Nothing
R/derive_annual_results_offshore.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
derive_annual_results_offshore
#
# derive_annual_results_offshore.R
#
#' derive set of results for offshore only and write to files
#'
#' @param model model object
#' @param build model build object
#' @param output model output
#' @param aggregates aggregated model output
#'
#' @noRd
#
# ------------------------------------------------------------------------------
derive_annual_results_offshore <- 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_so <- elt(output, "detritus_so")
detritus_d <- elt(output, "detritus_d")
xR_detritus_d1 <- elt(output, "xR_detritus_d1")
xR_detritus_d2 <- elt(output, "xR_detritus_d2")
xR_detritus_d3 <- elt(output, "xR_detritus_d3")
discard_o <- elt(output, "discard_o")
ammonia_so <- elt(output, "ammonia_so")
ammonia_d <- elt(output, "ammonia_d")
nitrate_so <- elt(output, "nitrate_so")
nitrate_d <- elt(output, "nitrate_d")
phyt_so <- elt(output, "phyt_so")
phyt_d <- elt(output, "phyt_d")
omni_o <- elt(output, "omni_o")
carn_o <- elt(output, "carn_o")
benthslar_o <- elt(output, "benthslar_o")
benths_o <- elt(output, "benths_o")
benthclar_o <- elt(output, "benthclar_o")
benthc_o <- elt(output, "benthc_o")
fishplar_o <- elt(output, "fishplar_o")
fishp_o <- elt(output, "fishp_o")
fishm_o <- elt(output, "fishm_o")
fishdlar_o <- elt(output, "fishdlar_o")
fishd_o <- elt(output, "fishd_o")
bird_o <- elt(output, "bird_o")
seal_o <- elt(output, "seal_o")
ceta_o <- elt(output, "ceta_o")
fluxAMMinflow_o <- elt(output, "fluxAMMinflow_o")
fluxNITinflow_o <- elt(output, "fluxNITinflow_o")
fluxAMMoutflow_o <- elt(output, "fluxAMMoutflow_o")
fluxNIToutflow_o <- elt(output, "fluxNIToutflow_o")
fluxPHYTinflow_o <- elt(output, "fluxPHYTinflow_o")
fluxDETinflow_o <- elt(output, "fluxDETinflow_o")
fluxPHYToutflow_o <- elt(output, "fluxPHYToutflow_o")
fluxDEToutflow_o <- elt(output, "fluxDEToutflow_o")
atmosAMMinput_o <- elt(output, "atmosAMMinput_o")
atmosNITinput_o <- elt(output, "atmosNITinput_o")
vertnitflux <- elt(output, "vertnitflux")
fluxsedboundary_o <- elt(output, "fluxsedboundary_o")
mfish_imigration <- elt(output, "mfish_imigration")
mfish_emigration <- elt(output, "mfish_emigration")
netpprod_o <- elt(output, "netpprod_o")
NNCP_o <- elt(output, "NNCP_o")
fluxwcnit_phyt_o <- elt(output, "fluxwcnit_phyt_o")
fluxwcamm_phyt_o <- elt(output, "fluxwcamm_phyt_o")
phytgrossprod_o <- elt(output, "phytgrossprod_o")
omnigrossprod_o <- elt(output, "omnigrossprod_o")
carngrossprod_o <- elt(output, "carngrossprod_o")
pfishlargrossprod_o <- elt(output, "pfishlargrossprod_o")
dfishlargrossprod_o <- elt(output, "dfishlargrossprod_o")
pfishgrossprod_o <- elt(output, "pfishgrossprod_o")
mfishgrossprod_o <- elt(output, "mfishgrossprod_o")
dfishgrossprod_o <- elt(output, "dfishgrossprod_o")
benthslargrossprod_o <- elt(output, "benthslargrossprod_o")
benthclargrossprod_o <- elt(output, "benthclargrossprod_o")
benthsgrossprod_o <- elt(output, "benthsgrossprod_o")
benthcgrossprod_o <- elt(output, "benthcgrossprod_o")
birdgrossprod_o <- elt(output, "birdgrossprod_o")
sealgrossprod_o <- elt(output, "sealgrossprod_o")
cetagrossprod_o <- elt(output, "cetagrossprod_o")
omninetprod_o <- elt(output, "omninetprod_o")
carnnetprod_o <- elt(output, "carnnetprod_o")
pfishlarnetprod_o <- elt(output, "pfishlarnetprod_o")
dfishlarnetprod_o <- elt(output, "dfishlarnetprod_o")
pfishnetprod_o <- elt(output, "pfishnetprod_o")
mfishnetprod_o <- elt(output, "mfishnetprod_o")
dfishnetprod_o <- elt(output, "dfishnetprod_o")
benthslarnetprod_o <- elt(output, "benthslarnetprod_o")
benthclarnetprod_o <- elt(output, "benthclarnetprod_o")
benthsnetprod_o <- elt(output, "benthsnetprod_o")
benthcnetprod_o <- elt(output, "benthcnetprod_o")
birdnetprod_o <- elt(output, "birdnetprod_o")
sealnetprod_o <- elt(output, "sealnetprod_o")
cetanetprod_o <- elt(output, "cetanetprod_o")
landp_o <- elt(output, "landp_o")
landm_o <- elt(output, "landm_o")
landd_quota_o <- elt(output, "landd_quota_o")
landd_nonquota_o <- elt(output, "landd_nonquota_o")
landsb_o <- elt(output, "landsb_o")
landcb_o <- elt(output, "landcb_o")
landcz_o <- elt(output, "landcz_o")
landbd_o <- elt(output, "landbd_o")
landsl_o <- elt(output, "landsl_o")
landct_o <- elt(output, "landct_o")
discpel_o <- elt(output, "discpel_o")
discmig_o <- elt(output, "discmig_o")
discdem_quota_o <- elt(output, "discdem_quota_o")
discdem_nonquota_o <- elt(output, "discdem_nonquota_o")
discsb_o <- elt(output, "discsb_o")
disccb_o <- elt(output, "disccb_o")
disccz_o <- elt(output, "disccz_o")
discbd_o <- elt(output, "discbd_o")
discsl_o <- elt(output, "discsl_o")
discct_o <- elt(output, "discct_o")
offalpel_o <- elt(output, "offalpel_o")
offalmig_o <- elt(output, "offalmig_o")
offaldem_quota_o <- elt(output, "offaldem_quota_o")
offaldem_nonquota_o <- elt(output, "offaldem_nonquota_o")
offalsb_o <- elt(output, "offalsb_o")
offalcb_o <- elt(output, "offalcb_o")
offalcz_o <- elt(output, "offalcz_o")
offalbd_o <- elt(output, "offalbd_o")
offalsl_o <- elt(output, "offalsl_o")
offalct_o <- elt(output, "offalct_o")
# unpack aggregates:
x_detritus_o <- elt(aggregates, "x_detritus_o")
corpse_o <- elt(aggregates, "corpse_o")
x_ammonia_o <- elt(aggregates, "x_ammonia_o")
x_nitrate_o <- elt(aggregates, "x_nitrate_o")
totalN_o <- elt(aggregates, "totalN_o")
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")
NET_mfish_ext_o <- elt(aggregates, "NET_mfish_ext_o")
landd_o <- elt(aggregates, "landd_o")
discdem_o <- elt(aggregates, "discdem_o")
offaldem_o <- elt(aggregates, "offaldem_o")
#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_so[((nyears-1)*360+1):ndays])
aamass_d_detritus<-mean(detritus_d[((nyears-1)*360+1):ndays])
