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R/CredInt_make_daily_migration_results.R
In StrathE2E2: End-to-End Marine Food Web Model
Defines functions
CredInt_make_daily_migration_results
#
# CredInt_make_daily_migration_results.R
#
#' Save current set of fitted parameters to file
#'
#' @param model model object
#' @param lastyearstore inshore annual flux data
#' @param csv.output (TRUE or FALSE, default=TRUE) Set to FALSE to disable writing of CSV output files - useful for testing
#'
#' @importFrom graphics abline
#'
#' @noRd
#
# ------------------------------------------------------------------------------
CredInt_make_daily_migration_results <- function(model, lastyearstore,csv.output) {
pkg.env$csv.output <- csv.output # controls writing of CSV files
resultsdir <- elt(model, "setup", "resultsdir")
identifier <- elt(model, "setup", "model.ident")
credpath <- makepath(resultsdir, CREDINT_DIR)
#THIS VERSION PROCESSES THE FLUX DATA SAVED IN THE CUMULATIVE DAILY OUTPUT STORE
#
#THE FLUX DATA ARE CUMULATIVE SO FIRST THING TO DO IS MAKE A NEW DATAFRAME CONTAINING
#THE DAILY INCREMENTS.
lastyearstore$dummy<-1
# names(lastyearstore)
# [1] "time" "detritus_so" "detritus_d"
# [4] "x_detritus_s1" "x_detritus_s2" "x_detritus_s3"
# [7] "x_detritus_d1" "x_detritus_d2" "x_detritus_d3"
# [10] "xR_detritus_s1" "xR_detritus_s2" "xR_detritus_s3"
# [13] "xR_detritus_d1" "xR_detritus_d2" "xR_detritus_d3"
# [16] "discard_o" "corpse_s1" "corpse_s2"
# [19] "corpse_s3" "corpse_d1" "corpse_d2"
# [22] "corpse_d3" "ammonia_so" "ammonia_d"
# [25] "x_ammonia_s1" "x_ammonia_s2" "x_ammonia_s3"
# [28] "x_ammonia_d1" "x_ammonia_d2" "x_ammonia_d3"
# [31] "nitrate_so" "nitrate_d" "x_nitrate_s1"
# [34] "x_nitrate_s2" "x_nitrate_s3" "x_nitrate_d1"
# [37] "x_nitrate_d2" "x_nitrate_d3" "phyt_so"
# [40] "phyt_d" "omni_o" "carn_o"
# [43] "benthslar_o" "benths_o" "benthclar_o"
# [46] "benthc_o" "fishp_o" "fishplar_o"
# [49] "fishd_o" "fishdlar_o" "fishm_o"
# [52] "bird_o" "detritus_si" "ammonia_si"
# [55] "nitrate_si" "phyt_si" "benthslar_i"
# [58] "benthclar_i" "benths_i" "benthc_i"
# [61] "discard_i" "omni_i" "carn_i"
# [64] "fishplar_i" "fishdlar_i" "fishp_i"
# [67] "fishm_i" "fishd_i" "bird_i"
# [70] "seal_o" "seal_i" "ceta_o"
# [73] "ceta_i" "corpse_s0" "corpse_d0"
# [76] "kelpC" "kelpN" "kelpdebris"
# [79] "netpprod_o" "netpprod_i" "PNP_o"
# [82] "PNP_i" "phytgrossprod_o" "phytgrossprod_i"
# [85] "kelpCprod_i" "kelpCexud_i" "kelpNprod_i"
# [88] "omnigrossprod_o" "omnigrossprod_i" "carngrossprod_o"
# [91] "carngrossprod_i" "pfishlargrossprod_o" "pfishlargrossprod_i"
# [94] "dfishlargrossprod_o" "dfishlargrossprod_i" "pfishgrossprod_o"
# [97] "pfishgrossprod_i" "mfishgrossprod_o" "mfishgrossprod_i"
#[100] "dfishgrossprod_o" "dfishgrossprod_i" "benthslargrossprod_o"
#[103] "benthslargrossprod_i" "benthclargrossprod_o" "benthclargrossprod_i"
#[106] "benthsgrossprod_o" "benthsgrossprod_i" "benthcgrossprod_o"
#[109] "benthcgrossprod_i" "birdgrossprod_o" "birdgrossprod_i"
#[112] "sealgrossprod_o" "sealgrossprod_i" "cetagrossprod_o"
#[115] "cetagrossprod_i" "wcdenitrif_o" "wcdenitrif_i"
#[118] "seddenitrif_o" "seddenitrif_i" "fluxsedamm_wcamm"
#[121] "fluxwcdet_wcamm" "fluxomni_wcamm" "fluxcarn_wcamm"
#[124] "fluxpfishlar_wcamm" "fluxdfishlar_wcamm" "fluxpfish_wcamm"
#[127] "fluxmfish_wcamm" "fluxdfish_wcamm" "fluxbenthslar_wcamm"
#[130] "fluxbenthclar_wcamm" "fluxbenths_wcamm" "fluxbenthc_wcamm"
#[133] "fluxbird_wcamm" "fluxseal_wcamm" "fluxceta_wcamm"
#[136] "fluxxdet_sedamm" "fluxxRdet_sedamm" "fluxwcamm_wcnit"
#[139] "fluxsednit_wcnit" "fluxsedamm_sednit" "fluxxdet_wcdet"
