benthc_i")
fishplar_i <- elt(output, "fishplar_i")
fishp_i <- elt(output, "fishp_i")
fishm_i <- elt(output, "fishm_i")
fishdlar_i <- elt(output, "fishdlar_i")
fishd_i <- elt(output, "fishd_i")
bird_i <- elt(output, "bird_i")
seal_i <- elt(output, "seal_i")
ceta_i <- elt(output, "ceta_i")
fluxAMMinflow_i <- elt(output, "fluxAMMinflow_i")
fluxNITinflow_i <- elt(output, "fluxNITinflow_i")
fluxAMMoutflow_i <- elt(output, "fluxAMMoutflow_i")
fluxNIToutflow_i <- elt(output, "fluxNIToutflow_i")
fluxPHYTinflow_i <- elt(output, "fluxPHYTinflow_i")
fluxDETinflow_i <- elt(output, "fluxDETinflow_i")
fluxPHYToutflow_i <- elt(output, "fluxPHYToutflow_i")
fluxDEToutflow_i <- elt(output, "fluxDEToutflow_i")
atmosAMMinput_i <- elt(output, "atmosAMMinput_i")
atmosNITinput_i <- elt(output, "atmosNITinput_i")
rivAMMinflow <- elt(output, "rivAMMinflow")
rivNITinflow <- elt(output, "rivNITinflow")
rivPARTinflow <- elt(output, "rivPARTinflow")
fluxsedboundary_i <- elt(output, "fluxsedboundary_i")
fluxkelpdebris_beachexport <- elt(output, "fluxkelpdebris_beachexport")
netpprod_i <- elt(output, "netpprod_i")
nitrate_d <- elt(output, "nitrate_d")
PNP_i <- elt(output, "PNP_i")
fluxwcnit_phyt_i <- elt(output, "fluxwcnit_phyt_i")
fluxwcamm_phyt_i <- elt(output, "fluxwcamm_phyt_i")
fluxwcnit_kelp <- elt(output, "fluxwcnit_kelp")
fluxwcamm_kelp <- elt(output, "fluxwcamm_kelp")
kelpNprod_i <- elt(output, "kelpNprod_i")
phytgrossprod_i <- elt(output, "phytgrossprod_i")
herbgrossprod_i <- elt(output, "herbgrossprod_i")
carngrossprod_i <- elt(output, "carngrossprod_i")
pfishlargrossprod_i <- elt(output, "pfishlargrossprod_i")
dfishlargrossprod_i <- elt(output, "dfishlargrossprod_i")
pfishgrossprod_i <- elt(output, "pfishgrossprod_i")
mfishgrossprod_i <- elt(output, "mfishgrossprod_i")
dfishgrossprod_i <- elt(output, "dfishgrossprod_i")
benthslargrossprod_i <- elt(output, "benthslargrossprod_i")
benthclargrossprod_i <- elt(output, "benthclargrossprod_i")
benthsgrossprod_i <- elt(output, "benthsgrossprod_i")
benthcgrossprod_i <- elt(output, "benthcgrossprod_i")
birdgrossprod_i <- elt(output, "birdgrossprod_i")
sealgrossprod_i <- elt(output, "sealgrossprod_i")
cetagrossprod_i <- elt(output, "cetagrossprod_i")
herbnetprod_i <- elt(output, "herbnetprod_i")
carnnetprod_i <- elt(output, "carnnetprod_i")
pfishlarnetprod_i <- elt(output, "pfishlarnetprod_i")
dfishlarnetprod_i <- elt(output, "dfishlarnetprod_i")
pfishnetprod_i <- elt(output, "pfishnetprod_i")
mfishnetprod_i <- elt(output, "mfishnetprod_i")
dfishnetprod_i <- elt(output, "dfishnetprod_i")
benthslarnetprod_i <- elt(output, "benthslarnetprod_i")
benthclarnetprod_i <- elt(output, "benthclarnetprod_i")
benthsnetprod_i <- elt(output, "benthsnetprod_i")
benthcnetprod_i <- elt(output, "benthcnetprod_i")
birdnetprod_i <- elt(output, "birdnetprod_i")
sealnetprod_i <- elt(output, "sealnetprod_i")
cetanetprod_i <- elt(output, "cetanetprod_i")
fluxkelp_kelpdebris <- elt(output, "fluxkelp_kelpdebris")
fluxkelp_benthc <- elt(output, "fluxkelp_benthc")
fluxkelpdebris_benthc <- elt(output, "fluxkelpdebris_benthc")
landp_i <- elt(output, "landp_i")
landm_i <- elt(output, "landm_i")
landd_quota_i <- elt(output, "landd_quota_i")
landd_nonquota_i <- elt(output, "landd_nonquota_i")
landsb_i <- elt(output, "landsb_i")
landcb_i <- elt(output, "landcb_i")
landcz_i <- elt(output, "landcz_i")
landbd_i <- elt(output, "landbd_i")
landsl_i <- elt(output, "landsl_i")
landct_i <- elt(output, "landct_i")
landkp_i <- elt(output, "landkp_i")
discpel_i <- elt(output, "discpel_i")
discmig_i <- elt(output, "discmig_i")
discdem_quota_i <- elt(output, "discdem_quota_i")
discdem_nonquota_i <- elt(output, "discdem_nonquota_i")
discsb_i <- elt(output, "discsb_i")
disccb_i <- elt(output, "disccb_i")
disccz_i <- elt(output, "disccz_i")
discbd_i <- elt(output, "discbd_i")
discsl_i <- elt(output, "discsl_i")
discct_i <- elt(output, "discct_i")
disckp_i <- elt(output, "disckp_i")
offalpel_i <- elt(output, "offalpel_i")
offalmig_i <- elt(output, "offalmig_i")
offaldem_quota_i <- elt(output, "offaldem_quota_i")
offaldem_nonquota_i <- elt(output, "offaldem_nonquota_i")
offalsb_i <- elt(output, "offalsb_i")
offalcb_i <- elt(output, "offalcb_i")
offalcz_i <- elt(output, "offalcz_i")
offalbd_i <- elt(output, "offalbd_i")
offalsl_i <- elt(output, "offalsl_i")
offalct_i <- elt(output, "offalct_i")
offalkp_i <- elt(output, "offalkp_i")
# extract aggregates:
x_detritus_i <- elt(aggregates, "x_detritus_i")
corpse_i <- elt(aggregates, "corpse_i")
x_ammonia_i <- elt(aggregates, "x_ammonia_i")
x_nitrate_i <- elt(aggregates, "x_nitrate_i")
totalN_i <- elt(aggregates, "totalN_i")
DIN_NET_flux_o_i <- elt(aggregates, "DIN_NET_flux_o_i")
PART_NET_flux_o_i <- elt(aggregates, "PART_NET_flux_o_i")
NET_activemigpelfish_o_i<- elt(aggregates, "NET_activemigpelfish_o_i")
NET_activemigmigfish_o_i<- elt(aggregates, "NET_activemigmigfish_o_i")
NET_activemigdemfish_o_i<- elt(aggregates, "NET_activemigdemfish_o_i")
NET_activemigbird_o_i <- elt(aggregates, "NET_activemigbird_o_i")
NET_activemigseal_o_i <- elt(aggregates, "NET_activemigseal_o_i")
NET_activemigceta_o_i <- elt(aggregates, "NET_activemigceta_o_i")
landd_i <- elt(aggregates, "landd_i")
discdem_i <- elt(aggregates, "discdem_i")
offaldem_i <- elt(aggregates, "offaldem_i")
#Derive a load of stuff from the output and write to a file
#Extract annual average biomass in the final year for the OFFSHORE model domain
aamass_s_detritus<-mean(detritus_si[((nyears-1)*360+1):ndays])
#aamass_d_detritus<-mean(detritus_d[((nyears-1)*360+1):ndays])
aamass_d_detritus<-NA
aamass_x_detritus<-mean(x_detritus_i[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamass_xR_detritus<-mean(xR_detritus_s1[((nyears-1)*360+1):ndays]
+ xR_detritus_s2[((nyears-1)*360+1):ndays]
+ xR_detritus_s3[((nyears-1)*360+1):ndays])
aamass_discard<-mean(discard_i[((nyears-1)*360+1):ndays])
aamass_corpse<-mean(corpse_i[((nyears-1)*360+1):ndays])
aamass_kelpdebris<-mean(kelpdebris[((nyears-1)*360+1):ndays])
#aamass_kelpdebris<-NA
aamass_s_ammonia<-mean(ammonia_si[((nyears-1)*360+1):ndays])
#aamass_d_ammonia<-mean(ammonia_d[((nyears-1)*360+1):ndays])
aamass_d_ammonia<-NA
aamass_x_ammonia<-mean(x_ammonia_i[((nyears-1)*360+1):ndays])
aamass_s_nitrate<-mean(nitrate_si[((nyears-1)*360+1):ndays])
#aamass_d_nitrate<-mean(nitrate_d[((nyears-1)*360+1):ndays])
aamass_d_nitrate<-NA
aamass_x_nitrate<-mean(x_nitrate_i[((nyears-1)*360+1):ndays])
aamass_kelpN<-mean(kelpN[((nyears-1)*360+1):ndays])
#aamass_kelpN<-NA
aamass_s_phyt<-mean(phyt_si[((nyears-1)*360+1):ndays])
#aamass_d_phyt<-mean(phyt_d[((nyears-1)*360+1):ndays])
aamass_d_phyt<-NA
aamass_herb<-mean(herb_i[((nyears-1)*360+1):ndays])
aamass_carn<-mean(carn_i[((nyears-1)*360+1):ndays])
aamass_benthslar<-mean(benthslar_i[((nyears-1)*360+1):ndays])
aamass_benths<-mean(benths_i[((nyears-1)*360+1):ndays])
aamass_benthclar<-mean(benthclar_i[((nyears-1)*360+1):ndays])
aamass_benthc<-mean(benthc_i[((nyears-1)*360+1):ndays])
aamass_fishplar<-mean(fishplar_i[((nyears-1)*360+1):ndays])
aamass_fishp<-mean(fishp_i[((nyears-1)*360+1):ndays])
aamass_fishm<-mean(fishm_i[((nyears-1)*360+1):ndays])
aamass_fishdlar<-mean(fishdlar_i[((nyears-1)*360+1):ndays])
aamass_fishd<-mean(fishd_i[((nyears-1)*360+1):ndays])
aamass_bird<-mean(bird_i[((nyears-1)*360+1):ndays])
aamass_seal<-mean(seal_i[((nyears-1)*360+1):ndays])
aamass_ceta<-mean(ceta_i[((nyears-1)*360+1):ndays])
aamass_totalN<-mean(totalN_i[((nyears-1)*360+1):ndays])
#.........................................