aamass_x_detritus<-mean(x_detritus_o[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamass_xR_detritus<-mean(xR_detritus_d1[((nyears-1)*360+1):ndays]
+ xR_detritus_d2[((nyears-1)*360+1):ndays]
+ xR_detritus_d3[((nyears-1)*360+1):ndays])
aamass_discard<-mean(discard_o[((nyears-1)*360+1):ndays])
aamass_corpse<-mean(corpse_o[((nyears-1)*360+1):ndays])
aamass_kelpdebris<-NA
aamass_s_ammonia<-mean(ammonia_so[((nyears-1)*360+1):ndays])
aamass_d_ammonia<-mean(ammonia_d[((nyears-1)*360+1):ndays])
aamass_x_ammonia<-mean(x_ammonia_o[((nyears-1)*360+1):ndays])
aamass_s_nitrate<-mean(nitrate_so[((nyears-1)*360+1):ndays])
aamass_d_nitrate<-mean(nitrate_d[((nyears-1)*360+1):ndays])
aamass_x_nitrate<-mean(x_nitrate_o[((nyears-1)*360+1):ndays])
aamass_kelpN<-NA
aamass_s_phyt<-mean(phyt_so[((nyears-1)*360+1):ndays])
aamass_d_phyt<-mean(phyt_d[((nyears-1)*360+1):ndays])
aamass_omni<-mean(omni_o[((nyears-1)*360+1):ndays])
aamass_carn<-mean(carn_o[((nyears-1)*360+1):ndays])
aamass_benthslar<-mean(benthslar_o[((nyears-1)*360+1):ndays])
aamass_benths<-mean(benths_o[((nyears-1)*360+1):ndays])
aamass_benthclar<-mean(benthclar_o[((nyears-1)*360+1):ndays])
aamass_benthc<-mean(benthc_o[((nyears-1)*360+1):ndays])
aamass_fishplar<-mean(fishplar_o[((nyears-1)*360+1):ndays])
aamass_fishp<-mean(fishp_o[((nyears-1)*360+1):ndays])
aamass_fishm<-mean(fishm_o[((nyears-1)*360+1):ndays])
aamass_fishdlar<-mean(fishdlar_o[((nyears-1)*360+1):ndays])
aamass_fishd<-mean(fishd_o[((nyears-1)*360+1):ndays])
aamass_bird<-mean(bird_o[((nyears-1)*360+1):ndays])
aamass_seal<-mean(seal_o[((nyears-1)*360+1):ndays])
aamass_ceta<-mean(ceta_o[((nyears-1)*360+1):ndays])
aamass_totalN<-mean(totalN_o[((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_omni
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
#Text descriptions of units set here for each row of output data
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]<-mass_results_descriptions
#The vector of text descriptions for each row of output is set in internal.R
colnames(mass_results)<-c("Model_annual_mean","Units","Description")
mass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "OFFSHORE_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_so[((nyears-1)*360+1):ndays])
aamaxmass_d_detritus<-max(detritus_d[((nyears-1)*360+1):ndays])
aamaxmass_x_detritus<-max(x_detritus_o[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamaxmass_xR_detritus<-max(xR_detritus_d1[((nyears-1)*360+1):ndays]
+ xR_detritus_d2[((nyears-1)*360+1):ndays]
+ xR_detritus_d3[((nyears-1)*360+1):ndays])
aamaxmass_discard<-max(discard_o[((nyears-1)*360+1):ndays])
aamaxmass_corpse<-max(corpse_o[((nyears-1)*360+1):ndays])
aamaxmass_kelpdebris<-NA
aamaxmass_s_ammonia<-max(ammonia_so[((nyears-1)*360+1):ndays])
aamaxmass_d_ammonia<-max(ammonia_d[((nyears-1)*360+1):ndays])
aamaxmass_x_ammonia<-max(x_ammonia_o[((nyears-1)*360+1):ndays])
aamaxmass_s_nitrate<-max(nitrate_so[((nyears-1)*360+1):ndays])
aamaxmass_d_nitrate<-max(nitrate_d[((nyears-1)*360+1):ndays])
aamaxmass_x_nitrate<-max(x_nitrate_o[((nyears-1)*360+1):ndays])
aamaxmass_kelpN<-NA
aamaxmass_s_phyt<-max(phyt_so[((nyears-1)*360+1):ndays])
aamaxmass_d_phyt<-max(phyt_d[((nyears-1)*360+1):ndays])
aamaxmass_omni<-max(omni_o[((nyears-1)*360+1):ndays])
aamaxmass_carn<-max(carn_o[((nyears-1)*360+1):ndays])
aamaxmass_benthslar<-max(benthslar_o[((nyears-1)*360+1):ndays])
aamaxmass_benths<-max(benths_o[((nyears-1)*360+1):ndays])
aamaxmass_benthclar<-max(benthclar_o[((nyears-1)*360+1):ndays])
aamaxmass_benthc<-max(benthc_o[((nyears-1)*360+1):ndays])
aamaxmass_fishplar<-max(fishplar_o[((nyears-1)*360+1):ndays])
aamaxmass_fishp<-max(fishp_o[((nyears-1)*360+1):ndays])
aamaxmass_fishm<-max(fishm_o[((nyears-1)*360+1):ndays])
aamaxmass_fishdlar<-max(fishdlar_o[((nyears-1)*360+1):ndays])
aamaxmass_fishd<-max(fishd_o[((nyears-1)*360+1):ndays])
aamaxmass_bird<-max(bird_o[((nyears-1)*360+1):ndays])
aamaxmass_seal<-max(seal_o[((nyears-1)*360+1):ndays])
aamaxmass_ceta<-max(ceta_o[((nyears-1)*360+1):ndays])
aamaxmass_totalN<-max(totalN_o[((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_omni
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, "OFFSHORE_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_so[((nyears-1)*360+1):ndays])
aaminmass_d_detritus<-min(detritus_d[((nyears-1)*360+1):ndays])
aaminmass_x_detritus<-min(x_detritus_o[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aaminmass_xR_detritus<-min(xR_detritus_d1[((nyears-1)*360+1):ndays]
+ xR_detritus_d2[((nyears-1)*360+1):ndays]
+ xR_detritus_d3[((nyears-1)*360+1):ndays])
aaminmass_discard<-min(discard_o[((nyears-1)*360+1):ndays])
aaminmass_corpse<-min(corpse_o[((nyears-1)*360+1):ndays])
aaminmass_kelpdebris<-NA
aaminmass_s_ammonia<-min(ammonia_so[((nyears-1)*360+1):ndays])
aaminmass_d_ammonia<-min(ammonia_d[((nyears-1)*360+1):ndays])
aaminmass_x_ammonia<-min(x_ammonia_o[((nyears-1)*360+1):ndays])
aaminmass_s_nitrate<-min(nitrate_so[((nyears-1)*360+1):ndays])
aaminmass_d_nitrate<-min(nitrate_d[((nyears-1)*360+1):ndays])
aaminmass_x_nitrate<-min(x_nitrate_o[((nyears-1)*360+1):ndays])
aaminmass_kelpN<-NA
aaminmass_s_phyt<-min(phyt_so[((nyears-1)*360+1):ndays])
aaminmass_d_phyt<-min(phyt_d[((nyears-1)*360+1):ndays])
aaminmass_omni<-min(omni_o[((nyears-1)*360+1):ndays])
aaminmass_carn<-min(carn_o[((nyears-1)*360+1):ndays])
aaminmass_benthslar<-min(benthslar_o[((nyears-1)*360+1):ndays])
aaminmass_benths<-min(benths_o[((nyears-1)*360+1):ndays])
aaminmass_benthclar<-min(benthclar_o[((nyears-1)*360+1):ndays])
aaminmass_benthc<-min(benthc_o[((nyears-1)*360+1):ndays])
aaminmass_fishplar<-min(fishplar_o[((nyears-1)*360+1):ndays])
aaminmass_fishp<-min(fishp_o[((nyears-1)*360+1):ndays])
aaminmass_fishm<-min(fishm_o[((nyears-1)*360+1):ndays])
aaminmass_fishdlar<-min(fishdlar_o[((nyears-1)*360+1):ndays])
aaminmass_fishd<-min(fishd_o[((nyears-1)*360+1):ndays])