#[142] "fluxkelpdebris_wcdet" "fluxcorp_wcdet" "fluxphyt_wcdet"
#[145] "fluxomni_wcdet" "fluxcarn_wcdet" "fluxpfishlar_wcdet"
#[148] "fluxdfishlar_wcdet" "fluxpfish_wcdet" "fluxmfish_wcdet"
#[151] "fluxdfish_wcdet" "fluxbenthslar_wcdet" "fluxbenthclar_wcdet"
#[154] "fluxbenths_wcdet" "fluxbenthc_wcdet" "fluxbird_wcdet"
#[157] "fluxseal_wcdet" "fluxceta_wcdet" "fluxwcdet_xdet"
#[160] "fluxcorp_xdet" "fluxbenths_xdet" "fluxbenthc_xdet"
#[163] "fluxxdet_xRdet" "fluxkelpdebris_xRdet" "fluxcorp_xRdet"
#[166] "fluxkelp_kelpdebris" "fluxdisc_corp" "fluxpfish_corp"
#[169] "fluxmfish_corp" "fluxdfish_corp" "fluxbenths_corp"
#[172] "fluxbenthc_corp" "fluxbird_corp" "fluxseal_corp"
#[175] "fluxceta_corp" "fluxwcamm_kelp" "fluxwcnit_kelp"
#[178] "fluxwcamm_phyt_o" "fluxwcamm_phyt_i" "fluxwcnit_phyt_o"
#[181] "fluxwcnit_phyt_i" "fluxwcdet_omni" "fluxphyt_omni"
#[184] "fluxbenthslar_omni" "fluxbenthclar_omni" "fluxomni_carn"
#[187] "fluxpfishlar_carn" "fluxdfishlar_carn" "fluxbenthslar_carn"
#[190] "fluxbenthclar_carn" "fluxomni_pfishlar" "fluxbenthslar_pfishlar"
#[193] "fluxbenthclar_pfishlar" "fluxomni_dfishlar" "fluxbenthslar_dfishlar"
#[196] "fluxbenthclar_dfishlar" "fluxomni_pfish" "fluxcarn_pfish"
#[199] "fluxpfishlar_pfish" "fluxdfishlar_pfish" "fluxbenthslar_pfish"
#[202] "fluxbenthclar_pfish" "fluxomni_mfish" "fluxcarn_mfish"
#[205] "fluxpfishlar_mfish" "fluxdfishlar_mfish" "fluxbenthslar_mfish"
#[208] "fluxbenthclar_mfish" "fluxcorp_dfish" "fluxdisc_dfish"
#[211] "fluxcarn_dfish" "fluxpfishlar_dfish" "fluxdfishlar_dfish"
#[214] "fluxpfish_dfish" "fluxmfish_dfish" "fluxdfish_dfish"
#[217] "fluxbenths_dfish" "fluxbenthc_dfish" "fluxwcdet_benthslar"
#[220] "fluxphyt_benthslar" "fluxwcdet_benthclar" "fluxphyt_benthclar"
#[223] "fluxwcdet_benths" "fluxxdet_benths" "fluxxRdet_benths"
#[226] "fluxphyt_benths" "fluxkelp_benthc" "fluxkelpdebris_benthc"
#[229] "fluxcorp_benthc" "fluxbenths_benthc" "fluxcorp_bird"
#[232] "fluxdisc_bird" "fluxcarn_bird" "fluxpfish_bird"
#[235] "fluxmfish_bird" "fluxdfish_bird" "fluxbenths_bird"
#[238] "fluxbenthc_bird" "fluxcorp_seal" "fluxdisc_seal"
#[241] "fluxcarn_seal" "fluxpfish_seal" "fluxmfish_seal"
#[244] "fluxdfish_seal" "fluxbenths_seal" "fluxbenthc_seal"
#[247] "fluxbird_seal" "fluxdisc_ceta" "fluxomni_ceta"
#[250] "fluxcarn_ceta" "fluxpfish_ceta" "fluxmfish_ceta"
#[253] "fluxdfish_ceta" "fluxbenths_ceta" "fluxbenthc_ceta"
#[256] "fluxbird_ceta" "fluxseal_ceta" "Bs_spawn"
#[259] "Bs_recruit" "Bc_spawn" "Bc_recruit"
#[262] "Pfish_spawn" "Pfish_recruit" "Dfish_spawn"
#[265] "Dfish_recruit" "fluxwcnit_Ngas" "fluxsednit_Ngas"
#[268] "fluxkelpdebris_beachexport" "fluxAMMoutflow_o" "fluxNIToutflow_o"
#[271] "fluxAMMoutflow_i" "fluxNIToutflow_i" "fluxPHYToutflow_o"
#[274] "fluxDEToutflow_o" "fluxPHYToutflow_i" "fluxDEToutflow_i"
#[277] "mfish_emigration" "fluxsedboundary_o" "fluxsedboundary_i"
#[280] "fluxAMMinflow_o" "fluxNITinflow_o" "fluxAMMinflow_i"
#[283] "fluxNITinflow_i" "fluxPHYTinflow_o" "fluxDETinflow_o"
#[286] "fluxPHYTinflow_i" "fluxDETinflow_i" "mfish_imigration"
#[289] "atmosAMMinput_o" "atmosNITinput_o" "atmosAMMinput_i"
#[292] "atmosNITinput_i" "rivAMMinflow" "rivNITinflow"
#[295] "rivPARTinflow" "DINflux_i_o" "DINflux_o_i"
#[298] "PARTflux_i_o" "PARTflux_o_i" "activemigpelfish_i_o"
#[301] "activemigmigfish_i_o" "activemigdemfish_i_o" "activemigbird_i_o"
#[304] "activemigseal_i_o" "activemigceta_i_o" "activemigpelfish_o_i"
#[307] "activemigmigfish_o_i" "activemigdemfish_o_i" "activemigbird_o_i"
#[310] "activemigseal_o_i" "activemigceta_o_i" "vertnitflux"
#[313] "horiznitflux" "landp_o" "landd_quota_o"