mass_results<-data.frame(rep(0,55))
mass_results[1,1]<-aamass_s_detritus
mass_results[2,1]<-aamass_d_detritus
mass_results[3,1]<-aamass_x_detritus
mass_results[4,1]<-aamass_xR_detritus
mass_results[5,1]<-aamass_discard
mass_results[6,1]<-aamass_corpse
mass_results[7,1]<-aamass_kelpdebris
mass_results[8,1]<-aamass_s_ammonia
mass_results[9,1]<-aamass_d_ammonia
mass_results[10,1]<-aamass_x_ammonia
mass_results[11,1]<-aamass_s_nitrate
mass_results[12,1]<-aamass_d_nitrate
mass_results[13,1]<-aamass_x_nitrate
mass_results[14,1]<-aamass_kelpN
mass_results[15,1]<-aamass_s_phyt
mass_results[16,1]<-aamass_d_phyt
mass_results[17,1]<-aamass_herb
mass_results[18,1]<-aamass_carn
mass_results[19,1]<-aamass_benthslar
mass_results[20,1]<-aamass_benths
mass_results[21,1]<-aamass_benthclar
mass_results[22,1]<-aamass_benthc
mass_results[23,1]<-aamass_fishplar
mass_results[24,1]<-aamass_fishp
mass_results[25,1]<-aamass_fishm
mass_results[26,1]<-aamass_fishdlar
mass_results[27,1]<-aamass_fishd
mass_results[28,1]<-aamass_bird
mass_results[29,1]<-aamass_seal
mass_results[30,1]<-aamass_ceta
mass_results[31,1]<-aamass_totalN
mass_results[32,1]<-x_shallowprop
mass_results[33,1]<-si_depth
mass_results[34,1]<-so_depth
mass_results[35,1]<-d_depth
mass_results[36,1]<-x_area_s0
mass_results[37,1]<-x_area_s1
mass_results[38,1]<-x_area_s2
mass_results[39,1]<-x_area_s3
mass_results[40,1]<-x_area_d0
mass_results[41,1]<-x_area_d1
mass_results[42,1]<-x_area_d2
mass_results[43,1]<-x_area_d3
mass_results[44,1]<-x_depth_s1
mass_results[45,1]<-x_depth_s2
mass_results[46,1]<-x_depth_s3
mass_results[47,1]<-x_depth_d1
mass_results[48,1]<-x_depth_d2
mass_results[49,1]<-x_depth_d3
mass_results[50,1]<-x_poros_s1
mass_results[51,1]<-x_poros_s2
mass_results[52,1]<-x_poros_s3
mass_results[53,1]<-x_poros_d1
mass_results[54,1]<-x_poros_d2
mass_results[55,1]<-x_poros_d3
mass_results[,2]<-"mMN_in_the_whole model_domain_(1m2)"
mass_results[c(32,36:43,50:55),2]<-"dimensionless"
mass_results[c(33:35,44:49),2]<-"m"
mass_results[,3]<-c(
"Surface_layer_detritus",
"Deep_layer_detritus",
"Sediment_labile_plus_refractory_detritus",
"Sediment_refractory_detritus",
"Fishery_discards",
"Corpses",
"Kelp_debris",
"Surface_layer_ammonia",
"Deep_layer_ammonia",
"Sediment_porewater_ammonia",
"Surface_layer_nitrate",
"Deep_layer_nitrate",
"Sediment_porewater_nitrate",
"Kelp_nitrogen",
"Surface_layer_phytoplankton",
"Deep_layer_phytoplankton",
"Omnivorous_zooplankton",
"Carnivorous_zooplankton",
"Benthos_susp/dep_feeders_larvae",
"Benthos_susp/dep_feeders",
"Benthos_carn/scav_feeders_larvae",
"Benthos_carn/scav_feeders",
"Planktivorous_fish_larvae",
"Planktivorous_fish",
"Migratory_fish",
"Demersal_fish_larvae",
"Demersal_fish",
"Bird",
"Seals",
"Cetaceans",
"Total_nitrogen_mass",
"Area_proportion_of_inshore_zone",
"Thickness_of_inshore_surface_layer",
"Thickness_of_offshore_surface_layer",
"Thickness_of_offshore_deep_layer",
"Area_proportion_inshore_rock",
"Area_proportion_inshore_sediment_s1",
"Area_proportion_inshore_sediment_s2",
"Area_proportion_inshore_sediment_s3",
"Area_proportion_offshore_rock",
"Area_proportion_offshore_sediment_d1",
"Area_proportion_offshore_sediment_d2",
"Area_proportion_offshore_sediment_d3",
"Thickness_of_inshore_sediment_layer_s1",
"Thickness_of_inshore_sediment_layer_s2",
"Thickness_of_inshore_sediment_layer_s3",
"Thickness_of_offshore_sediment_layer_d1",
"Thickness_of_offshore_sediment_layer_d2",
"Thickness_of_offshore_sediment_layer_d3",
"Porosity_of_inshore_sediment_layer_s1",
"Porosity_of_inshore_sediment_layer_s2",
"Porosity_of_inshore_sediment_layer_s3",
"Porosity_of_offshore_sediment_layer_d1",
"Porosity_of_offshore_sediment_layer_d2",
"Porosity_of_offshore_sediment_layer_d3")
colnames(mass_results)<-c("Model_annual_mean","Units","Description")
mass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_anav_biomass", identifier)
writecsv(mass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#copy the mass_results dataframe as a template for the annual maximum data
maxmass_results<-mass_results
maxmass_results[1:31,1]<-0
aamaxmass_s_detritus<-max(detritus_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_detritus<-max(detritus_d[((nyears-1)*360+1):ndays])
aamaxmass_d_detritus<-NA
aamaxmass_x_detritus<-max(x_detritus_i[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamaxmass_xR_detritus<-max(xR_detritus_s1[((nyears-1)*360+1):ndays]
+ xR_detritus_s2[((nyears-1)*360+1):ndays]
+ xR_detritus_s3[((nyears-1)*360+1):ndays])
aamaxmass_discard<-max(discard_i[((nyears-1)*360+1):ndays])
aamaxmass_corpse<-max(corpse_i[((nyears-1)*360+1):ndays])
aamaxmass_kelpdebris<-max(kelpdebris[((nyears-1)*360+1):ndays])
#aamaxmass_kelpdebris<-NA
aamaxmass_s_ammonia<-max(ammonia_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_ammonia<-max(ammonia_d[((nyears-1)*360+1):ndays])
aamaxmass_d_ammonia<-NA
aamaxmass_x_ammonia<-max(x_ammonia_i[((nyears-1)*360+1):ndays])
aamaxmass_s_nitrate<-max(nitrate_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_nitrate<-max(nitrate_d[((nyears-1)*360+1):ndays])
aamaxmass_d_nitrate<-NA
aamaxmass_x_nitrate<-max(x_nitrate_i[((nyears-1)*360+1):ndays])
aamaxmass_kelpN<-max(kelpN[((nyears-1)*360+1):ndays])
#aamaxmass_kelpN<-NA
aamaxmass_s_phyt<-max(phyt_si[((nyears-1)*360+1):ndays])
#aamaxmass_d_phyt<-max(phyt_d[((nyears-1)*360+1):ndays])
aamaxmass_d_phyt<-NA
aamaxmass_herb<-max(herb_i[((nyears-1)*360+1):ndays])
aamaxmass_carn<-max(carn_i[((nyears-1)*360+1):ndays])
aamaxmass_benthslar<-max(benthslar_i[((nyears-1)*360+1):ndays])
aamaxmass_benths<-max(benths_i[((nyears-1)*360+1):ndays])
aamaxmass_benthclar<-max(benthclar_i[((nyears-1)*360+1):ndays])
aamaxmass_benthc<-max(benthc_i[((nyears-1)*360+1):ndays])
aamaxmass_fishplar<-max(fishplar_i[((nyears-1)*360+1):ndays])
aamaxmass_fishp<-max(fishp_i[((nyears-1)*360+1):ndays])
aamaxmass_fishm<-max(fishm_i[((nyears-1)*360+1):ndays])
aamaxmass_fishdlar<-max(fishdlar_i[((nyears-1)*360+1):ndays])
aamaxmass_fishd<-max(fishd_i[((nyears-1)*360+1):ndays])
aamaxmass_bird<-max(bird_i[((nyears-1)*360+1):ndays])
aamaxmass_seal<-max(seal_i[((nyears-1)*360+1):ndays])
aamaxmass_ceta<-max(ceta_i[((nyears-1)*360+1):ndays])
aamaxmass_totalN<-max(totalN_i[((nyears-1)*360+1):ndays])
#..........................................
maxmass_results[1,1]<-aamaxmass_s_detritus
maxmass_results[2,1]<-aamaxmass_d_detritus
maxmass_results[3,1]<-aamaxmass_x_detritus
maxmass_results[4,1]<-aamaxmass_xR_detritus
maxmass_results[5,1]<-aamaxmass_discard
maxmass_results[6,1]<-aamaxmass_corpse
maxmass_results[7,1]<-aamaxmass_kelpdebris
maxmass_results[8,1]<-aamaxmass_s_ammonia
maxmass_results[9,1]<-aamaxmass_d_ammonia
maxmass_results[10,1]<-aamaxmass_x_ammonia
maxmass_results[11,1]<-aamaxmass_s_nitrate
maxmass_results[12,1]<-aamaxmass_d_nitrate
maxmass_results[13,1]<-aamaxmass_x_nitrate
maxmass_results[14,1]<-aamaxmass_kelpN
maxmass_results[15,1]<-aamaxmass_s_phyt
maxmass_results[16,1]<-aamaxmass_d_phyt
maxmass_results[17,1]<-aamaxmass_herb
maxmass_results[18,1]<-aamaxmass_carn
maxmass_results[19,1]<-aamaxmass_benthslar
maxmass_results[20,1]<-aamaxmass_benths
maxmass_results[21,1]<-aamaxmass_benthclar
maxmass_results[22,1]<-aamaxmass_benthc
maxmass_results[23,1]<-aamaxmass_fishplar
maxmass_results[24,1]<-aamaxmass_fishp
maxmass_results[25,1]<-aamaxmass_fishm
maxmass_results[26,1]<-aamaxmass_fishdlar
maxmass_results[27,1]<-aamaxmass_fishd
maxmass_results[28,1]<-aamaxmass_bird
maxmass_results[29,1]<-aamaxmass_seal
maxmass_results[30,1]<-aamaxmass_ceta
maxmass_results[31,1]<-aamaxmass_totalN
colnames(maxmass_results)<-c("Model_annual_maximum","Units","Description")
maxmass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_maximum_biomass", identifier)
writecsv(maxmass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#copy the mass_results dataframe as a template for the annual minimum data
minmass_results<-mass_results
minmass_results[1:31,1]<-0
aaminmass_s_detritus<-min(detritus_si[((nyears-1)*360+1):ndays])
#aaminmass_d_detritus<-min(detritus_d[((nyears-1)*360+1):ndays])
aaminmass_d_detritus<-NA
aaminmass_x_detritus<-min(x_detritus_i[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aaminmass_xR_detritus<-min(xR_detritus_s1[((nyears-1)*360+1):ndays]
+ xR_detritus_s2[((nyears-1)*360+1):ndays]
+ xR_detritus_s3[((nyears-1)*360+1):ndays])
aaminmass_discard<-min(discard_i[((nyears-1)*360+1):ndays])
aaminmass_corpse<-min(corpse_i[((nyears-1)*360+1):ndays])
aaminmass_kelpdebris<-min(kelpdebris[((nyears-1)*360+1):ndays])
#aaminmass_kelpdebris<-NA
aaminmass_s_ammonia<-min(ammonia_si[((nyears-1)*360+1):ndays])
#aaminmass_d_ammonia<-min(ammonia_d[((nyears-1)*360+1):ndays])
aaminmass_d_ammonia<-NA
aaminmass_x_ammonia<-min(x_ammonia_i[((nyears-1)*360+1):ndays])
aaminmass_s_nitrate<-min(nitrate_si[((nyears-1)*360+1):ndays])
#aaminmass_d_nitrate<-min(nitrate_d[((nyears-1)*360+1):ndays])
aaminmass_d_nitrate<-NA
aaminmass_x_nitrate<-min(x_nitrate_i[((nyears-1)*360+1):ndays])
aaminmass_kelpN<-min(kelpN[((nyears-1)*360+1):ndays])
#aaminmass_kelpN<-NA
aaminmass_s_phyt<-min(phyt_si[((nyears-1)*360+1):ndays])
#aaminmass_d_phyt<-min(phyt_d[((nyears-1)*360+1):ndays])
aaminmass_d_phyt<-NA
aaminmass_herb<-min(herb_i[((nyears-1)*360+1):ndays])
aaminmass_carn<-min(carn_i[((nyears-1)*360+1):ndays])
aaminmass_benthslar<-min(benthslar_i[((nyears-1)*360+1):ndays])
aaminmass_benths<-min(benths_i[((nyears-1)*360+1):ndays])
aaminmass_benthclar<-min(benthclar_i[((nyears-1)*360+1):ndays])
aaminmass_benthc<-min(benthc_i[((nyears-1)*360+1):ndays])
aaminmass_fishplar<-min(fishplar_i[((nyears-1)*360+1):ndays])
aaminmass_fishp<-min(fishp_i[((nyears-1)*360+1):ndays])
aaminmass_fishm<-min(fishm_i[((nyears-1)*360+1):ndays])
aaminmass_fishdlar<-min(fishdlar_i[((nyears-1)*360+1):ndays])
aaminmass_fishd<-min(fishd_i[((nyears-1)*360+1):ndays])
aaminmass_bird<-min(bird_i[((nyears-1)*360+1):ndays])
aaminmass_seal<-min(seal_i[((nyears-1)*360+1):ndays])
aaminmass_ceta<-min(ceta_i[((nyears-1)*360+1):ndays])
aaminmass_totalN<-min(totalN_i[((nyears-1)*360+1):ndays])
#..........................................