aaminmass_bird<-min(bird_o[((nyears-1)*360+1):ndays])
aaminmass_seal<-min(seal_o[((nyears-1)*360+1):ndays])
aaminmass_ceta<-min(ceta_o[((nyears-1)*360+1):ndays])
aaminmass_totalN<-min(totalN_o[((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_omni
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, "OFFSHORE_model_minimum_biomass", identifier)
writecsv(minmass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#Extract all of the derived rate variables for the final year
DINinflow<-(fluxAMMinflow_o[ndays]-fluxAMMinflow_o[((nyears-1)*360+1)]) + (fluxNITinflow_o[ndays]-fluxNITinflow_o[((nyears-1)*360+1)])
DINoutflow<-(fluxAMMoutflow_o[ndays]-fluxAMMoutflow_o[((nyears-1)*360+1)]) + (fluxNIToutflow_o[ndays]-fluxNIToutflow_o[((nyears-1)*360+1)])
PARTinflow<-(fluxPHYTinflow_o[ndays]-fluxPHYTinflow_o[((nyears-1)*360+1)]) + (fluxDETinflow_o[ndays]-fluxDETinflow_o[((nyears-1)*360+1)])
PARToutflow<-(fluxPHYToutflow_o[ndays]-fluxPHYToutflow_o[((nyears-1)*360+1)]) + (fluxDEToutflow_o[ndays]-fluxDEToutflow_o[((nyears-1)*360+1)])
atmosphereDINinput<-(atmosAMMinput_o[ndays]-atmosAMMinput_o[((nyears-1)*360+1)]) + (atmosNITinput_o[ndays]-atmosNITinput_o[((nyears-1)*360+1)])
riverDINinflow<-0
riverPARTinflow<-0
sumDINinflow<-(fluxAMMinflow_o[ndays-90]-fluxAMMinflow_o[((nyears-1)*360+1+89)]) + (fluxNITinflow_o[ndays-90]-fluxNITinflow_o[((nyears-1)*360+1+89)])
sumDINoutflow<-(fluxAMMoutflow_o[ndays-90]-fluxAMMoutflow_o[((nyears-1)*360+1+89)]) + (fluxNIToutflow_o[ndays-90]-fluxNIToutflow_o[((nyears-1)*360+1+89)])
sumPARTinflow<-(fluxPHYTinflow_o[ndays-90]-fluxPHYTinflow_o[((nyears-1)*360+1+89)]) + (fluxDETinflow_o[ndays-90]-fluxDETinflow_o[((nyears-1)*360+1+89)])
sumPARToutflow<-(fluxPHYToutflow_o[ndays-90]-fluxPHYToutflow_o[((nyears-1)*360+1+89)]) + (fluxDEToutflow_o[ndays-90]-fluxDEToutflow_o[((nyears-1)*360+1+89)])
sumriverDINinflow<-0
sumatmosDINinput<-(atmosAMMinput_o[ndays-90]-atmosAMMinput_o[((nyears-1)*360+1+89)]) + (atmosNITinput_o[ndays-90]-atmosNITinput_o[((nyears-1)*360+1+89)])
surfvertnitflux<-vertnitflux[ndays]-vertnitflux[((nyears-1)*360+1)]
surfhoriznitflux<-NA
sumriverNITinflow<-0
sumatmosNITinput<-(atmosNITinput_o[ndays-90]-atmosNITinput_o[((nyears-1)*360+1+89)]) # April - September inclusive
Flux_sedboundary <- (fluxsedboundary_o[ndays]-fluxsedboundary_o[((nyears-1)*360+1)])
#kelp_beachcast<-((fluxkelpdebris_beachexport[ndays]-fluxkelpdebris_beachexport[((nyears-1)*360+1)]))
kelp_beachcast<-NA
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)]
Mfish_annual_imig <- mfish_imigration[ndays]-mfish_imigration[((nyears-1)*360+1)]
Mfish_annual_emig <- mfish_emigration[ndays]-mfish_emigration[((nyears-1)*360+1)]
NETPrimaryP<-netpprod_o[ndays]-netpprod_o[((nyears-1)*360+1)]
MMP<-(max(nitrate_so[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays])) - (min(nitrate_so[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays]))
NNCP<-NNCP_o[ndays]-NNCP_o[((nyears-1)*360+1)]
PhytNitUp<-fluxwcnit_phyt_o[ndays]-fluxwcnit_phyt_o[((nyears-1)*360+1)]
PhytAmmUp<-fluxwcamm_phyt_o[ndays]-fluxwcamm_phyt_o[((nyears-1)*360+1)]
PNP<-MMP+sumriverNITinflow+sumatmosNITinput
fratio<-PNP/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 <- NA
Phytgrossprod <- phytgrossprod_o[ndays] - phytgrossprod_o[((nyears-1)*360+1)]
omnigrossprod <- omnigrossprod_o[ndays] - omnigrossprod_o[((nyears-1)*360+1)]
Carngrossprod <- carngrossprod_o[ndays] - carngrossprod_o[((nyears-1)*360+1)]
Fishplargrossprod <- pfishlargrossprod_o[ndays] - pfishlargrossprod_o[((nyears-1)*360+1)]
Fishdlargrossprod <- dfishlargrossprod_o[ndays] - dfishlargrossprod_o[((nyears-1)*360+1)]
Fishpgrossprod <- pfishgrossprod_o[ndays] - pfishgrossprod_o[((nyears-1)*360+1)]
Fishmgrossprod <- mfishgrossprod_o[ndays] - mfishgrossprod_o[((nyears-1)*360+1)]
Fishdgrossprod <- dfishgrossprod_o[ndays] - dfishgrossprod_o[((nyears-1)*360+1)]
Benthslargrossprod <- benthslargrossprod_o[ndays] - benthslargrossprod_o[((nyears-1)*360+1)]
Benthclargrossprod <- benthclargrossprod_o[ndays] - benthclargrossprod_o[((nyears-1)*360+1)]
Benthsgrossprod <- benthsgrossprod_o[ndays] - benthsgrossprod_o[((nyears-1)*360+1)]
Benthcgrossprod <- benthcgrossprod_o[ndays] - benthcgrossprod_o[((nyears-1)*360+1)]
Birdgrossprod <- birdgrossprod_o[ndays] - birdgrossprod_o[((nyears-1)*360+1)]
Sealgrossprod <- sealgrossprod_o[ndays] - sealgrossprod_o[((nyears-1)*360+1)]
Cetagrossprod <- cetagrossprod_o[ndays] - cetagrossprod_o[((nyears-1)*360+1)]
omninetprod <- omninetprod_o[ndays] - omninetprod_o[((nyears-1)*360+1)]
Carnnetprod <- carnnetprod_o[ndays] - carnnetprod_o[((nyears-1)*360+1)]
Fishplarnetprod <- pfishlarnetprod_o[ndays] - pfishlarnetprod_o[((nyears-1)*360+1)]
Fishdlarnetprod <- dfishlarnetprod_o[ndays] - dfishlarnetprod_o[((nyears-1)*360+1)]
Fishpnetprod <- pfishnetprod_o[ndays] - pfishnetprod_o[((nyears-1)*360+1)]
Fishmnetprod <- mfishnetprod_o[ndays] - mfishnetprod_o[((nyears-1)*360+1)]
Fishdnetprod <- dfishnetprod_o[ndays] - dfishnetprod_o[((nyears-1)*360+1)]
Benthslarnetprod <- benthslarnetprod_o[ndays] - benthslarnetprod_o[((nyears-1)*360+1)]
Benthclarnetprod <- benthclarnetprod_o[ndays] - benthclarnetprod_o[((nyears-1)*360+1)]
Benthsnetprod <- benthsnetprod_o[ndays] - benthsnetprod_o[((nyears-1)*360+1)]
Benthcnetprod <- benthcnetprod_o[ndays] - benthcnetprod_o[((nyears-1)*360+1)]
Birdnetprod <- birdnetprod_o[ndays] - birdnetprod_o[((nyears-1)*360+1)]
Sealnetprod <- sealnetprod_o[ndays] - sealnetprod_o[((nyears-1)*360+1)]
Cetanetprod <- cetanetprod_o[ndays] - cetanetprod_o[((nyears-1)*360+1)]
WCdetritusprod <- NA
#SEDdetritusprod <- fluxcorp_xdet[ndays] - fluxcorp_xdet[((nyears-1)*360+1)] +
SEDdetritusprod <- NA
Kelpdebrisprod <- NA
Corpseprod <- NA
#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
#Excludes mineralisation of detritus
Pelagammprod <- NA