#[316] "landd_nonquota_o" "landm_o" "landsb_o"
#[319] "landcb_o" "landcz_o" "landbd_o"
#[322] "landsl_o" "landct_o" "discpel_o"
#[325] "discdem_quota_o" "discdem_nonquota_o" "discmig_o"
#[328] "discsb_o" "disccb_o" "disccz_o"
#[331] "discbd_o" "discsl_o" "discct_o"
#[334] "landp_i" "landd_quota_i" "landd_nonquota_i"
#[337] "landm_i" "landsb_i" "landcb_i"
#[340] "landcz_i" "landbd_i" "landsl_i"
#[343] "landct_i" "landkp_i" "discpel_i"
#[346] "discdem_quota_i" "discdem_nonquota_i" "discmig_i"
#[349] "discsb_i" "disccb_i" "disccz_i"
#[352] "discbd_i" "discsl_i" "discct_i"
#[355] "disckp_i" "offalpel_o" "offaldem_quota_o"
#[358] "offaldem_nonquota_o" "offalmig_o" "offalsb_o"
#[361] "offalcb_o" "offalcz_o" "offalbd_o"
#[364] "offalsl_o" "offalct_o" "offalpel_i"
#[367] "offaldem_quota_i" "offaldem_nonquota_i" "offalmig_i"
#[370] "offalsb_i" "offalcb_i" "offalcz_i"
#[373] "offalbd_i" "offalsl_i" "offalct_i"
#[376] "offalkp_i" "omninetprod_o" "omninetprod_i"
#[379] "carnnetprod_o" "carnnetprod_i" "pfishlarnetprod_o"
#[382] "pfishlarnetprod_i" "dfishlarnetprod_o" "dfishlarnetprod_i"
#[385] "pfishnetprod_o" "pfishnetprod_i" "mfishnetprod_o"
#[388] "mfishnetprod_i" "dfishnetprod_o" "dfishnetprod_i"
#[391] "benthslarnetprod_o" "benthslarnetprod_i" "benthclarnetprod_o"
#[394] "benthclarnetprod_i" "benthsnetprod_o" "benthsnetprod_i"
#[397] "benthcnetprod_o" "benthcnetprod_i" "birdnetprod_o"
#[400] "birdnetprod_i" "sealnetprod_o" "sealnetprod_i"
#[403] "cetanetprod_o" "cetanetprod_i" "totalN"
#[406] "totalN_o" "totalN_i" "x_detritus"
#[409] "x_detritus_o" "x_detritus_i" "corpse"
#[412] "corpse_o" "corpse_i" "x_ammonia"
#[415] "x_ammonia_o" "x_ammonia_i" "x_nitrate"
#[418] "x_nitrate_o" "x_nitrate_i" "s_detritus"
#[421] "s_ammonia" "s_nitrate" "s_phyt"
#[424] "benthslar" "benthclar" "benths"
#[427] "benthc" "discard" "omni"
#[430] "carn" "fishp" "fishd"
#[433] "fishm" "bird" "seal"
#[436] "ceta" "fishplar" "fishdlar"
#[439] "PNP" "netpprod" "fluxwcamm_phyt"
#[442] "fluxwcnit_phyt" "phytgrossprod" "omnigrossprod"
#[445] "carngrossprod" "pfishlargrossprod" "dfishlargrossprod"
#[448] "pfishgrossprod" "mfishgrossprod" "dfishgrossprod"
#[451] "benthslargrossprod" "benthclargrossprod" "benthsgrossprod"
#[454] "benthcgrossprod" "birdgrossprod" "sealgrossprod"
#[457] "cetagrossprod" "omninetprod" "carnnetprod"
#[460] "pfishlarnetprod" "dfishlarnetprod" "pfishnetprod"
#[463] "mfishnetprod" "dfishnetprod" "benthslarnetprod"
#[466] "benthclarnetprod" "benthsnetprod" "benthcnetprod"
#[469] "birdnetprod" "sealnetprod" "cetanetprod"
#[472] "wcdenitrif" "seddenitrif" "fluxsedboundary"
#[475] "DIN_NET_flux_o_i" "PART_NET_flux_o_i" "NET_activemigpelfish_o_i"
#[478] "NET_activemigmigfish_o_i" "NET_activemigdemfish_o_i" "NET_activemigbird_o_i"
#[481] "NET_activemigseal_o_i" "NET_activemigceta_o_i" "NET_mfish_ext_o"
#[484] "fluxDINinflow" "fluxDINoutflow" "fluxPARTinflow"
#[487] "fluxPARToutflow" "atmosDINinput" "rivDINinflow"
#[490] "landp" "landd" "landd_o"
#[493] "landd_i" "landd_quota" "landd_nonquota"
#[496] "landm" "landsb" "landcb"
#[499] "landcz" "landbd" "landsl"
#[502] "landct" "discpel" "discdem"
#[505] "discdem_o" "discdem_i" "discdem_quota"
#[508] "discdem_nonquota" "discmig" "discsb"
#[511] "disccb" "disccz" "discbd"
#[514] "discsl" "discct" "offalpel"
#[517] "offaldem" "offaldem_o" "offaldem_i"
#[520] "offaldem_quota" "offaldem_nonquota" "offalmig"
#[523] "offalsb" "offalcb" "offalcz"
#[526] "offalbd" "offalsl" "offalct"
#[529] "shallowprop" "depth_si" "depth_so"
#[532] "depth_d" "area_s0" "area_s1"
#[535] "area_s2" "area_s3" "area_d0"
#[538] "area_d1" "area_d2" "area_d3"