minmass_results[1,1]<-aaminmass_s_detritus
minmass_results[2,1]<-aaminmass_d_detritus
minmass_results[3,1]<-aaminmass_x_detritus
minmass_results[4,1]<-aaminmass_xR_detritus
minmass_results[5,1]<-aaminmass_discard
minmass_results[6,1]<-aaminmass_corpse
minmass_results[7,1]<-aaminmass_kelpdebris
minmass_results[8,1]<-aaminmass_s_ammonia
minmass_results[9,1]<-aaminmass_d_ammonia
minmass_results[10,1]<-aaminmass_x_ammonia
minmass_results[11,1]<-aaminmass_s_nitrate
minmass_results[12,1]<-aaminmass_d_nitrate
minmass_results[13,1]<-aaminmass_x_nitrate
minmass_results[14,1]<-aaminmass_kelpN
minmass_results[15,1]<-aaminmass_s_phyt
minmass_results[16,1]<-aaminmass_d_phyt
minmass_results[17,1]<-aaminmass_herb
minmass_results[18,1]<-aaminmass_carn
minmass_results[19,1]<-aaminmass_benthslar
minmass_results[20,1]<-aaminmass_benths
minmass_results[21,1]<-aaminmass_benthclar
minmass_results[22,1]<-aaminmass_benthc
minmass_results[23,1]<-aaminmass_fishplar
minmass_results[24,1]<-aaminmass_fishp
minmass_results[25,1]<-aaminmass_fishm
minmass_results[26,1]<-aaminmass_fishdlar
minmass_results[27,1]<-aaminmass_fishd
minmass_results[28,1]<-aaminmass_bird
minmass_results[29,1]<-aaminmass_seal
minmass_results[30,1]<-aaminmass_ceta
minmass_results[31,1]<-aaminmass_totalN
colnames(minmass_results)<-c("Model_annual_minimum","Units","Description")
minmass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_minimum_biomass", identifier)
writecsv(minmass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#Extract all of the derived rate variables for the final year
#!!!!!!
DINinflow<-(fluxAMMinflow_i[ndays]-fluxAMMinflow_i[((nyears-1)*360+1)]) + (fluxNITinflow_i[ndays]-fluxNITinflow_i[((nyears-1)*360+1)])
DINoutflow<-(fluxAMMoutflow_i[ndays]-fluxAMMoutflow_i[((nyears-1)*360+1)]) + (fluxNIToutflow_i[ndays]-fluxNIToutflow_i[((nyears-1)*360+1)])
PARTinflow<-(fluxPHYTinflow_i[ndays]-fluxPHYTinflow_i[((nyears-1)*360+1)]) + (fluxDETinflow_i[ndays]-fluxDETinflow_i[((nyears-1)*360+1)])
PARToutflow<-(fluxPHYToutflow_i[ndays]-fluxPHYToutflow_i[((nyears-1)*360+1)]) + (fluxDEToutflow_i[ndays]-fluxDEToutflow_i[((nyears-1)*360+1)])
atmosphereDINinput<-(atmosAMMinput_i[ndays]-atmosAMMinput_i[((nyears-1)*360+1)]) + (atmosNITinput_i[ndays]-atmosNITinput_i[((nyears-1)*360+1)])
riverDINinflow<-(rivAMMinflow[ndays]-rivAMMinflow[((nyears-1)*360+1)]) + (rivNITinflow[ndays]-rivNITinflow[((nyears-1)*360+1)])
riverPARTinflow<-rivPARTinflow[ndays]-rivPARTinflow[((nyears-1)*360+1)]
#riverDINinflow<-0
#riverPARTinflow<-0
#!!!!!!
sumDINinflow<-(fluxAMMinflow_i[ndays-90]-fluxAMMinflow_i[((nyears-1)*360+1+89)]) + (fluxNITinflow_i[ndays-90]-fluxNITinflow_i[((nyears-1)*360+1+89)])
sumDINoutflow<-(fluxAMMoutflow_i[ndays-90]-fluxAMMoutflow_i[((nyears-1)*360+1+89)]) + (fluxNIToutflow_i[ndays-90]-fluxNIToutflow_i[((nyears-1)*360+1+89)])
sumPARTinflow<-(fluxPHYTinflow_i[ndays-90]-fluxPHYTinflow_i[((nyears-1)*360+1+89)]) + (fluxDETinflow_i[ndays-90]-fluxDETinflow_i[((nyears-1)*360+1+89)])
sumPARToutflow<-(fluxPHYToutflow_i[ndays-90]-fluxPHYToutflow_i[((nyears-1)*360+1+89)]) + (fluxDEToutflow_i[ndays-90]-fluxDEToutflow_i[((nyears-1)*360+1+89)])
sumriverDINinflow<-(rivAMMinflow[ndays-90]-rivAMMinflow[((nyears-1)*360+1+89)]) + (rivNITinflow[ndays-90]-rivNITinflow[((nyears-1)*360+1+89)])
sumatmosDINinput<-(atmosAMMinput_i[ndays-90]-atmosAMMinput_i[((nyears-1)*360+1+89)]) + (atmosNITinput_i[ndays-90]-atmosNITinput_i[((nyears-1)*360+1+89)])
#surfvertnitflux<-vertnitflux[ndays]-vertnitflux[((nyears-1)*360+1)]
surfvertnitflux<-NA
#surfhoriznitflux<-horiznitflux[ndays]-horiznitflux[((nyears-1)*360+1)]
surfhoriznitflux<-NA
#!!!!!!
Flux_sedboundary <- (fluxsedboundary_i[ndays]-fluxsedboundary_i[((nyears-1)*360+1)])
kelp_beachcast<-((fluxkelpdebris_beachexport[ndays]-fluxkelpdebris_beachexport[((nyears-1)*360+1)]))
DIN_NET_flux_o_i <- DIN_NET_flux_o_i[ndays]-DIN_NET_flux_o_i[((nyears-1)*360+1)]
PART_NET_flux_o_i <- PART_NET_flux_o_i[ndays]-PART_NET_flux_o_i[((nyears-1)*360+1)]
NET_activemigpelfish_o_i <- NET_activemigpelfish_o_i[ndays]-NET_activemigpelfish_o_i[((nyears-1)*360+1)]
NET_activemigmigfish_o_i <- NET_activemigmigfish_o_i[ndays]-NET_activemigmigfish_o_i[((nyears-1)*360+1)]
NET_activemigdemfish_o_i <- NET_activemigdemfish_o_i[ndays]-NET_activemigdemfish_o_i[((nyears-1)*360+1)]
NET_activemigbird_o_i <- NET_activemigbird_o_i[ndays]-NET_activemigbird_o_i[((nyears-1)*360+1)]
NET_activemigseal_o_i <- NET_activemigseal_o_i[ndays]-NET_activemigseal_o_i[((nyears-1)*360+1)]
NET_activemigceta_o_i <- NET_activemigceta_o_i[ndays]-NET_activemigceta_o_i[((nyears-1)*360+1)]
#NET_mfish_ext_o <- NET_mfish_ext_o[ndays]-NET_mfish_ext_o[((nyears-1)*360+1)]
NET_mfish_ext_o<-NA
#Mfish_annual_imig <- mfish_imigration[ndays]-mfish_imigration[((nyears-1)*360+1)]
#Mfish_annual_emig <- mfish_emigration[ndays]-mfish_emigration[((nyears-1)*360+1)]
Mfish_annual_imig <- NA
Mfish_annual_emig <- NA
NETPrimaryP<-netpprod_i[ndays]-netpprod_i[((nyears-1)*360+1)]
MMP<-(max(nitrate_si[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays])) - (min(nitrate_si[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays]))
PNP<-PNP_i[ndays]-PNP_i[((nyears-1)*360+1)]
PhytNitUp<-fluxwcnit_phyt_i[ndays]-fluxwcnit_phyt_i[((nyears-1)*360+1)]
PhytAmmUp<-fluxwcamm_phyt_i[ndays]-fluxwcamm_phyt_i[((nyears-1)*360+1)]
NewP<-MMP+sumriverDINinflow+sumatmosDINinput+sumDINinflow-sumDINoutflow
fratio<-NewP/NETPrimaryP
Tfratio<-PhytNitUp/(PhytNitUp+PhytAmmUp)
KelpNitUp<-fluxwcnit_kelp[ndays]-fluxwcnit_kelp[((nyears-1)*360+1)]
KelpAmmUp<-fluxwcamm_kelp[ndays]-fluxwcamm_kelp[((nyears-1)*360+1)]
#KelpNitUp<-NA
#KelpAmmUp<-NA
KelpNprod <- kelpNprod_i[ndays] - kelpNprod_i[((nyears-1)*360+1)]
#KelpNprod <- NA
Phytgrossprod <- phytgrossprod_i[ndays] - phytgrossprod_i[((nyears-1)*360+1)]
Herbgrossprod <- herbgrossprod_i[ndays] - herbgrossprod_i[((nyears-1)*360+1)]
Carngrossprod <- carngrossprod_i[ndays] - carngrossprod_i[((nyears-1)*360+1)]
Fishplargrossprod <- pfishlargrossprod_i[ndays] - pfishlargrossprod_i[((nyears-1)*360+1)]
Fishdlargrossprod <- dfishlargrossprod_i[ndays] - dfishlargrossprod_i[((nyears-1)*360+1)]
Fishpgrossprod <- pfishgrossprod_i[ndays] - pfishgrossprod_i[((nyears-1)*360+1)]
Fishmgrossprod <- mfishgrossprod_i[ndays] - mfishgrossprod_i[((nyears-1)*360+1)]
Fishdgrossprod <- dfishgrossprod_i[ndays] - dfishgrossprod_i[((nyears-1)*360+1)]
Benthslargrossprod <- benthslargrossprod_i[ndays] - benthslargrossprod_i[((nyears-1)*360+1)]
Benthclargrossprod <- benthclargrossprod_i[ndays] - benthclargrossprod_i[((nyears-1)*360+1)]
Benthsgrossprod <- benthsgrossprod_i[ndays] - benthsgrossprod_i[((nyears-1)*360+1)]
Benthcgrossprod <- benthcgrossprod_i[ndays] - benthcgrossprod_i[((nyears-1)*360+1)]
Birdgrossprod <- birdgrossprod_i[ndays] - birdgrossprod_i[((nyears-1)*360+1)]
Sealgrossprod <- sealgrossprod_i[ndays] - sealgrossprod_i[((nyears-1)*360+1)]
Cetagrossprod <- cetagrossprod_i[ndays] - cetagrossprod_i[((nyears-1)*360+1)]
Herbnetprod <- herbnetprod_i[ndays] - herbnetprod_i[((nyears-1)*360+1)]
Carnnetprod <- carnnetprod_i[ndays] - carnnetprod_i[((nyears-1)*360+1)]
Fishplarnetprod <- pfishlarnetprod_i[ndays] - pfishlarnetprod_i[((nyears-1)*360+1)]
Fishdlarnetprod <- dfishlarnetprod_i[ndays] - dfishlarnetprod_i[((nyears-1)*360+1)]
Fishpnetprod <- pfishnetprod_i[ndays] - pfishnetprod_i[((nyears-1)*360+1)]
Fishmnetprod <- mfishnetprod_i[ndays] - mfishnetprod_i[((nyears-1)*360+1)]
Fishdnetprod <- dfishnetprod_i[ndays] - dfishnetprod_i[((nyears-1)*360+1)]