#Excludes mineralisation of detritus
Benthammprod <- NA
WCmineralisation <- NA
SEDmineralisation <- NA
WCnitrification <- NA
SEDnitrification <- NA
WCdenitrification <- NA
SEDdenitrification <- NA
#Includes excretion by benthos
SEDWCammflux <- NA
SEDWCnitflux <- NA
Fluxdet_omni <- NA
Fluxphyt_omni <- NA
Fluxbenthslar_omni <- NA
Fluxbenthclar_omni <- NA
Fluxomni_carn <- NA
Fluxpfishlar_carn <- NA
Fluxdfishlar_carn <- NA
Fluxbenthslar_carn <- NA
Fluxbenthclar_carn <- NA
Fluxomni_pfishlar <- NA
Fluxbenthslar_pfishlar <- NA
Fluxbenthclar_pfishlar <- NA
Fluxomni_dfishlar <- NA
Fluxbenthslar_dfishlar <- NA
Fluxbenthclar_dfishlar <- NA
Fluxomni_pfish <- NA
Fluxcarn_pfish <- NA
Fluxpfishlar_pfish <- NA
Fluxdfishlar_pfish <- NA
Fluxbenthslar_pfish <- NA
Fluxbenthclar_pfish <- NA
Fluxomni_mfish <- NA
Fluxcarn_mfish <- NA
Fluxpfishlar_mfish <- NA
Fluxdfishlar_mfish <- NA
Fluxbenthslar_mfish <- NA
Fluxbenthclar_mfish <- NA
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 <- NA
Fluxphyt_benthslar <- NA
Fluxdet_benthclar <- NA
Fluxphyt_benthclar <- NA
Fluxdet_benths <- NA
Fluxseddet_benths <- NA
Fluxphyt_benths <- NA
Fluxkelp_benthc <- NA
Fluxkelpdebris_benthc <- NA
Fluxcorp_benthc <- NA
Fluxbenths_benthc <- NA
Fluxcorp_bird <- NA
Fluxdisc_bird <- NA
#Fluxomni_bird <- NA
Fluxcarn_bird <- NA
Fluxpfish_bird <- NA
Fluxmfish_bird <- NA
Fluxdfish_bird <- NA
Fluxbenths_bird <- NA
Fluxbenthc_bird <- NA
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 <- NA
Fluxomni_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<- omninetprod +
+ Carnnetprod +
+ Benthsnetprod +
+ Benthcnetprod +
+ Benthslarnetprod +
+ Benthclarnetprod +
+ Fishplarnetprod +
+ Fishdlarnetprod +
+ Fishpnetprod +
+ Fishmnetprod +
+ Fishdnetprod +
+ Birdnetprod +
+ Sealnetprod +
+ Cetanetprod
export_from_2prod<- NA
Pfish_annual_spawn <- NA
Pfish_annual_recruit <- NA
Dfish_annual_spawn <- NA
Dfish_annual_recruit <- NA
Benths_annual_spawn <- NA
Benths_annual_recruit <- NA
Benthc_annual_spawn <- NA
Benthc_annual_recruit <- NA
FishpLand_livewt<-landp_o[ndays]-landp_o[((nyears-1)*360+1)]
FishmLand_livewt<-landm_o[ndays]-landm_o[((nyears-1)*360+1)]
FishdLand_livewt<-landd_o[ndays]-landd_o[((nyears-1)*360+1)]
Fishd_qLand_livewt<-landd_quota_o[ndays]-landd_quota_o[((nyears-1)*360+1)]
Fishd_nqLand_livewt<-landd_nonquota_o[ndays]-landd_nonquota_o[((nyears-1)*360+1)]
BenthsLand_livewt <- landsb_o[ndays]-landsb_o[((nyears-1)*360+1)]
BenthcLand_livewt <- landcb_o[ndays]-landcb_o[((nyears-1)*360+1)]
CarnzLand_livewt <- landcz_o[ndays]-landcz_o[((nyears-1)*360+1)]
BirdLand_livewt <- landbd_o[ndays]-landbd_o[((nyears-1)*360+1)]
SealLand_livewt <- landsl_o[ndays]-landsl_o[((nyears-1)*360+1)]
CetaLand_livewt <- landct_o[ndays]-landct_o[((nyears-1)*360+1)]
KelpLand_livewt <- NA
FishpDiscard<-discpel_o[ndays]-discpel_o[((nyears-1)*360+1)]
FishmDiscard<-discmig_o[ndays]-discmig_o[((nyears-1)*360+1)]
FishdDiscard<-discdem_o[ndays]-discdem_o[((nyears-1)*360+1)]
Fishd_qDiscard<-discdem_quota_o[ndays]-discdem_quota_o[((nyears-1)*360+1)]
Fishd_nqDiscard<-discdem_nonquota_o[ndays]-discdem_nonquota_o[((nyears-1)*360+1)]
BenthsDiscard <- discsb_o[ndays]-discsb_o[((nyears-1)*360+1)]
BenthcDiscard <- disccb_o[ndays]-disccb_o[((nyears-1)*360+1)]
CarnzDiscard <- disccz_o[ndays]-disccz_o[((nyears-1)*360+1)]
BirdDiscard <- discbd_o[ndays]-discbd_o[((nyears-1)*360+1)]
SealDiscard <- discsl_o[ndays]-discsl_o[((nyears-1)*360+1)]
CetaDiscard <- discct_o[ndays]-discct_o[((nyears-1)*360+1)]
KelpDiscard <- NA
FishpOffal<-offalpel_o[ndays]-offalpel_o[((nyears-1)*360+1)]
FishmOffal<-offalmig_o[ndays]-offalmig_o[((nyears-1)*360+1)]
FishdOffal<-offaldem_o[ndays]-offaldem_o[((nyears-1)*360+1)]
Fishd_qOffal<-offaldem_quota_o[ndays]-offaldem_quota_o[((nyears-1)*360+1)]
Fishd_nqOffal<-offaldem_nonquota_o[ndays]-offaldem_nonquota_o[((nyears-1)*360+1)]
BenthsOffal <- offalsb_o[ndays]-offalsb_o[((nyears-1)*360+1)]
BenthcOffal <- offalcb_o[ndays]-offalcb_o[((nyears-1)*360+1)]
CarnzOffal <- offalcz_o[ndays]-offalcz_o[((nyears-1)*360+1)]
BirdOffal <- offalbd_o[ndays]-offalbd_o[((nyears-1)*360+1)]
SealOffal <- offalsl_o[ndays]-offalsl_o[((nyears-1)*360+1)]
CetaOffal <- offalct_o[ndays]-offalct_o[((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]<-NNCP
annual_flux_results[33,1]<-PhytNitUp
annual_flux_results[34,1]<-PhytAmmUp
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]<-omnigrossprod
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]<-omninetprod
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_omni
annual_flux_results[85,1]<-Fluxphyt_omni
annual_flux_results[86,1]<-Fluxbenthslar_omni
annual_flux_results[87,1]<-Fluxbenthclar_omni
annual_flux_results[88,1]<-Fluxomni_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]<-Fluxomni_pfishlar
annual_flux_results[94,1]<-Fluxbenthslar_pfishlar
annual_flux_results[95,1]<-Fluxbenthclar_pfishlar
annual_flux_results[96,1]<-Fluxomni_dfishlar
annual_flux_results[97,1]<-Fluxbenthslar_dfishlar
annual_flux_results[98,1]<-Fluxbenthclar_dfishlar
annual_flux_results[99,1]<-Fluxomni_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]<-Fluxomni_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]<-Fluxomni_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]<-Fluxomni_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
#Text descriptions of units set here for each row of output data
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]<-annual_flux_descriptions
#The vector of text descriptions for each row of output is set in internal.R
names(annual_flux_results)<-c("Model_annual_flux","Units","Description")
filename = csvname(resultsdir, "OFFSHORE_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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Defines functions derive_annual_results_offshore