#[541] "depth_s1" "depth_s2" "depth_s3"
#[544] "depth_d1" "depth_d2" "depth_d3"
#[547] "poros_s1" "poros_s2" "poros_s3"
#[550] "poros_d1" "poros_d2" "poros_d3"
#[553] "iteration" "likelihood" "dummy"
creds<-c(0.005,0.25,0.5,0.75,0.995) # This can be any lenth of vector in any order. All values must be between 0 and 1
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Build_Cred_Timeseries_Fluxes<-function(VtoPid,areaid,thikid,io,creds,varname){
#io = 0 means offshore
#io = 1 means inshore
#io = 2 means whole domain
rownamesvec<-rep(NA,(length(creds)+1))
for(kkk in 1:(length(creds)+1)){
if(kkk==1) rownamesvec[kkk]<-paste(varname,"-maxlik",sep="")
if(kkk>1) rownamesvec[kkk]<-paste(varname,"-",creds[kkk-1],sep="")
}
Resultdata<-data.frame(rep(NA,(length(creds)+1)))
for(kkk in 1:360){
Resultdata[,kkk+1]<-(rep(NA,(length(creds)+1)))
}
names(Resultdata)<-seq(0,360)
row.names(Resultdata)<-rownamesvec
template<-data.frame(newlastyearstore$time)
names(template)<-"time"
if(io==2) template$VtoP<-newlastyearstore[,VtoPid]
if(io==1) template$VtoP<-newlastyearstore[,VtoPid]/(newlastyearstore[,areaid]*newlastyearstore[,thikid])
if(io==0) template$VtoP<-newlastyearstore[,VtoPid]/((1-newlastyearstore[,areaid])*newlastyearstore[,thikid])
template$iteration<-newlastyearstore$iteration
template$likelihood<-newlastyearstore$likelihood
for(ii in 0:360){
Resultdata[1,ii+1]<-template$VtoP[which(template$time==ii&template$iteration==1)]
modresvector<-template$VtoP[which(template$time==ii)]
likevector<-template$likelihood[which(template$time==ii)]
#message("\n","Processing ",varname," data")
credvals<-GetCredInt(modresvector,likevector,creds,var=varname,plotgraph=FALSE)
Resultdata[2:(length(credvals)+1),ii+1]<-credvals
}
return(Resultdata)
}
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# CONVERT CUMULATIVE FLUX COLUMNS INTO DAILY FLUXES
#Find the number of runs that were stored
n_datasets<-nrow(lastyearstore)/361
newlastyearstore<-data.frame(lastyearstore$time)
names(newlastyearstore)<-"time"
newlastyearstore$dummy<-1
newlastyearstore$iteration<-lastyearstore$iteration
newlastyearstore$likelihood<-lastyearstore$likelihood
newlastyearstore$shallowprop<-lastyearstore$shallowprop
tempset<-rep(0,361)
#################################################
col2proc<-477 # Pelagic fish migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-478 # Migratory fish migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-479 # Demersal fish migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-480 # Bird migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-481 # Seal migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-482 # Cetacean migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
################################################################
newlastyearstore$NET_activemigpelfish_o_i_propbiom <- newlastyearstore$NET_activemigpelfish_o_i/(lastyearstore$fishp_o+lastyearstore$fishp_i)
newlastyearstore$NET_activemigmigfish_o_i_propbiom <- newlastyearstore$NET_activemigmigfish_o_i/(lastyearstore$fishm_o+lastyearstore$fishm_i)
newlastyearstore$NET_activemigdemfish_o_i_propbiom <- newlastyearstore$NET_activemigdemfish_o_i/(lastyearstore$fishd_o+lastyearstore$fishd_i)
newlastyearstore$NET_activemigbird_o_i_propbiom <- newlastyearstore$NET_activemigbird_o_i/(lastyearstore$bird_o+lastyearstore$bird_i)
newlastyearstore$NET_activemigseal_o_i_propbiom <- newlastyearstore$NET_activemigseal_o_i/(lastyearstore$seal_o+lastyearstore$seal_i)
newlastyearstore$NET_activemigceta_o_i_propbiom <- newlastyearstore$NET_activemigceta_o_i/(lastyearstore$ceta_o+lastyearstore$ceta_i)