Benthslarnetprod <- benthslarnetprod_i[ndays] - benthslarnetprod_i[((nyears-1)*360+1)]
Benthclarnetprod <- benthclarnetprod_i[ndays] - benthclarnetprod_i[((nyears-1)*360+1)]
Benthsnetprod <- benthsnetprod_i[ndays] - benthsnetprod_i[((nyears-1)*360+1)]
Benthcnetprod <- benthcnetprod_i[ndays] - benthcnetprod_i[((nyears-1)*360+1)]
Birdnetprod <- birdnetprod_i[ndays] - birdnetprod_i[((nyears-1)*360+1)]
Sealnetprod <- sealnetprod_i[ndays] - sealnetprod_i[((nyears-1)*360+1)]
Cetanetprod <- cetanetprod_i[ndays] - cetanetprod_i[((nyears-1)*360+1)]
#WCdetritusprod <- fluxcorp_wcdet[ndays] - fluxcorp_wcdet[((nyears-1)*360+1)] +
# +fluxkelpdebris_wcdet[ndays] - fluxkelpdebris_wcdet[((nyears-1)*360+1)] +
# +fluxphyt_wcdet[ndays] - fluxphyt_wcdet[((nyears-1)*360+1)] +
# +fluxherb_wcdet[ndays] - fluxherb_wcdet[((nyears-1)*360+1)] +
# +fluxcarn_wcdet[ndays] - fluxcarn_wcdet[((nyears-1)*360+1)] +
# +fluxpfishlar_wcdet[ndays] - fluxpfishlar_wcdet[((nyears-1)*360+1)] +
# +fluxdfishlar_wcdet[ndays] - fluxdfishlar_wcdet[((nyears-1)*360+1)] +
# +fluxpfish_wcdet[ndays] - fluxpfish_wcdet[((nyears-1)*360+1)] +
# +fluxmfish_wcdet[ndays] - fluxmfish_wcdet[((nyears-1)*360+1)] +
# +fluxdfish_wcdet[ndays] - fluxdfish_wcdet[((nyears-1)*360+1)] +
# +fluxbenthslar_wcdet[ndays] - fluxbenthslar_wcdet[((nyears-1)*360+1)] +
# +fluxbenthclar_wcdet[ndays] - fluxbenthclar_wcdet[((nyears-1)*360+1)] +
# +fluxbenths_wcdet[ndays] - fluxbenths_wcdet[((nyears-1)*360+1)] +
# +fluxbenthc_wcdet[ndays] - fluxbenthc_wcdet[((nyears-1)*360+1)] +
# +fluxbird_wcdet[ndays] - fluxbird_wcdet[((nyears-1)*360+1)] +
# +fluxseal_wcdet[ndays] - fluxseal_wcdet[((nyears-1)*360+1)] +
# +fluxceta_wcdet[ndays] - fluxceta_wcdet[((nyears-1)*360+1)]
WCdetritusprod <- NA
#SEDdetritusprod <- fluxcorp_xdet[ndays] - fluxcorp_xdet[((nyears-1)*360+1)] +
# +fluxbenths_xdet[ndays] - fluxbenths_xdet[((nyears-1)*360+1)] +
# +fluxbenthc_xdet[ndays] - fluxbenthc_xdet[((nyears-1)*360+1)]
SEDdetritusprod <- NA
Kelpdebrisprod <- fluxkelp_kelpdebris[ndays] - fluxkelp_kelpdebris[((nyears-1)*360+1)]
#Kelpdebrisprod <- NA
#Corpseprod <- fluxdisc_corp[ndays] - fluxdisc_corp[((nyears-1)*360+1)] +
# +fluxpfish_corp[ndays] - fluxpfish_corp[((nyears-1)*360+1)] +
# +fluxmfish_corp[ndays] - fluxmfish_corp[((nyears-1)*360+1)] +
# +fluxdfish_corp[ndays] - fluxdfish_corp[((nyears-1)*360+1)] +
# +fluxbenths_corp[ndays] - fluxbenths_corp[((nyears-1)*360+1)] +
# +fluxbenthc_corp[ndays] - fluxbenthc_corp[((nyears-1)*360+1)] +
# +fluxbird_corp[ndays] - fluxbird_corp[((nyears-1)*360+1)] +
# +fluxseal_corp[ndays] - fluxseal_corp[((nyears-1)*360+1)] +
# +fluxceta_corp[ndays] - fluxceta_corp[((nyears-1)*360+1)]
Corpseprod <- NA
#Fluxpartwc_sed <- fluxwcdet_xdet[ndays] - fluxwcdet_xdet[((nyears-1)*360+1)] +
# +fluxdisc_corp[ndays] - fluxdisc_corp[((nyears-1)*360+1)] +
# +fluxpfish_corp[ndays] - fluxpfish_corp[((nyears-1)*360+1)] +
# +fluxmfish_corp[ndays] - fluxmfish_corp[((nyears-1)*360+1)] +
# +fluxdfish_corp[ndays] - fluxdfish_corp[((nyears-1)*360+1)] +
# +fluxbird_corp[ndays] - fluxbird_corp[((nyears-1)*360+1)] +
# +fluxphyt_benths[ndays] - fluxphyt_benths[((nyears-1)*360+1)]+
# +fluxwcdet_benths[ndays] - fluxwcdet_benths[((nyears-1)*360+1)]
##Includes the water column feeding flux of benthos
Fluxpartwc_sed <- NA
#Fluxdisc_corp <- fluxdisc_corp[ndays] - fluxdisc_corp[((nyears-1)*360+1)]
Fluxdisc_corp <- NA
#Pelagammprod <- fluxherb_wcamm[ndays] - fluxherb_wcamm[((nyears-1)*360+1)] +
# +fluxcarn_wcamm[ndays] - fluxcarn_wcamm[((nyears-1)*360+1)] +
# +fluxpfishlar_wcamm[ndays] - fluxpfishlar_wcamm[((nyears-1)*360+1)] +
# +fluxdfishlar_wcamm[ndays] - fluxdfishlar_wcamm[((nyears-1)*360+1)] +
# +fluxpfish_wcamm[ndays] - fluxpfish_wcamm[((nyears-1)*360+1)] +
# +fluxmfish_wcamm[ndays] - fluxmfish_wcamm[((nyears-1)*360+1)] +
# +fluxdfish_wcamm[ndays] - fluxdfish_wcamm[((nyears-1)*360+1)] +
# +fluxbenthslar_wcamm[ndays] - fluxbenthslar_wcamm[((nyears-1)*360+1)] +
# +fluxbenthclar_wcamm[ndays] - fluxbenthclar_wcamm[((nyears-1)*360+1)] +
# +fluxbird_wcamm[ndays] - fluxbird_wcamm[((nyears-1)*360+1)] +
# +fluxseal_wcamm[ndays] - fluxseal_wcamm[((nyears-1)*360+1)] +
# +fluxceta_wcamm[ndays] - fluxceta_wcamm[((nyears-1)*360+1)]
##Excludes mineralisation of detritus
Pelagammprod <- NA
#Benthammprod <- fluxbenths_wcamm[ndays] - fluxbenths_wcamm[((nyears-1)*360+1)]+
# +fluxbenthc_wcamm[ndays] - fluxbenthc_wcamm[((nyears-1)*360+1)]
##Excludes mineralisation of detritus
Benthammprod <- NA
#WCmineralisation <- fluxwcdet_wcamm[ndays] - fluxwcdet_wcamm[((nyears-1)*360+1)]
WCmineralisation <- NA
#SEDmineralisation <- fluxxdet_sedamm[ndays] - fluxxdet_sedamm[((nyears-1)*360+1)]+
# +fluxxRdet_sedamm[ndays] - fluxxRdet_sedamm[((nyears-1)*360+1)]
SEDmineralisation <- NA
#WCnitrification <- fluxwcamm_wcnit[ndays] - fluxwcamm_wcnit[((nyears-1)*360+1)]
WCnitrification <- NA
#SEDnitrification <- fluxsedamm_sednit[ndays] - fluxsedamm_sednit[((nyears-1)*360+1)]
SEDnitrification <- NA
#WCdenitrification <- wcdenitrif[ndays] - wcdenitrif[((nyears-1)*360+1)]
WCdenitrification <- NA
#SEDdenitrification <- seddenitrif[ndays] - seddenitrif[((nyears-1)*360+1)]
SEDdenitrification <- NA
#SEDWCammflux <- fluxsedamm_wcamm[ndays] - fluxsedamm_wcamm[((nyears-1)*360+1)]+
# +fluxbenths_wcamm[ndays] - fluxbenths_wcamm[((nyears-1)*360+1)]+
# +fluxbenthc_wcamm[ndays] - fluxbenthc_wcamm[((nyears-1)*360+1)]
##Includes excretion by benthos
SEDWCammflux <- NA
#SEDWCnitflux <- fluxsednit_wcnit[ndays] - fluxsednit_wcnit[((nyears-1)*360+1)]
SEDWCnitflux <- NA
#Fluxdet_herb <- fluxwcdet_herb[ndays] - fluxwcdet_herb[((nyears-1)*360+1)]
#Fluxphyt_herb <- fluxphyt_herb[ndays] - fluxphyt_herb[((nyears-1)*360+1)]
#Fluxbenthslar_herb <- fluxbenthslar_herb[ndays] - fluxbenthslar_herb[((nyears-1)*360+1)]
#Fluxbenthclar_herb <- fluxbenthclar_herb[ndays] - fluxbenthclar_herb[((nyears-1)*360+1)]
Fluxdet_herb <- NA
Fluxphyt_herb <- NA
Fluxbenthslar_herb <- NA
Fluxbenthclar_herb <- NA
#Fluxherb_carn <- fluxherb_carn[ndays] - fluxherb_carn[((nyears-1)*360+1)]
#Fluxpfishlar_carn <- fluxpfishlar_carn[ndays] - fluxpfishlar_carn[((nyears-1)*360+1)]
#Fluxdfishlar_carn <- fluxdfishlar_carn[ndays] - fluxdfishlar_carn[((nyears-1)*360+1)]
#Fluxbenthslar_carn <- fluxbenthslar_carn[ndays] - fluxbenthslar_carn[((nyears-1)*360+1)]
#Fluxbenthclar_carn <- fluxbenthclar_carn[ndays] - fluxbenthclar_carn[((nyears-1)*360+1)]
Fluxherb_carn <- NA
Fluxpfishlar_carn <- NA
Fluxdfishlar_carn <- NA
Fluxbenthslar_carn <- NA
Fluxbenthclar_carn <- NA
#Fluxherb_pfishlar <- fluxherb_pfishlar[ndays] - fluxherb_pfishlar[((nyears-1)*360+1)]
#Fluxbenthslar_pfishlar <- fluxbenthslar_pfishlar[ndays] - fluxbenthslar_pfishlar[((nyears-1)*360+1)]
#Fluxbenthclar_pfishlar <- fluxbenthclar_pfishlar[ndays] - fluxbenthclar_pfishlar[((nyears-1)*360+1)]
Fluxherb_pfishlar <- NA
Fluxbenthslar_pfishlar <- NA
Fluxbenthclar_pfishlar <- NA
#Fluxherb_dfishlar <- fluxherb_dfishlar[ndays] - fluxherb_dfishlar[((nyears-1)*360+1)]
#Fluxbenthslar_dfishlar <- fluxbenthslar_dfishlar[ndays] - fluxbenthslar_dfishlar[((nyears-1)*360+1)]
#Fluxbenthclar_dfishlar <- fluxbenthclar_dfishlar[ndays] - fluxbenthclar_dfishlar[((nyears-1)*360+1)]
Fluxherb_dfishlar <- NA
Fluxbenthslar_dfishlar <- NA
Fluxbenthclar_dfishlar <- NA
#Fluxherb_pfish <- fluxherb_pfish[ndays] - fluxherb_pfish[((nyears-1)*360+1)]
#Fluxcarn_pfish <- fluxcarn_pfish[ndays] - fluxcarn_pfish[((nyears-1)*360+1)]
#Fluxpfishlar_pfish <- fluxpfishlar_pfish[ndays] - fluxpfishlar_pfish[((nyears-1)*360+1)]
#Fluxdfishlar_pfish <- fluxdfishlar_pfish[ndays] - fluxdfishlar_pfish[((nyears-1)*360+1)]