#
# derive_annual_results_offshore.R
#
#' derive set of results for offshore only and write to files
#'
#' @param model model object
#' @param build model build object
#' @param output model output
#' @param aggregates aggregated model output
#'
#' @noRd
#
# ------------------------------------------------------------------------------
derive_annual_results_offshore <- 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_so <- elt(output, "detritus_so")
detritus_d <- elt(output, "detritus_d")
xR_detritus_d1 <- elt(output, "xR_detritus_d1")
xR_detritus_d2 <- elt(output, "xR_detritus_d2")
xR_detritus_d3 <- elt(output, "xR_detritus_d3")
discard_o <- elt(output, "discard_o")
ammonia_so <- elt(output, "ammonia_so")
ammonia_d <- elt(output, "ammonia_d")
nitrate_so <- elt(output, "nitrate_so")
nitrate_d <- elt(output, "nitrate_d")
phyt_so <- elt(output, "phyt_so")
phyt_d <- elt(output, "phyt_d")
omni_o <- elt(output, "omni_o")
carn_o <- elt(output, "carn_o")
benthslar_o <- elt(output, "benthslar_o")
benths_o <- elt(output, "benths_o")
benthclar_o <- elt(output, "benthclar_o")
benthc_o <- elt(output, "benthc_o")
fishplar_o <- elt(output, "fishplar_o")
fishp_o <- elt(output, "fishp_o")
fishm_o <- elt(output, "fishm_o")
fishdlar_o <- elt(output, "fishdlar_o")
fishd_o <- elt(output, "fishd_o")
bird_o <- elt(output, "bird_o")
seal_o <- elt(output, "seal_o")
ceta_o <- elt(output, "ceta_o")
fluxAMMinflow_o <- elt(output, "fluxAMMinflow_o")
fluxNITinflow_o <- elt(output, "fluxNITinflow_o")
fluxAMMoutflow_o <- elt(output, "fluxAMMoutflow_o")
fluxNIToutflow_o <- elt(output, "fluxNIToutflow_o")
fluxPHYTinflow_o <- elt(output, "fluxPHYTinflow_o")
fluxDETinflow_o <- elt(output, "fluxDETinflow_o")
fluxPHYToutflow_o <- elt(output, "fluxPHYToutflow_o")
fluxDEToutflow_o <- elt(output, "fluxDEToutflow_o")
atmosAMMinput_o <- elt(output, "atmosAMMinput_o")
atmosNITinput_o <- elt(output, "atmosNITinput_o")
vertnitflux <- elt(output, "vertnitflux")
fluxsedboundary_o <- elt(output, "fluxsedboundary_o")
mfish_imigration <- elt(output, "mfish_imigration")
mfish_emigration <- elt(output, "mfish_emigration")
netpprod_o <- elt(output, "netpprod_o")
NNCP_o <- elt(output, "NNCP_o")
fluxwcnit_phyt_o <- elt(output, "fluxwcnit_phyt_o")
fluxwcamm_phyt_o <- elt(output, "fluxwcamm_phyt_o")
phytgrossprod_o <- elt(output, "phytgrossprod_o")
omnigrossprod_o <- elt(output, "omnigrossprod_o")
carngrossprod_o <- elt(output, "carngrossprod_o")
pfishlargrossprod_o <- elt(output, "pfishlargrossprod_o")
dfishlargrossprod_o <- elt(output, "dfishlargrossprod_o")
pfishgrossprod_o <- elt(output, "pfishgrossprod_o")
mfishgrossprod_o <- elt(output, "mfishgrossprod_o")
dfishgrossprod_o <- elt(output, "dfishgrossprod_o")
benthslargrossprod_o <- elt(output, "benthslargrossprod_o")
benthclargrossprod_o <- elt(output, "benthclargrossprod_o")
benthsgrossprod_o <- elt(output, "benthsgrossprod_o")
benthcgrossprod_o <- elt(output, "benthcgrossprod_o")
birdgrossprod_o <- elt(output, "birdgrossprod_o")
sealgrossprod_o <- elt(output, "sealgrossprod_o")
cetagrossprod_o <- elt(output, "cetagrossprod_o")
omninetprod_o <- elt(output, "omninetprod_o")
carnnetprod_o <- elt(output, "carnnetprod_o")
pfishlarnetprod_o <- elt(output, "pfishlarnetprod_o")
dfishlarnetprod_o <- elt(output, "dfishlarnetprod_o")
pfishnetprod_o <- elt(output, "pfishnetprod_o")
mfishnetprod_o <- elt(output, "mfishnetprod_o")
dfishnetprod_o <- elt(output, "dfishnetprod_o")
benthslarnetprod_o <- elt(output, "benthslarnetprod_o")
benthclarnetprod_o <- elt(output, "benthclarnetprod_o")
benthsnetprod_o <- elt(output, "benthsnetprod_o")
benthcnetprod_o <- elt(output, "benthcnetprod_o")
birdnetprod_o <- elt(output, "birdnetprod_o")
sealnetprod_o <- elt(output, "sealnetprod_o")
cetanetprod_o <- elt(output, "cetanetprod_o")
landp_o <- elt(output, "landp_o")
landm_o <- elt(output, "landm_o")
landd_quota_o <- elt(output, "landd_quota_o")
landd_nonquota_o <- elt(output, "landd_nonquota_o")
landsb_o <- elt(output, "landsb_o")
landcb_o <- elt(output, "landcb_o")
landcz_o <- elt(output, "landcz_o")
landbd_o <- elt(output, "landbd_o")
landsl_o <- elt(output, "landsl_o")
landct_o <- elt(output, "landct_o")
discpel_o <- elt(output, "discpel_o")
discmig_o <- elt(output, "discmig_o")
discdem_quota_o <- elt(output, "discdem_quota_o")
discdem_nonquota_o <- elt(output, "discdem_nonquota_o")
discsb_o <- elt(output, "discsb_o")
disccb_o <- elt(output, "disccb_o")
disccz_o <- elt(output, "disccz_o")
discbd_o <- elt(output, "discbd_o")
discsl_o <- elt(output, "discsl_o")
discct_o <- elt(output, "discct_o")
offalpel_o <- elt(output, "offalpel_o")
offalmig_o <- elt(output, "offalmig_o")
offaldem_quota_o <- elt(output, "offaldem_quota_o")
offaldem_nonquota_o <- elt(output, "offaldem_nonquota_o")
offalsb_o <- elt(output, "offalsb_o")
offalcb_o <- elt(output, "offalcb_o")
offalcz_o <- elt(output, "offalcz_o")
offalbd_o <- elt(output, "offalbd_o")
offalsl_o <- elt(output, "offalsl_o")
offalct_o <- elt(output, "offalct_o")
# unpack aggregates:
x_detritus_o <- elt(aggregates, "x_detritus_o")
corpse_o <- elt(aggregates, "corpse_o")
x_ammonia_o <- elt(aggregates, "x_ammonia_o")
x_nitrate_o <- elt(aggregates, "x_nitrate_o")
totalN_o <- elt(aggregates, "totalN_o")
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")
NET_mfish_ext_o <- elt(aggregates, "NET_mfish_ext_o")
landd_o <- elt(aggregates, "landd_o")
discdem_o <- elt(aggregates, "discdem_o")
offaldem_o <- elt(aggregates, "offaldem_o")
#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_so[((nyears-1)*360+1):ndays])
aamass_d_detritus<-mean(detritus_d[((nyears-1)*360+1):ndays])
aamass_x_detritus<-mean(x_detritus_o[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamass_xR_detritus<-mean(xR_detritus_d1[((nyears-1)*360+1):ndays]
+ xR_detritus_d2[((nyears-1)*360+1):ndays]