#################################################
#Pelagic fish migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigpelfish_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Planktivorous_fish_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-Result_data
#Pelagic fish migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigpelfish_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Planktivorous_fish_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#migratory fish migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigmigfish_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Migratory_fish_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#migratory fish migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigmigfish_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Migratory_fish_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Demersal fish migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigdemfish_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Demersal_fish_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Demersal fish migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigdemfish_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Demersal_fish_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Bird migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigbird_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Birds_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Bird migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigbird_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Birds_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Seals migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigseal_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Pinnipeds_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Seals migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigseal_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Pinnipeds_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Cetaceans migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigceta_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Cetaceans_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Cetaceans migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigceta_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Cetaceans_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
# goes into resultsdir/CredInt/datafile-ident.csv
csvfile <- csvname(credpath, "CredInt_processed_daily_migrations", identifier)
writecsv(Result_data_store, csvfile)
Result_data_store
}
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Defines functions CredInt_make_daily_migration_results
#
# CredInt_make_daily_migration_results.R
#
#' Save current set of fitted parameters to file
#'
#' @param model model object
#' @param lastyearstore inshore annual flux data
#' @param csv.output (TRUE or FALSE, default=TRUE) Set to FALSE to disable writing of CSV output files - useful for testing
#'
#' @importFrom graphics abline
#'
#' @noRd
#
# ------------------------------------------------------------------------------
CredInt_make_daily_migration_results <- function(model, lastyearstore,csv.output) {
pkg.env$csv.output <- csv.output # controls writing of CSV files
resultsdir <- elt(model, "setup", "resultsdir")
identifier <- elt(model, "setup", "model.ident")
credpath <- makepath(resultsdir, CREDINT_DIR)
#THIS VERSION PROCESSES THE FLUX DATA SAVED IN THE CUMULATIVE DAILY OUTPUT STORE
#
#THE FLUX DATA ARE CUMULATIVE SO FIRST THING TO DO IS MAKE A NEW DATAFRAME CONTAINING
#THE DAILY INCREMENTS.