#Fluxbenthslar_pfish <- fluxbenthslar_pfish[ndays] - fluxbenthslar_pfish[((nyears-1)*360+1)]
#Fluxbenthclar_pfish <- fluxbenthclar_pfish[ndays] - fluxbenthclar_pfish[((nyears-1)*360+1)]
Fluxherb_pfish <- NA
Fluxcarn_pfish <- NA
Fluxpfishlar_pfish <- NA
Fluxdfishlar_pfish <- NA
Fluxbenthslar_pfish <- NA
Fluxbenthclar_pfish <- NA
#Fluxherb_mfish <- fluxherb_mfish[ndays] - fluxherb_mfish[((nyears-1)*360+1)]
#Fluxcarn_mfish <- fluxcarn_mfish[ndays] - fluxcarn_mfish[((nyears-1)*360+1)]
#Fluxpfishlar_mfish <- fluxpfishlar_mfish[ndays] - fluxpfishlar_mfish[((nyears-1)*360+1)]
#Fluxdfishlar_mfish <- fluxdfishlar_mfish[ndays] - fluxdfishlar_mfish[((nyears-1)*360+1)]
#Fluxbenthslar_mfish <- fluxbenthslar_mfish[ndays] - fluxbenthslar_mfish[((nyears-1)*360+1)]
#Fluxbenthclar_mfish <- fluxbenthclar_mfish[ndays] - fluxbenthclar_mfish[((nyears-1)*360+1)]
Fluxherb_mfish <- NA
Fluxcarn_mfish <- NA
Fluxpfishlar_mfish <- NA
Fluxdfishlar_mfish <- NA
Fluxbenthslar_mfish <- NA
Fluxbenthclar_mfish <- NA
#Fluxcorp_dfish <- fluxcorp_dfish[ndays] - fluxcorp_dfish[((nyears-1)*360+1)]
#Fluxdisc_dfish <- fluxdisc_dfish[ndays] - fluxdisc_dfish[((nyears-1)*360+1)]
#Fluxcarn_dfish <- fluxcarn_dfish[ndays] - fluxcarn_dfish[((nyears-1)*360+1)]
#Fluxpfishlar_dfish <- fluxpfishlar_dfish[ndays] - fluxpfishlar_dfish[((nyears-1)*360+1)]
#Fluxdfishlar_dfish <- fluxdfishlar_dfish[ndays] - fluxdfishlar_dfish[((nyears-1)*360+1)]
#Fluxpfish_dfish <- fluxpfish_dfish[ndays] - fluxpfish_dfish[((nyears-1)*360+1)]
#Fluxmfish_dfish <- fluxmfish_dfish[ndays] - fluxmfish_dfish[((nyears-1)*360+1)]
#Fluxdfish_dfish <- fluxdfish_dfish[ndays] - fluxdfish_dfish[((nyears-1)*360+1)]
#Fluxbenths_dfish <- fluxbenths_dfish[ndays] - fluxbenths_dfish[((nyears-1)*360+1)]
#Fluxbenthc_dfish <- fluxbenthc_dfish[ndays] - fluxbenthc_dfish[((nyears-1)*360+1)]
Fluxcorp_dfish <- NA
Fluxdisc_dfish <- NA
Fluxcarn_dfish <- NA
Fluxpfishlar_dfish <- NA
Fluxdfishlar_dfish <- NA
Fluxpfish_dfish <- NA
Fluxmfish_dfish <- NA
Fluxdfish_dfish <- NA
Fluxbenths_dfish <- NA
Fluxbenthc_dfish <- NA
#Fluxdet_benthslar <- fluxwcdet_benthslar[ndays] - fluxwcdet_benthslar[((nyears-1)*360+1)]
#Fluxphyt_benthslar <- fluxphyt_benthslar[ndays] - fluxphyt_benthslar[((nyears-1)*360+1)]
Fluxdet_benthslar <- NA
Fluxphyt_benthslar <- NA
#Fluxdet_benthclar <- fluxwcdet_benthclar[ndays] - fluxwcdet_benthclar[((nyears-1)*360+1)]
#Fluxphyt_benthclar <- fluxphyt_benthclar[ndays] - fluxphyt_benthclar[((nyears-1)*360+1)]
Fluxdet_benthclar <- NA
Fluxphyt_benthclar <- NA
#Fluxdet_benths <- fluxwcdet_benths[ndays] - fluxwcdet_benths[((nyears-1)*360+1)]
#Fluxseddet_benths <- fluxxdet_benths[ndays] - fluxxdet_benths[((nyears-1)*360+1)] +
#Fluxphyt_benths <- fluxphyt_benths[ndays] - fluxphyt_benths[((nyears-1)*360+1)]
Fluxdet_benths <- NA
Fluxseddet_benths <- NA
Fluxphyt_benths <- NA
Fluxkelp_benthc <- fluxkelp_benthc[ndays] - fluxkelp_benthc[((nyears-1)*360+1)]
Fluxkelpdebris_benthc <- fluxkelpdebris_benthc[ndays] - fluxkelpdebris_benthc[((nyears-1)*360+1)]
#Fluxkelp_benthc <- NA
#Fluxkelpdebris_benthc <- NA
#Fluxcorp_benthc <- fluxcorp_benthc[ndays] - fluxcorp_benthc[((nyears-1)*360+1)]
#Fluxbenths_benthc <- fluxbenths_benthc[ndays] - fluxbenths_benthc[((nyears-1)*360+1)]
Fluxcorp_benthc <- NA
Fluxbenths_benthc <- NA
#Fluxcorp_bird <- fluxcorp_bird[ndays] - fluxcorp_bird[((nyears-1)*360+1)]
#Fluxdisc_bird <- fluxdisc_bird[ndays] - fluxdisc_bird[((nyears-1)*360+1)]
##Fluxherb_bird <- fluxherb_bird[ndays] - fluxherb_bird[((nyears-1)*360+1)]
#Fluxcarn_bird <- fluxcarn_bird[ndays] - fluxcarn_bird[((nyears-1)*360+1)]
#Fluxpfish_bird <- fluxpfish_bird[ndays] - fluxpfish_bird[((nyears-1)*360+1)]
#Fluxmfish_bird <- fluxmfish_bird[ndays] - fluxmfish_bird[((nyears-1)*360+1)]
#Fluxdfish_bird <- fluxdfish_bird[ndays] - fluxdfish_bird[((nyears-1)*360+1)]
#Fluxbenths_bird <- fluxbenths_bird[ndays] - fluxbenths_bird[((nyears-1)*360+1)]
#Fluxbenthc_bird <- fluxbenthc_bird[ndays] - fluxbenthc_bird[((nyears-1)*360+1)]
Fluxcorp_bird <- NA
Fluxdisc_bird <- NA
#Fluxherb_bird <- NA
Fluxcarn_bird <- NA
Fluxpfish_bird <- NA
Fluxmfish_bird <- NA
Fluxdfish_bird <- NA
Fluxbenths_bird <- NA
Fluxbenthc_bird <- NA
#Fluxcorp_seal <- fluxcorp_seal[ndays] - fluxcorp_seal[((nyears-1)*360+1)]
#Fluxdisc_seal <- fluxdisc_seal[ndays] - fluxdisc_seal[((nyears-1)*360+1)]
#Fluxcarn_seal <- fluxcarn_seal[ndays] - fluxcarn_seal[((nyears-1)*360+1)]
#Fluxpfish_seal <- fluxpfish_seal[ndays] - fluxpfish_seal[((nyears-1)*360+1)]
#Fluxmfish_seal <- fluxmfish_seal[ndays] - fluxmfish_seal[((nyears-1)*360+1)]
#Fluxdfish_seal <- fluxdfish_seal[ndays] - fluxdfish_seal[((nyears-1)*360+1)]
#Fluxbenths_seal <- fluxbenths_seal[ndays] - fluxbenths_seal[((nyears-1)*360+1)]
#Fluxbenthc_seal <- fluxbenthc_seal[ndays] - fluxbenthc_seal[((nyears-1)*360+1)]
#Fluxbird_seal <- fluxbird_seal[ndays] - fluxbird_seal[((nyears-1)*360+1)]
Fluxcorp_seal <- NA
Fluxdisc_seal <- NA
Fluxcarn_seal <- NA
Fluxpfish_seal <- NA
Fluxmfish_seal <- NA
Fluxdfish_seal <- NA
Fluxbenths_seal <- NA
Fluxbenthc_seal <- NA
Fluxbird_seal <- NA
#Fluxdisc_ceta <- fluxdisc_ceta[ndays] - fluxdisc_ceta[((nyears-1)*360+1)]
#Fluxherb_ceta <- fluxherb_ceta[ndays] - fluxherb_ceta[((nyears-1)*360+1)]
#Fluxcarn_ceta <- fluxcarn_ceta[ndays] - fluxcarn_ceta[((nyears-1)*360+1)]
#Fluxpfish_ceta <- fluxpfish_ceta[ndays] - fluxpfish_ceta[((nyears-1)*360+1)]
#Fluxmfish_ceta <- fluxmfish_ceta[ndays] - fluxmfish_ceta[((nyears-1)*360+1)]
#Fluxdfish_ceta <- fluxdfish_ceta[ndays] - fluxdfish_ceta[((nyears-1)*360+1)]
#Fluxbenths_ceta <- fluxbenths_ceta[ndays] - fluxbenths_ceta[((nyears-1)*360+1)]
#Fluxbenthc_ceta <- fluxbenthc_ceta[ndays] - fluxbenthc_ceta[((nyears-1)*360+1)]
#Fluxbird_ceta <- fluxbird_ceta[ndays] - fluxbird_ceta[((nyears-1)*360+1)]
#Fluxseal_ceta <- fluxseal_ceta[ndays] - fluxseal_ceta[((nyears-1)*360+1)]
Fluxdisc_ceta <- NA
Fluxherb_ceta <- NA
Fluxcarn_ceta <- NA
Fluxpfish_ceta <- NA
Fluxmfish_ceta <- NA
Fluxdfish_ceta <- NA
Fluxbenths_ceta <- NA
Fluxbenthc_ceta <- NA
Fluxbird_ceta <- NA
Fluxseal_ceta <- NA
HTLP<- Herbnetprod +
+ Carnnetprod +
+ Benthsnetprod +
+ Benthcnetprod +
+ Benthslarnetprod +
+ Benthclarnetprod +
+ Fishplarnetprod +
+ Fishdlarnetprod +
+ Fishpnetprod +
+ Fishmnetprod +
+ Fishdnetprod +
+ Birdnetprod +
+ Sealnetprod +
+ Cetanetprod
#export_from_2prod<- Fluxherb_carn +
# + Fluxherb_pfishlar +
# + Fluxherb_dfishlar +
# + Fluxherb_pfish +
# + Fluxherb_ceta +
# + Fluxbenths_dfish +
# + Fluxbenths_benthc +
# + Fluxbenths_bird +
# + Fluxbenths_seal +
# + Fluxbenths_ceta
export_from_2prod<- NA
#Pfish_annual_spawn <- Pfish_spawn[ndays]-Pfish_spawn[((nyears-1)*360+1)]
#Pfish_annual_recruit <- Pfish_recruit[ndays]-Pfish_recruit[((nyears-1)*360+1)]
#Dfish_annual_spawn <- Dfish_spawn[ndays]-Dfish_spawn[((nyears-1)*360+1)]
#Dfish_annual_recruit <- Dfish_recruit[ndays]-Dfish_recruit[((nyears-1)*360+1)]
Pfish_annual_spawn <- NA
Pfish_annual_recruit <- NA
Dfish_annual_spawn <- NA
Dfish_annual_recruit <- NA
#Benths_annual_spawn <- Bs_spawn[ndays]-Bs_spawn[((nyears-1)*360+1)]
#Benths_annual_recruit <- Bs_recruit[ndays]-Bs_recruit[((nyears-1)*360+1)]
#Benthc_annual_spawn <- Bc_spawn[ndays]-Bc_spawn[((nyears-1)*360+1)]
#Benthc_annual_recruit <- Bc_recruit[ndays]-Bc_recruit[((nyears-1)*360+1)]
Benths_annual_spawn <- NA
Benths_annual_recruit <- NA
Benthc_annual_spawn <- NA
Benthc_annual_recruit <- NA
FishpLand_livewt<-landp_i[ndays]-landp_i[((nyears-1)*360+1)]
FishmLand_livewt<-landm_i[ndays]-landm_i[((nyears-1)*360+1)]