+ xR_detritus_d3[((nyears-1)*360+1):ndays])
aamass_discard<-mean(discard_o[((nyears-1)*360+1):ndays])
aamass_corpse<-mean(corpse_o[((nyears-1)*360+1):ndays])
aamass_kelpdebris<-NA
aamass_s_ammonia<-mean(ammonia_so[((nyears-1)*360+1):ndays])
aamass_d_ammonia<-mean(ammonia_d[((nyears-1)*360+1):ndays])
aamass_x_ammonia<-mean(x_ammonia_o[((nyears-1)*360+1):ndays])
aamass_s_nitrate<-mean(nitrate_so[((nyears-1)*360+1):ndays])
aamass_d_nitrate<-mean(nitrate_d[((nyears-1)*360+1):ndays])
aamass_x_nitrate<-mean(x_nitrate_o[((nyears-1)*360+1):ndays])
aamass_kelpN<-NA
aamass_s_phyt<-mean(phyt_so[((nyears-1)*360+1):ndays])
aamass_d_phyt<-mean(phyt_d[((nyears-1)*360+1):ndays])
aamass_omni<-mean(omni_o[((nyears-1)*360+1):ndays])
aamass_carn<-mean(carn_o[((nyears-1)*360+1):ndays])
aamass_benthslar<-mean(benthslar_o[((nyears-1)*360+1):ndays])
aamass_benths<-mean(benths_o[((nyears-1)*360+1):ndays])
aamass_benthclar<-mean(benthclar_o[((nyears-1)*360+1):ndays])
aamass_benthc<-mean(benthc_o[((nyears-1)*360+1):ndays])
aamass_fishplar<-mean(fishplar_o[((nyears-1)*360+1):ndays])
aamass_fishp<-mean(fishp_o[((nyears-1)*360+1):ndays])
aamass_fishm<-mean(fishm_o[((nyears-1)*360+1):ndays])
aamass_fishdlar<-mean(fishdlar_o[((nyears-1)*360+1):ndays])
aamass_fishd<-mean(fishd_o[((nyears-1)*360+1):ndays])
aamass_bird<-mean(bird_o[((nyears-1)*360+1):ndays])
aamass_seal<-mean(seal_o[((nyears-1)*360+1):ndays])
aamass_ceta<-mean(ceta_o[((nyears-1)*360+1):ndays])
aamass_totalN<-mean(totalN_o[((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_omni
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
#Text descriptions of units set here for each row of output data
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]<-mass_results_descriptions
#The vector of text descriptions for each row of output is set in internal.R
colnames(mass_results)<-c("Model_annual_mean","Units","Description")
mass_results
#Print the data to a csv file
#-----------------------------------------------------------------
filename = csvname(resultsdir, "OFFSHORE_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_so[((nyears-1)*360+1):ndays])
aamaxmass_d_detritus<-max(detritus_d[((nyears-1)*360+1):ndays])
aamaxmass_x_detritus<-max(x_detritus_o[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aamaxmass_xR_detritus<-max(xR_detritus_d1[((nyears-1)*360+1):ndays]
+ xR_detritus_d2[((nyears-1)*360+1):ndays]
+ xR_detritus_d3[((nyears-1)*360+1):ndays])
aamaxmass_discard<-max(discard_o[((nyears-1)*360+1):ndays])
aamaxmass_corpse<-max(corpse_o[((nyears-1)*360+1):ndays])
aamaxmass_kelpdebris<-NA
aamaxmass_s_ammonia<-max(ammonia_so[((nyears-1)*360+1):ndays])
aamaxmass_d_ammonia<-max(ammonia_d[((nyears-1)*360+1):ndays])
aamaxmass_x_ammonia<-max(x_ammonia_o[((nyears-1)*360+1):ndays])
aamaxmass_s_nitrate<-max(nitrate_so[((nyears-1)*360+1):ndays])
aamaxmass_d_nitrate<-max(nitrate_d[((nyears-1)*360+1):ndays])
aamaxmass_x_nitrate<-max(x_nitrate_o[((nyears-1)*360+1):ndays])
aamaxmass_kelpN<-NA
aamaxmass_s_phyt<-max(phyt_so[((nyears-1)*360+1):ndays])
aamaxmass_d_phyt<-max(phyt_d[((nyears-1)*360+1):ndays])
aamaxmass_omni<-max(omni_o[((nyears-1)*360+1):ndays])
aamaxmass_carn<-max(carn_o[((nyears-1)*360+1):ndays])
aamaxmass_benthslar<-max(benthslar_o[((nyears-1)*360+1):ndays])
aamaxmass_benths<-max(benths_o[((nyears-1)*360+1):ndays])
aamaxmass_benthclar<-max(benthclar_o[((nyears-1)*360+1):ndays])
aamaxmass_benthc<-max(benthc_o[((nyears-1)*360+1):ndays])
aamaxmass_fishplar<-max(fishplar_o[((nyears-1)*360+1):ndays])
aamaxmass_fishp<-max(fishp_o[((nyears-1)*360+1):ndays])
aamaxmass_fishm<-max(fishm_o[((nyears-1)*360+1):ndays])
aamaxmass_fishdlar<-max(fishdlar_o[((nyears-1)*360+1):ndays])
aamaxmass_fishd<-max(fishd_o[((nyears-1)*360+1):ndays])
aamaxmass_bird<-max(bird_o[((nyears-1)*360+1):ndays])
aamaxmass_seal<-max(seal_o[((nyears-1)*360+1):ndays])
aamaxmass_ceta<-max(ceta_o[((nyears-1)*360+1):ndays])
aamaxmass_totalN<-max(totalN_o[((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_omni
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, "OFFSHORE_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_so[((nyears-1)*360+1):ndays])
aaminmass_d_detritus<-min(detritus_d[((nyears-1)*360+1):ndays])
aaminmass_x_detritus<-min(x_detritus_o[((nyears-1)*360+1):ndays]) #Includes both labile and refractory detritus
aaminmass_xR_detritus<-min(xR_detritus_d1[((nyears-1)*360+1):ndays]
+ xR_detritus_d2[((nyears-1)*360+1):ndays]
+ xR_detritus_d3[((nyears-1)*360+1):ndays])
aaminmass_discard<-min(discard_o[((nyears-1)*360+1):ndays])
aaminmass_corpse<-min(corpse_o[((nyears-1)*360+1):ndays])
aaminmass_kelpdebris<-NA
aaminmass_s_ammonia<-min(ammonia_so[((nyears-1)*360+1):ndays])
aaminmass_d_ammonia<-min(ammonia_d[((nyears-1)*360+1):ndays])
aaminmass_x_ammonia<-min(x_ammonia_o[((nyears-1)*360+1):ndays])
aaminmass_s_nitrate<-min(nitrate_so[((nyears-1)*360+1):ndays])
aaminmass_d_nitrate<-min(nitrate_d[((nyears-1)*360+1):ndays])
aaminmass_x_nitrate<-min(x_nitrate_o[((nyears-1)*360+1):ndays])
aaminmass_kelpN<-NA
aaminmass_s_phyt<-min(phyt_so[((nyears-1)*360+1):ndays])
aaminmass_d_phyt<-min(phyt_d[((nyears-1)*360+1):ndays])
aaminmass_omni<-min(omni_o[((nyears-1)*360+1):ndays])
aaminmass_carn<-min(carn_o[((nyears-1)*360+1):ndays])
aaminmass_benthslar<-min(benthslar_o[((nyears-1)*360+1):ndays])
aaminmass_benths<-min(benths_o[((nyears-1)*360+1):ndays])
aaminmass_benthclar<-min(benthclar_o[((nyears-1)*360+1):ndays])
aaminmass_benthc<-min(benthc_o[((nyears-1)*360+1):ndays])
aaminmass_fishplar<-min(fishplar_o[((nyears-1)*360+1):ndays])
aaminmass_fishp<-min(fishp_o[((nyears-1)*360+1):ndays])
aaminmass_fishm<-min(fishm_o[((nyears-1)*360+1):ndays])
aaminmass_fishdlar<-min(fishdlar_o[((nyears-1)*360+1):ndays])
aaminmass_fishd<-min(fishd_o[((nyears-1)*360+1):ndays])
aaminmass_bird<-min(bird_o[((nyears-1)*360+1):ndays])
aaminmass_seal<-min(seal_o[((nyears-1)*360+1):ndays])
aaminmass_ceta<-min(ceta_o[((nyears-1)*360+1):ndays])
aaminmass_totalN<-min(totalN_o[((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_omni
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, "OFFSHORE_model_minimum_biomass", identifier)
writecsv(minmass_results, filename, row.names=FALSE)
#-------------------------------------------------------------------------------------------------------
#Extract all of the derived rate variables for the final year
DINinflow<-(fluxAMMinflow_o[ndays]-fluxAMMinflow_o[((nyears-1)*360+1)]) + (fluxNITinflow_o[ndays]-fluxNITinflow_o[((nyears-1)*360+1)])
DINoutflow<-(fluxAMMoutflow_o[ndays]-fluxAMMoutflow_o[((nyears-1)*360+1)]) + (fluxNIToutflow_o[ndays]-fluxNIToutflow_o[((nyears-1)*360+1)])
PARTinflow<-(fluxPHYTinflow_o[ndays]-fluxPHYTinflow_o[((nyears-1)*360+1)]) + (fluxDETinflow_o[ndays]-fluxDETinflow_o[((nyears-1)*360+1)])
PARToutflow<-(fluxPHYToutflow_o[ndays]-fluxPHYToutflow_o[((nyears-1)*360+1)]) + (fluxDEToutflow_o[ndays]-fluxDEToutflow_o[((nyears-1)*360+1)])
atmosphereDINinput<-(atmosAMMinput_o[ndays]-atmosAMMinput_o[((nyears-1)*360+1)]) + (atmosNITinput_o[ndays]-atmosNITinput_o[((nyears-1)*360+1)])
riverDINinflow<-0
riverPARTinflow<-0
sumDINinflow<-(fluxAMMinflow_o[ndays-90]-fluxAMMinflow_o[((nyears-1)*360+1+89)]) + (fluxNITinflow_o[ndays-90]-fluxNITinflow_o[((nyears-1)*360+1+89)])
sumDINoutflow<-(fluxAMMoutflow_o[ndays-90]-fluxAMMoutflow_o[((nyears-1)*360+1+89)]) + (fluxNIToutflow_o[ndays-90]-fluxNIToutflow_o[((nyears-1)*360+1+89)])
sumPARTinflow<-(fluxPHYTinflow_o[ndays-90]-fluxPHYTinflow_o[((nyears-1)*360+1+89)]) + (fluxDETinflow_o[ndays-90]-fluxDETinflow_o[((nyears-1)*360+1+89)])
sumPARToutflow<-(fluxPHYToutflow_o[ndays-90]-fluxPHYToutflow_o[((nyears-1)*360+1+89)]) + (fluxDEToutflow_o[ndays-90]-fluxDEToutflow_o[((nyears-1)*360+1+89)])
sumriverDINinflow<-0
sumatmosDINinput<-(atmosAMMinput_o[ndays-90]-atmosAMMinput_o[((nyears-1)*360+1+89)]) + (atmosNITinput_o[ndays-90]-atmosNITinput_o[((nyears-1)*360+1+89)])
surfvertnitflux<-vertnitflux[ndays]-vertnitflux[((nyears-1)*360+1)]
surfhoriznitflux<-NA
sumriverNITinflow<-0
sumatmosNITinput<-(atmosNITinput_o[ndays-90]-atmosNITinput_o[((nyears-1)*360+1+89)]) # April - September inclusive
Flux_sedboundary <- (fluxsedboundary_o[ndays]-fluxsedboundary_o[((nyears-1)*360+1)])
#kelp_beachcast<-((fluxkelpdebris_beachexport[ndays]-fluxkelpdebris_beachexport[((nyears-1)*360+1)]))
kelp_beachcast<-NA
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)]
Mfish_annual_imig <- mfish_imigration[ndays]-mfish_imigration[((nyears-1)*360+1)]
Mfish_annual_emig <- mfish_emigration[ndays]-mfish_emigration[((nyears-1)*360+1)]
NETPrimaryP<-netpprod_o[ndays]-netpprod_o[((nyears-1)*360+1)]
MMP<-(max(nitrate_so[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays])) - (min(nitrate_so[((nyears-1)*360+1):ndays]+nitrate_d[((nyears-1)*360+1):ndays]))
NNCP<-NNCP_o[ndays]-NNCP_o[((nyears-1)*360+1)]
PhytNitUp<-fluxwcnit_phyt_o[ndays]-fluxwcnit_phyt_o[((nyears-1)*360+1)]
PhytAmmUp<-fluxwcamm_phyt_o[ndays]-fluxwcamm_phyt_o[((nyears-1)*360+1)]
PNP<-MMP+sumriverNITinflow+sumatmosNITinput
fratio<-PNP/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 <- NA
Phytgrossprod <- phytgrossprod_o[ndays] - phytgrossprod_o[((nyears-1)*360+1)]
omnigrossprod <- omnigrossprod_o[ndays] - omnigrossprod_o[((nyears-1)*360+1)]
Carngrossprod <- carngrossprod_o[ndays] - carngrossprod_o[((nyears-1)*360+1)]
Fishplargrossprod <- pfishlargrossprod_o[ndays] - pfishlargrossprod_o[((nyears-1)*360+1)]
Fishdlargrossprod <- dfishlargrossprod_o[ndays] - dfishlargrossprod_o[((nyears-1)*360+1)]
Fishpgrossprod <- pfishgrossprod_o[ndays] - pfishgrossprod_o[((nyears-1)*360+1)]
Fishmgrossprod <- mfishgrossprod_o[ndays] - mfishgrossprod_o[((nyears-1)*360+1)]
Fishdgrossprod <- dfishgrossprod_o[ndays] - dfishgrossprod_o[((nyears-1)*360+1)]
Benthslargrossprod <- benthslargrossprod_o[ndays] - benthslargrossprod_o[((nyears-1)*360+1)]
Benthclargrossprod <- benthclargrossprod_o[ndays] - benthclargrossprod_o[((nyears-1)*360+1)]
Benthsgrossprod <- benthsgrossprod_o[ndays] - benthsgrossprod_o[((nyears-1)*360+1)]
Benthcgrossprod <- benthcgrossprod_o[ndays] - benthcgrossprod_o[((nyears-1)*360+1)]
Birdgrossprod <- birdgrossprod_o[ndays] - birdgrossprod_o[((nyears-1)*360+1)]
Sealgrossprod <- sealgrossprod_o[ndays] - sealgrossprod_o[((nyears-1)*360+1)]
Cetagrossprod <- cetagrossprod_o[ndays] - cetagrossprod_o[((nyears-1)*360+1)]
omninetprod <- omninetprod_o[ndays] - omninetprod_o[((nyears-1)*360+1)]
Carnnetprod <- carnnetprod_o[ndays] - carnnetprod_o[((nyears-1)*360+1)]
Fishplarnetprod <- pfishlarnetprod_o[ndays] - pfishlarnetprod_o[((nyears-1)*360+1)]
Fishdlarnetprod <- dfishlarnetprod_o[ndays] - dfishlarnetprod_o[((nyears-1)*360+1)]
Fishpnetprod <- pfishnetprod_o[ndays] - pfishnetprod_o[((nyears-1)*360+1)]
Fishmnetprod <- mfishnetprod_o[ndays] - mfishnetprod_o[((nyears-1)*360+1)]
Fishdnetprod <- dfishnetprod_o[ndays] - dfishnetprod_o[((nyears-1)*360+1)]
Benthslarnetprod <- benthslarnetprod_o[ndays] - benthslarnetprod_o[((nyears-1)*360+1)]
Benthclarnetprod <- benthclarnetprod_o[ndays] - benthclarnetprod_o[((nyears-1)*360+1)]
Benthsnetprod <- benthsnetprod_o[ndays] - benthsnetprod_o[((nyears-1)*360+1)]
Benthcnetprod <- benthcnetprod_o[ndays] - benthcnetprod_o[((nyears-1)*360+1)]
Birdnetprod <- birdnetprod_o[ndays] - birdnetprod_o[((nyears-1)*360+1)]
Sealnetprod <- sealnetprod_o[ndays] - sealnetprod_o[((nyears-1)*360+1)]
Cetanetprod <- cetanetprod_o[ndays] - cetanetprod_o[((nyears-1)*360+1)]
WCdetritusprod <- NA
#SEDdetritusprod <- fluxcorp_xdet[ndays] - fluxcorp_xdet[((nyears-1)*360+1)] +
SEDdetritusprod <- NA
Kelpdebrisprod <- NA
Corpseprod <- NA
#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