FishdLand_livewt<-landd_i[ndays]-landd_i[((nyears-1)*360+1)]
Fishd_qLand_livewt<-landd_quota_i[ndays]-landd_quota_i[((nyears-1)*360+1)]
Fishd_nqLand_livewt<-landd_nonquota_i[ndays]-landd_nonquota_i[((nyears-1)*360+1)]
BenthsLand_livewt <- landsb_i[ndays]-landsb_i[((nyears-1)*360+1)]
BenthcLand_livewt <- landcb_i[ndays]-landcb_i[((nyears-1)*360+1)]
CarnzLand_livewt <- landcz_i[ndays]-landcz_i[((nyears-1)*360+1)]
BirdLand_livewt <- landbd_i[ndays]-landbd_i[((nyears-1)*360+1)]
SealLand_livewt <- landsl_i[ndays]-landsl_i[((nyears-1)*360+1)]
CetaLand_livewt <- landct_i[ndays]-landct_i[((nyears-1)*360+1)]
KelpLand_livewt <- landkp_i[ndays]-landkp_i[((nyears-1)*360+1)]
#KelpLand_livewt <- NA
FishpDiscard<-discpel_i[ndays]-discpel_i[((nyears-1)*360+1)]
FishmDiscard<-discmig_i[ndays]-discmig_i[((nyears-1)*360+1)]
FishdDiscard<-discdem_i[ndays]-discdem_i[((nyears-1)*360+1)]
Fishd_qDiscard<-discdem_quota_i[ndays]-discdem_quota_i[((nyears-1)*360+1)]
Fishd_nqDiscard<-discdem_nonquota_i[ndays]-discdem_nonquota_i[((nyears-1)*360+1)]
BenthsDiscard <- discsb_i[ndays]-discsb_i[((nyears-1)*360+1)]
BenthcDiscard <- disccb_i[ndays]-disccb_i[((nyears-1)*360+1)]
CarnzDiscard <- disccz_i[ndays]-disccz_i[((nyears-1)*360+1)]
BirdDiscard <- discbd_i[ndays]-discbd_i[((nyears-1)*360+1)]
SealDiscard <- discsl_i[ndays]-discsl_i[((nyears-1)*360+1)]
CetaDiscard <- discct_i[ndays]-discct_i[((nyears-1)*360+1)]
KelpDiscard <- disckp_i[ndays]-disckp_i[((nyears-1)*360+1)]
#KelpDiscard <- NA
FishpOffal<-offalpel_i[ndays]-offalpel_i[((nyears-1)*360+1)]
FishmOffal<-offalmig_i[ndays]-offalmig_i[((nyears-1)*360+1)]
FishdOffal<-offaldem_i[ndays]-offaldem_i[((nyears-1)*360+1)]
Fishd_qOffal<-offaldem_quota_i[ndays]-offaldem_quota_i[((nyears-1)*360+1)]
Fishd_nqOffal<-offaldem_nonquota_i[ndays]-offaldem_nonquota_i[((nyears-1)*360+1)]
BenthsOffal <- offalsb_i[ndays]-offalsb_i[((nyears-1)*360+1)]
BenthcOffal <- offalcb_i[ndays]-offalcb_i[((nyears-1)*360+1)]
CarnzOffal <- offalcz_i[ndays]-offalcz_i[((nyears-1)*360+1)]
BirdOffal <- offalbd_i[ndays]-offalbd_i[((nyears-1)*360+1)]
SealOffal <- offalsl_i[ndays]-offalsl_i[((nyears-1)*360+1)]
CetaOffal <- offalct_i[ndays]-offalct_i[((nyears-1)*360+1)]
KelpOffal <- offalkp_i[ndays]-offalkp_i[((nyears-1)*360+1)]
#KelpOffal <- NA
FishpLand_processedwt<- FishpLand_livewt - FishpOffal
FishmLand_processedwt<- FishmLand_livewt - FishmOffal
FishdLand_processedwt<- FishdLand_livewt - FishdOffal
Fishd_qLand_processedwt<- Fishd_qLand_livewt - Fishd_qOffal
Fishd_nqLand_processedwt<- Fishd_nqLand_livewt - Fishd_nqOffal
BenthsLand_processedwt <- BenthsLand_livewt - BenthsOffal
BenthcLand_processedwt <- BenthcLand_livewt - BenthcOffal
CarnzLand_processedwt <- CarnzLand_livewt - CarnzOffal
BirdLand_processedwt <- BirdLand_livewt - BirdOffal
SealLand_processedwt <- SealLand_livewt - SealOffal
CetaLand_processedwt <- CetaLand_livewt - CetaOffal
KelpLand_processedwt <- KelpLand_livewt - KelpOffal
#KelpLand_processedwt <- NA
annual_flux_results<-data.frame(rep(0,240))
#EXTRACT THE RESULTS INTO A DATA FRAME
#COLUMN 1 IS IN NITROGEN UNITS (mM N/m2/y)
#DERIVED ANNUAL VALUES IN UNITS OF mM N/m2 and fluxes in mMN/m2/y
annual_flux_results[1,1]<-DINinflow
annual_flux_results[2,1]<-DINoutflow
annual_flux_results[3,1]<-PARTinflow
annual_flux_results[4,1]<-PARToutflow
annual_flux_results[5,1]<-atmosphereDINinput
annual_flux_results[6,1]<-riverDINinflow
annual_flux_results[7,1]<-riverPARTinflow
annual_flux_results[8,1]<-sumDINinflow
annual_flux_results[9,1]<-sumDINoutflow
annual_flux_results[10,1]<-sumPARTinflow
annual_flux_results[11,1]<-sumPARToutflow
annual_flux_results[12,1]<-sumriverDINinflow
annual_flux_results[13,1]<-sumatmosDINinput
annual_flux_results[14,1]<-surfvertnitflux
annual_flux_results[15,1]<-surfhoriznitflux
annual_flux_results[16,1]<-Flux_sedboundary
annual_flux_results[17,1]<-kelp_beachcast
annual_flux_results[18,1]<-DIN_NET_flux_o_i
annual_flux_results[19,1]<-PART_NET_flux_o_i
annual_flux_results[20,1]<-NET_activemigpelfish_o_i
annual_flux_results[21,1]<-NET_activemigmigfish_o_i
annual_flux_results[22,1]<-NET_activemigdemfish_o_i
annual_flux_results[23,1]<-NET_activemigbird_o_i
annual_flux_results[24,1]<-NET_activemigseal_o_i
annual_flux_results[25,1]<-NET_activemigceta_o_i
annual_flux_results[26,1]<-NET_mfish_ext_o
annual_flux_results[27,1]<-Mfish_annual_imig
annual_flux_results[28,1]<-Mfish_annual_emig
annual_flux_results[29,1]<-NETPrimaryP
annual_flux_results[30,1]<-MMP
annual_flux_results[31,1]<-PNP
annual_flux_results[32,1]<-PhytNitUp
annual_flux_results[33,1]<-PhytAmmUp
annual_flux_results[34,1]<-NewP
annual_flux_results[35,1]<-fratio
annual_flux_results[36,1]<-Tfratio
annual_flux_results[37,1]<-KelpNitUp
annual_flux_results[38,1]<-KelpAmmUp
annual_flux_results[39,1]<-KelpNprod
annual_flux_results[40,1]<-Phytgrossprod
annual_flux_results[41,1]<-Herbgrossprod
annual_flux_results[42,1]<-Carngrossprod
annual_flux_results[43,1]<-Fishplargrossprod
annual_flux_results[44,1]<-Fishdlargrossprod
annual_flux_results[45,1]<-Fishpgrossprod
annual_flux_results[46,1]<-Fishmgrossprod
annual_flux_results[47,1]<-Fishdgrossprod
annual_flux_results[48,1]<-Benthslargrossprod
annual_flux_results[49,1]<-Benthclargrossprod
annual_flux_results[50,1]<-Benthsgrossprod
annual_flux_results[51,1]<-Benthcgrossprod
annual_flux_results[52,1]<-Birdgrossprod
annual_flux_results[53,1]<-Sealgrossprod
annual_flux_results[54,1]<-Cetagrossprod
annual_flux_results[55,1]<-Herbnetprod
annual_flux_results[56,1]<-Carnnetprod
annual_flux_results[57,1]<-Fishplarnetprod
annual_flux_results[58,1]<-Fishdlarnetprod
annual_flux_results[59,1]<-Fishpnetprod
annual_flux_results[60,1]<-Fishmnetprod
annual_flux_results[61,1]<-Fishdnetprod
annual_flux_results[62,1]<-Benthslarnetprod
annual_flux_results[63,1]<-Benthclarnetprod
annual_flux_results[64,1]<-Benthsnetprod
annual_flux_results[65,1]<-Benthcnetprod
annual_flux_results[66,1]<-Birdnetprod
annual_flux_results[67,1]<-Sealnetprod
annual_flux_results[68,1]<-Cetanetprod
annual_flux_results[69,1]<-WCdetritusprod
annual_flux_results[70,1]<-SEDdetritusprod
annual_flux_results[71,1]<-Corpseprod
annual_flux_results[72,1]<-Fluxpartwc_sed
annual_flux_results[73,1]<-Fluxdisc_corp
annual_flux_results[74,1]<-Pelagammprod
annual_flux_results[75,1]<-Benthammprod
annual_flux_results[76,1]<-WCmineralisation
annual_flux_results[77,1]<-SEDmineralisation
annual_flux_results[78,1]<-WCnitrification
annual_flux_results[79,1]<-SEDnitrification
annual_flux_results[80,1]<-WCdenitrification
annual_flux_results[81,1]<-SEDdenitrification
annual_flux_results[82,1]<-SEDWCammflux
annual_flux_results[83,1]<-SEDWCnitflux
annual_flux_results[84,1]<-Fluxdet_herb
annual_flux_results[85,1]<-Fluxphyt_herb
annual_flux_results[85,1]<-Fluxbenthslar_herb
annual_flux_results[87,1]<-Fluxbenthclar_herb
annual_flux_results[88,1]<-Fluxherb_carn
annual_flux_results[89,1]<-Fluxpfishlar_carn
annual_flux_results[90,1]<-Fluxdfishlar_carn
annual_flux_results[91,1]<-Fluxbenthslar_carn
annual_flux_results[92,1]<-Fluxbenthclar_carn
annual_flux_results[93,1]<-Fluxherb_pfishlar
annual_flux_results[94,1]<-Fluxbenthslar_pfishlar
annual_flux_results[95,1]<-Fluxbenthclar_pfishlar
annual_flux_results[96,1]<-Fluxherb_dfishlar
annual_flux_results[97,1]<-Fluxbenthslar_dfishlar
annual_flux_results[98,1]<-Fluxbenthclar_dfishlar
annual_flux_results[99,1]<-Fluxherb_pfish
annual_flux_results[100,1]<-Fluxcarn_pfish
annual_flux_results[101,1]<-Fluxpfishlar_pfish
annual_flux_results[102,1]<-Fluxdfishlar_pfish
annual_flux_results[103,1]<-Fluxbenthslar_pfish
annual_flux_results[104,1]<-Fluxbenthclar_pfish
annual_flux_results[105,1]<-Fluxherb_mfish
annual_flux_results[106,1]<-Fluxcarn_mfish
annual_flux_results[107,1]<-Fluxpfishlar_mfish
annual_flux_results[108,1]<-Fluxdfishlar_mfish
annual_flux_results[109,1]<-Fluxbenthslar_mfish
annual_flux_results[110,1]<-Fluxbenthclar_mfish
annual_flux_results[111,1]<-Fluxcorp_dfish
annual_flux_results[112,1]<-Fluxdisc_dfish
annual_flux_results[113,1]<-Fluxcarn_dfish
annual_flux_results[114,1]<-Fluxpfishlar_dfish
annual_flux_results[115,1]<-Fluxdfishlar_dfish
annual_flux_results[116,1]<-Fluxpfish_dfish
annual_flux_results[117,1]<-Fluxmfish_dfish
annual_flux_results[118,1]<-Fluxdfish_dfish
annual_flux_results[119,1]<-Fluxbenths_dfish
annual_flux_results[120,1]<-Fluxbenthc_dfish
annual_flux_results[121,1]<-Fluxdet_benthslar
annual_flux_results[122,1]<-Fluxphyt_benthslar
annual_flux_results[123,1]<-Fluxdet_benthclar
annual_flux_results[124,1]<-Fluxphyt_benthclar
annual_flux_results[125,1]<-Fluxdet_benths
annual_flux_results[126,1]<-Fluxseddet_benths
annual_flux_results[127,1]<-Fluxphyt_benths
annual_flux_results[128,1]<-Fluxkelpdebris_benthc
annual_flux_results[129,1]<-Fluxcorp_benthc
annual_flux_results[130,1]<-Fluxkelp_benthc
annual_flux_results[131,1]<-Fluxbenths_benthc
annual_flux_results[132,1]<-Fluxcorp_bird
annual_flux_results[133,1]<-Fluxdisc_bird
#annual_flux_results[xxx,1]<-Fluxherb_bird
annual_flux_results[134,1]<-Fluxcarn_bird
annual_flux_results[135,1]<-Fluxpfish_bird
annual_flux_results[136,1]<-Fluxmfish_bird
annual_flux_results[137,1]<-Fluxdfish_bird
annual_flux_results[138,1]<-Fluxbenths_bird
annual_flux_results[139,1]<-Fluxbenthc_bird
annual_flux_results[140,1]<-Fluxcorp_seal
annual_flux_results[141,1]<-Fluxdisc_seal
annual_flux_results[142,1]<-Fluxcarn_seal
annual_flux_results[143,1]<-Fluxpfish_seal
annual_flux_results[144,1]<-Fluxmfish_seal
annual_flux_results[145,1]<-Fluxdfish_seal
annual_flux_results[146,1]<-Fluxbenths_seal
annual_flux_results[147,1]<-Fluxbenthc_seal
annual_flux_results[148,1]<-Fluxbird_seal
annual_flux_results[149,1]<-Fluxdisc_ceta
annual_flux_results[150,1]<-Fluxherb_ceta
annual_flux_results[151,1]<-Fluxcarn_ceta
annual_flux_results[152,1]<-Fluxpfish_ceta
annual_flux_results[153,1]<-Fluxmfish_ceta
annual_flux_results[154,1]<-Fluxdfish_ceta
annual_flux_results[155,1]<-Fluxbenths_ceta
annual_flux_results[156,1]<-Fluxbenthc_ceta
annual_flux_results[157,1]<-Fluxbird_ceta
annual_flux_results[158,1]<-Fluxseal_ceta
annual_flux_results[159,1]<-HTLP
annual_flux_results[160,1]<-export_from_2prod
annual_flux_results[161,1]<-Pfish_annual_spawn
annual_flux_results[162,1]<-Pfish_annual_recruit
annual_flux_results[163,1]<-Dfish_annual_spawn
annual_flux_results[164,1]<-Dfish_annual_recruit
annual_flux_results[165,1]<-Benths_annual_spawn
annual_flux_results[166,1]<-Benths_annual_recruit
annual_flux_results[167,1]<-Benthc_annual_spawn
annual_flux_results[168,1]<-Benthc_annual_recruit
annual_flux_results[169,1]<-FishpLand_livewt
annual_flux_results[170,1]<-FishmLand_livewt
annual_flux_results[171,1]<-FishdLand_livewt
annual_flux_results[172,1]<-Fishd_qLand_livewt
annual_flux_results[173,1]<-Fishd_nqLand_livewt
annual_flux_results[174,1]<-BenthsLand_livewt
annual_flux_results[175,1]<-BenthcLand_livewt
annual_flux_results[176,1]<-CarnzLand_livewt
annual_flux_results[177,1]<-BirdLand_livewt
annual_flux_results[178,1]<-SealLand_livewt
annual_flux_results[179,1]<-CetaLand_livewt
annual_flux_results[180,1]<-KelpLand_livewt
annual_flux_results[181,1]<-FishpDiscard
annual_flux_results[182,1]<-FishmDiscard
annual_flux_results[183,1]<-FishdDiscard
annual_flux_results[184,1]<-Fishd_qDiscard
annual_flux_results[185,1]<-Fishd_nqDiscard
annual_flux_results[186,1]<-BenthsDiscard
annual_flux_results[187,1]<-BenthcDiscard
annual_flux_results[188,1]<-CarnzDiscard
annual_flux_results[189,1]<-BirdDiscard
annual_flux_results[190,1]<-SealDiscard
annual_flux_results[191,1]<-CetaDiscard
annual_flux_results[192,1]<-KelpDiscard
annual_flux_results[193,1]<-FishpOffal
annual_flux_results[194,1]<-FishmOffal
annual_flux_results[195,1]<-FishdOffal
annual_flux_results[196,1]<-Fishd_qOffal
annual_flux_results[197,1]<-Fishd_nqOffal
annual_flux_results[198,1]<-BenthsOffal
annual_flux_results[199,1]<-BenthcOffal
annual_flux_results[200,1]<-CarnzOffal
annual_flux_results[201,1]<-BirdOffal
annual_flux_results[202,1]<-SealOffal
annual_flux_results[203,1]<-CetaOffal
annual_flux_results[204,1]<-KelpOffal
annual_flux_results[205,1]<-FishpLand_processedwt
annual_flux_results[206,1]<-FishmLand_processedwt
annual_flux_results[207,1]<-FishdLand_processedwt
annual_flux_results[208,1]<-Fishd_qLand_processedwt
annual_flux_results[209,1]<-Fishd_nqLand_processedwt
annual_flux_results[210,1]<-BenthsLand_processedwt
annual_flux_results[211,1]<-BenthcLand_processedwt
annual_flux_results[212,1]<-CarnzLand_processedwt
annual_flux_results[213,1]<-BirdLand_processedwt
annual_flux_results[214,1]<-SealLand_processedwt
annual_flux_results[215,1]<-CetaLand_processedwt
annual_flux_results[216,1]<-KelpLand_processedwt
annual_flux_results[217,1]<-x_shallowprop
annual_flux_results[218,1]<-si_depth
annual_flux_results[219,1]<-so_depth
annual_flux_results[220,1]<-d_depth
annual_flux_results[221,1]<-x_area_s0
annual_flux_results[222,1]<-x_area_s1
annual_flux_results[223,1]<-x_area_s2
annual_flux_results[224,1]<-x_area_s3
annual_flux_results[225,1]<-x_area_d0
annual_flux_results[226,1]<-x_area_d1
annual_flux_results[227,1]<-x_area_d2
annual_flux_results[228,1]<-x_area_d3
annual_flux_results[229,1]<-x_depth_s1
annual_flux_results[230,1]<-x_depth_s2
annual_flux_results[231,1]<-x_depth_s3
annual_flux_results[232,1]<-x_depth_d1
annual_flux_results[233,1]<-x_depth_d2
annual_flux_results[234,1]<-x_depth_d3
annual_flux_results[235,1]<-x_poros_s1
annual_flux_results[236,1]<-x_poros_s2
annual_flux_results[237,1]<-x_poros_s3
annual_flux_results[238,1]<-x_poros_d1
annual_flux_results[239,1]<-x_poros_d2
annual_flux_results[240,1]<-x_poros_d3
annual_flux_results[,2]<-rep("mMN/whole_model_domain_(1m2)/y",240)
annual_flux_results[8:13,2]<-("mMN/whole_model_domain_(1m2)/summer_period_AMJJAS")
annual_flux_results[c(217,221:228,235:240),2]<-"dimensionless"
annual_flux_results[c(218:220,229:234),2]<-"m"
annual_flux_results[,3]<-c(
"DIN_inflow",
"DIN_outflow",
"Particulate_inflow",
"Particulate_outflow",
"Atmosphere_DIN_input",
"River_DIN_inflow",
"River_particulate_inflow",
"Summer_DIN_inflow",
"Summer_DIN_outflow",
"Summer_particulate_inflow",
"Summer_particulate_outflow",
"Summer_river_DIN_inflow",
"Summer_atmosphere_DIN_input",
"Vertical_nitrate_flux",
"Surface_horizontal_nitrate_flux",
"Net_import/export_flux_in_the_sediment",
"Beachcast_export_of_kelp_debris",
"DIN_Net_flux_offshore_to_inshore",
"Particulate_net_flux_offshore_to_inshore",
"Plank.fish_net_active_migration_offshore_to_inshore",
"Mig.fish_net_active_migration_offshore_to_inshore",
"Dem.fish_net_active_migration_offshore_to_inshore",
"Bird_net_active_migration_offshore_to_inshore",
"Seal_net_active_migration_offshore_to_inshore",
"Cetacean_net_active_migration_offshore_to_inshore",
"Mig.fish_net_migration_external_offshore",
"Mig.fish_annual_immigration",
"Mig.fish_annual_emigration",
"Phytoplankton_net_primary_production",
"Phytoplankton_new_production_(nitrate_drawdown)",
"Phytoplankton_new_production_(traditional)",
"Phytoplankton_new_production_(Heath&Beare)",
"Phytoplankton_nitrate_uptake",
"Phytoplankton_ammonia_uptake",