#Excludes mineralisation of detritus
Pelagammprod <- NA
#Excludes mineralisation of detritus
Benthammprod <- NA
WCmineralisation <- NA
SEDmineralisation <- NA
WCnitrification <- NA
SEDnitrification <- NA
WCdenitrification <- NA
SEDdenitrification <- NA
#Includes excretion by benthos
SEDWCammflux <- NA
SEDWCnitflux <- NA
Fluxdet_omni <- NA
Fluxphyt_omni <- NA
Fluxbenthslar_omni <- NA
Fluxbenthclar_omni <- NA
Fluxomni_carn <- NA
Fluxpfishlar_carn <- NA
Fluxdfishlar_carn <- NA
Fluxbenthslar_carn <- NA
Fluxbenthclar_carn <- NA
Fluxomni_pfishlar <- NA
Fluxbenthslar_pfishlar <- NA
Fluxbenthclar_pfishlar <- NA
Fluxomni_dfishlar <- NA
Fluxbenthslar_dfishlar <- NA
Fluxbenthclar_dfishlar <- NA
Fluxomni_pfish <- NA
Fluxcarn_pfish <- NA
Fluxpfishlar_pfish <- NA
Fluxdfishlar_pfish <- NA
Fluxbenthslar_pfish <- NA
Fluxbenthclar_pfish <- NA
Fluxomni_mfish <- NA
Fluxcarn_mfish <- NA
Fluxpfishlar_mfish <- NA
Fluxdfishlar_mfish <- NA
Fluxbenthslar_mfish <- NA
Fluxbenthclar_mfish <- NA
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 <- NA
Fluxphyt_benthslar <- NA
Fluxdet_benthclar <- NA
Fluxphyt_benthclar <- NA
Fluxdet_benths <- NA
Fluxseddet_benths <- NA
Fluxphyt_benths <- NA
Fluxkelp_benthc <- NA
Fluxkelpdebris_benthc <- NA
Fluxcorp_benthc <- NA
Fluxbenths_benthc <- NA
Fluxcorp_bird <- NA
Fluxdisc_bird <- NA
#Fluxomni_bird <- NA
Fluxcarn_bird <- NA
Fluxpfish_bird <- NA
Fluxmfish_bird <- NA
Fluxdfish_bird <- NA
Fluxbenths_bird <- NA
Fluxbenthc_bird <- NA
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 <- NA
Fluxomni_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<- omninetprod +
+ Carnnetprod +
+ Benthsnetprod +
+ Benthcnetprod +
+ Benthslarnetprod +
+ Benthclarnetprod +
+ Fishplarnetprod +
+ Fishdlarnetprod +
+ Fishpnetprod +
+ Fishmnetprod +
+ Fishdnetprod +
+ Birdnetprod +
+ Sealnetprod +
+ Cetanetprod
export_from_2prod<- NA
Pfish_annual_spawn <- NA
Pfish_annual_recruit <- NA
Dfish_annual_spawn <- NA
Dfish_annual_recruit <- NA
Benths_annual_spawn <- NA
Benths_annual_recruit <- NA
Benthc_annual_spawn <- NA
Benthc_annual_recruit <- NA
FishpLand_livewt<-landp_o[ndays]-landp_o[((nyears-1)*360+1)]
FishmLand_livewt<-landm_o[ndays]-landm_o[((nyears-1)*360+1)]
FishdLand_livewt<-landd_o[ndays]-landd_o[((nyears-1)*360+1)]
Fishd_qLand_livewt<-landd_quota_o[ndays]-landd_quota_o[((nyears-1)*360+1)]
Fishd_nqLand_livewt<-landd_nonquota_o[ndays]-landd_nonquota_o[((nyears-1)*360+1)]
BenthsLand_livewt <- landsb_o[ndays]-landsb_o[((nyears-1)*360+1)]
BenthcLand_livewt <- landcb_o[ndays]-landcb_o[((nyears-1)*360+1)]
CarnzLand_livewt <- landcz_o[ndays]-landcz_o[((nyears-1)*360+1)]
BirdLand_livewt <- landbd_o[ndays]-landbd_o[((nyears-1)*360+1)]
SealLand_livewt <- landsl_o[ndays]-landsl_o[((nyears-1)*360+1)]
CetaLand_livewt <- landct_o[ndays]-landct_o[((nyears-1)*360+1)]
KelpLand_livewt <- NA
FishpDiscard<-discpel_o[ndays]-discpel_o[((nyears-1)*360+1)]
FishmDiscard<-discmig_o[ndays]-discmig_o[((nyears-1)*360+1)]
FishdDiscard<-discdem_o[ndays]-discdem_o[((nyears-1)*360+1)]
Fishd_qDiscard<-discdem_quota_o[ndays]-discdem_quota_o[((nyears-1)*360+1)]
Fishd_nqDiscard<-discdem_nonquota_o[ndays]-discdem_nonquota_o[((nyears-1)*360+1)]
BenthsDiscard <- discsb_o[ndays]-discsb_o[((nyears-1)*360+1)]
BenthcDiscard <- disccb_o[ndays]-disccb_o[((nyears-1)*360+1)]
CarnzDiscard <- disccz_o[ndays]-disccz_o[((nyears-1)*360+1)]
BirdDiscard <- discbd_o[ndays]-discbd_o[((nyears-1)*360+1)]
SealDiscard <- discsl_o[ndays]-discsl_o[((nyears-1)*360+1)]
CetaDiscard <- discct_o[ndays]-discct_o[((nyears-1)*360+1)]
KelpDiscard <- NA
FishpOffal<-offalpel_o[ndays]-offalpel_o[((nyears-1)*360+1)]
FishmOffal<-offalmig_o[ndays]-offalmig_o[((nyears-1)*360+1)]
FishdOffal<-offaldem_o[ndays]-offaldem_o[((nyears-1)*360+1)]
Fishd_qOffal<-offaldem_quota_o[ndays]-offaldem_quota_o[((nyears-1)*360+1)]
Fishd_nqOffal<-offaldem_nonquota_o[ndays]-offaldem_nonquota_o[((nyears-1)*360+1)]
BenthsOffal <- offalsb_o[ndays]-offalsb_o[((nyears-1)*360+1)]
BenthcOffal <- offalcb_o[ndays]-offalcb_o[((nyears-1)*360+1)]
CarnzOffal <- offalcz_o[ndays]-offalcz_o[((nyears-1)*360+1)]
BirdOffal <- offalbd_o[ndays]-offalbd_o[((nyears-1)*360+1)]
SealOffal <- offalsl_o[ndays]-offalsl_o[((nyears-1)*360+1)]
CetaOffal <- offalct_o[ndays]-offalct_o[((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]<-NNCP
annual_flux_results[33,1]<-PhytNitUp
annual_flux_results[34,1]<-PhytAmmUp
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]<-omnigrossprod
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]<-omninetprod
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_omni
annual_flux_results[85,1]<-Fluxphyt_omni
annual_flux_results[86,1]<-Fluxbenthslar_omni
annual_flux_results[87,1]<-Fluxbenthclar_omni
annual_flux_results[88,1]<-Fluxomni_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]<-Fluxomni_pfishlar
annual_flux_results[94,1]<-Fluxbenthslar_pfishlar
annual_flux_results[95,1]<-Fluxbenthclar_pfishlar
annual_flux_results[96,1]<-Fluxomni_dfishlar
annual_flux_results[97,1]<-Fluxbenthslar_dfishlar
annual_flux_results[98,1]<-Fluxbenthclar_dfishlar
annual_flux_results[99,1]<-Fluxomni_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]<-Fluxomni_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]<-Fluxomni_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]<-Fluxomni_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
#Text descriptions of units set here for each row of output data
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]<-annual_flux_descriptions
#The vector of text descriptions for each row of output is set in internal.R
names(annual_flux_results)<-c("Model_annual_flux","Units","Description")
filename = csvname(resultsdir, "OFFSHORE_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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