"Phytoplankton_fratio_(H&B/NetPP)",
"Phytoplankton_fratio_(traditional)",
"Kelp_nitrate_uptake",
"Kelp_ammonia_uptake",
"Kelp_gross_production",
"Phytoplankton_gross_production",
"Omniv.zooplankton_gross_production",
"Carniv.zooplankton_gross_production",
"Planktiv.fish_larvae_gross_production",
"Dem.fish_larvae_gross_production",
"Planktiv.fish_gross_production",
"Mig.fish_gross_production",
"Dem.fish_gross_production",
"Benthos_filt/dep_larvae_gross_production",
"Benthos_carn/scav_larvae_gross_production",
"Benthos_filt/dep_gross_production",
"Benthos_carn/scav_gross_production",
"Bird_gross_production",
"Seal_gross_production",
"Cetacean_gross_production",
"Omniv.zooplankton_net_production",
"Carniv.zooplankton_net_production",
"Planktiv.fish_larvae_net_production",
"Dem.fish_larvae_net_production",
"Planktiv.fish_net_production",
"Mig.fish_net_production",
"Dem.fish_net_production",
"Benthos_filt/dep_larvae_net_production",
"Benthos_carn/scav_larvae_net_production",
"Benthos_filt/dep_net_production",
"Benthos_carn/scav_net_production",
"Bird_net_production",
"Seal_net_production",
"Cetacean_net_production",
"Water_column_detritus_production",
"Sediment_detritus_production",
"Corpse_production",
"Flux_of_detritus_from_water_to_sediment",
"Flux_of_discards_to_corpses",
"Pelagic_fauna_ammonia_production",
"Benthic_fauna_ammonia_production",
"Water_column_detritus_mineralisation",
"Sediment_detritus_mineralisation",
"Water_column_nitrification",
"Sediment_nitrification",
"Water_column_denitrification",
"Sediment_denitrification",
"Sediment_to_water_ammonia_flux",
"Sediment_to_water_nitrate_flux",
"Flux_detritus_to_omniv.zooplankton",
"Flux_phytoplankton_to_omniv.zooplankton",
"Flux_benthosf/d.larvae_to_omniv.zooplankton",
"Flux_benthosc/s.larvae_to_omniv.zooplankton",
"Flux_omniv.zooplankton_to_carniv.zooplankton",
"Flux_plank.fish.larvae_to_carniv.zooplankton",
"Flux_dem.fish.larvae_to_carniv.zooplankton",
"Flux_benthosf/d.larvae_to_carniv.zooplankton",
"Flux_benthosc/s.larvae_to_carniv.zooplankton",
"Flux_omniv.zooplankton_to_plank.fish.larvae",
"Flux_benthosf/d.larvae_to_plank.fish.larvae",
"Flux_benthosc/s.larvae_to_plank.fish.larvae",
"Flux_omniv.zooplankton_to_dem.fish.larvae",
"Flux_benthosf/d.larvae_to_dem.fish.larvae",
"Flux_benthosc/s.larvae_to_dem.fish.larvae",
"Flux_omniv.zooplankton_to_plank.fish",
"Flux_carniv.zooplankton_to_plank.fish",
"Flux_plank.fish.larvae_to_plank.fish",
"Flux_dem.fish.larvae_to_plank.fish",
"Flux_benthosf/d.larvae_to_plank.fish",
"Flux_benthosc/s.larvae_to_plank.fish",
"Flux_omniv.zooplankton_to_mig.fish",
"Flux_carniv.zooplankton_to_mig.fish",
"Flux_plank.fish.larvae_to_mig.fish",
"Flux_dem.fish.larvae_to_mig.fish",
"Flux_benthosf/d.larvae_to_mig.fish",
"Flux_benthosc/s.larvae_to_mig.fish",
"Flux_corpses_to_dem.fish",
"Flux_discards_to_dem.fish",
"Flux_carniv.zooplankton_to_dem.fish",
"Flux_plank.fish.larvae_to_dem.fish",
"Flux_dem.fish.larvae_to_dem.fish",
"Flux_plank.fish_to_dem.fish",
"Flux_mig.fish_to_dem.fish",
"Flux_dem.fish_to_dem.fish",
"Flux_benthosf/d_to_dem.fish",
"Flux_benthosc/s_to_dem.fish",
"Flux_detritus_to_benthosf/d.larvae",
"Flux_phytoplankton_to_benthosf/d.larvae",
"Flux_detritus_to_benthosc/s.larvae",
"Flux_phytoplankton_to_benthosc/s.larvae",
"Flux_detritus_to_benthosf/d",
"Flux_sediment.detritus_to_benthosf/d",
"Flux_phytoplankton_to_benthosf/d",
"Flux_kelp.debris_to_benthosc/s",
"Flux_corpses_to_benthosc/s",
"Flux_kelp_to_benthosc/s",
"Flux_benthosf/d_to_benthosc/sc",
"Flux_corpses_to_birds",
"Flux_discards_to_birds",
#"Flux_ominiv.zooplankton_to_birds",
"Flux_carniv.zooplankton_to_birds",
"Flux_plank.fish_to_birds",
"Flux_mig.fish_to_birds",
"Flux_dem.fish_to_birds",
"Flux_benthosf/d_to_birds",
"Flux_benthosc/s_to_birds",
"Flux_corpses_to_seals",
"Flux_discards_to_seals",
"Flux_carniv.zooplankton_to_seals",
"Flux_plank.fish_to_seals",
"Flux_mig.fish_to_seals",
"Flux_dem.fish_to_seals",
"Flux_benthosf/d_to_seals",
"Flux_benthosc/s_to_seals",
"Flux_birds_to_seals",
"Flux_discards_to_cetaceans",
"Flux_ominiv.zooplankton_to_cetaceans",
"Flux_carniv.zooplankton_to_cetaceans",
"Flux_plank.fish_to_cetaceans",
"Flux_mig.fish_to_cetaceans",
"Flux_dem.fish_to_cetaceans",
"Flux_benthosf/d_to_cetaceans",
"Flux_benthosc/s_to_cetaceans",
"Flux_birds_to_cetaceans",
"Flux_seals_to_cetaceans",
"Net_production_of_all_secondary_and_higher_trophic_levels",
"Export_from_secondary_producers",
"Plank.fish_annual_spawning",
"Plank.fish_annual_recruitment",
"Dem.fish_annual_spawning",
"Dem.fish_annual_recruitment",
"Benthosf/d_annual_spawning",
"Benthosf/d_annual_recruitment",
"Benthosc/s_annual_spawning",
"Benthosc/sc_annual_recruitment",
"Plank.fish_landings_live_weight",
"Mig.fish_landings_live_weight",
"Dem.fish_landings_live_weight",
"Dem.fish_quota_limited_landings_live_weight",
"Dem.fish_non.quota_landings_live_weight",
"Benthosf/d_landings_live_weight",
"Benthosc/s_landings_live_weight",
"Carniv.zooplankton_landings_live_weight",
"Bird_landings_live_weight",
"Seal_landings_live_weight",
"Cetacean_landings_live_weight",
"Kelp_landings_live_weight",
"Plank.fish_discards",
"Mig.fish_discards",
"Dem.fish_discards",
"Dem.fish_quota_limited_discards",
"Dem.fish_non.quota_discards",
"Benthosf/d_discards",
"Benthosc/s_discards",
"Carniv.zooplankton_discards",
"Bird_discards",
"Seal_discards",
"Cetacean_discards",
"Kelp_discards",
"Plank.fish_offal",
"Mig.fish_offal",
"Dem.fish_offal",
"Dem.fish_quota_limited_offal",
"Dem.fish_non.quota_offal",
"Benthosf/d_offal",
"Benthosc/s_offal",
"Carniv.zooplankton_offal",
"Bird_offal",
"Seal_offal",
"Cetacean_offal",
"Kelp_offal",
"Plank.fish_landings_processed_weight",
"Mig.fish_landings_processed_weight",
"Dem.fish_landings_processed_weight",
"Dem.fish_quota_limited_landings_processed_weight",
"Dem.fish_non.quota_landings_processed_weight",
"Benthosf/d_landings_processed_weight",
"Benthosc/s_landings_processed_weight",
"Carniv.zooplankton_landings_processed_weight",
"Bird_landings_processed_weight",
"Seal_landings_processed_weight",
"Cetacean_landings_processed_weight",
"Kelp_landings_processed_weight",
"Area_proportion_of_inshore_zone",
"Thickness_of_inshore_surface_layer",
"Thickness_of_offshore_surface_layer",
"Thickness_of_offshore_deep_layer",
"Area_proportion_inshore_rock",
"Area_proportion_inshore_sediment_s1",
"Area_proportion_inshore_sediment_s2",
"Area_proportion_inshore_sediment_s3",
"Area_proportion_offshore_rock",
"Area_proportion_offshore_sediment_d1",
"Area_proportion_offshore_sediment_d2",
"Area_proportion_offshore_sediment_d3",
"Thickness_of_inshore_sediment_layer_s1",
"Thickness_of_inshore_sediment_layer_s2",
"Thickness_of_inshore_sediment_layer_s3",
"Thickness_of_offshore_sediment_layer_d1",
"Thickness_of_offshore_sediment_layer_d2",
"Thickness_of_offshore_sediment_layer_d3",
"Porosity_of_inshore_sediment_layer_s1",
"Porosity_of_inshore_sediment_layer_s2",
"Porosity_of_inshore_sediment_layer_s3",
"Porosity_of_offshore_sediment_layer_d1",
"Porosity_of_offshore_sediment_layer_d2",
"Porosity_of_offshore_sediment_layer_d3")
names(annual_flux_results)<-c("Model_annual_flux","Units","Description")
#annual_flux_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "INSHORE_model_annualresults", identifier)
writecsv(annual_flux_results, filename, row.names=FALSE)
list(
mass_results = mass_results,
maxmass_results = maxmass_results,
minmass_results = minmass_results,
annual_flux_results = annual_flux_results
)
}
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