lastyearstore$dummy<-1
# names(lastyearstore)
# [1] "time" "detritus_so" "detritus_d"
# [4] "x_detritus_s1" "x_detritus_s2" "x_detritus_s3"
# [7] "x_detritus_d1" "x_detritus_d2" "x_detritus_d3"
# [10] "xR_detritus_s1" "xR_detritus_s2" "xR_detritus_s3"
# [13] "xR_detritus_d1" "xR_detritus_d2" "xR_detritus_d3"
# [16] "discard_o" "corpse_s1" "corpse_s2"
# [19] "corpse_s3" "corpse_d1" "corpse_d2"
# [22] "corpse_d3" "ammonia_so" "ammonia_d"
# [25] "x_ammonia_s1" "x_ammonia_s2" "x_ammonia_s3"
# [28] "x_ammonia_d1" "x_ammonia_d2" "x_ammonia_d3"
# [31] "nitrate_so" "nitrate_d" "x_nitrate_s1"
# [34] "x_nitrate_s2" "x_nitrate_s3" "x_nitrate_d1"
# [37] "x_nitrate_d2" "x_nitrate_d3" "phyt_so"
# [40] "phyt_d" "omni_o" "carn_o"
# [43] "benthslar_o" "benths_o" "benthclar_o"
# [46] "benthc_o" "fishp_o" "fishplar_o"
# [49] "fishd_o" "fishdlar_o" "fishm_o"
# [52] "bird_o" "detritus_si" "ammonia_si"
# [55] "nitrate_si" "phyt_si" "benthslar_i"
# [58] "benthclar_i" "benths_i" "benthc_i"
# [61] "discard_i" "omni_i" "carn_i"
# [64] "fishplar_i" "fishdlar_i" "fishp_i"
# [67] "fishm_i" "fishd_i" "bird_i"
# [70] "seal_o" "seal_i" "ceta_o"
# [73] "ceta_i" "corpse_s0" "corpse_d0"
# [76] "kelpC" "kelpN" "kelpdebris"
# [79] "netpprod_o" "netpprod_i" "PNP_o"
# [82] "PNP_i" "phytgrossprod_o" "phytgrossprod_i"
# [85] "kelpCprod_i" "kelpCexud_i" "kelpNprod_i"
# [88] "omnigrossprod_o" "omnigrossprod_i" "carngrossprod_o"
# [91] "carngrossprod_i" "pfishlargrossprod_o" "pfishlargrossprod_i"
# [94] "dfishlargrossprod_o" "dfishlargrossprod_i" "pfishgrossprod_o"
# [97] "pfishgrossprod_i" "mfishgrossprod_o" "mfishgrossprod_i"
#[100] "dfishgrossprod_o" "dfishgrossprod_i" "benthslargrossprod_o"
#[103] "benthslargrossprod_i" "benthclargrossprod_o" "benthclargrossprod_i"
#[106] "benthsgrossprod_o" "benthsgrossprod_i" "benthcgrossprod_o"
#[109] "benthcgrossprod_i" "birdgrossprod_o" "birdgrossprod_i"
#[112] "sealgrossprod_o" "sealgrossprod_i" "cetagrossprod_o"
#[115] "cetagrossprod_i" "wcdenitrif_o" "wcdenitrif_i"
#[118] "seddenitrif_o" "seddenitrif_i" "fluxsedamm_wcamm"
#[121] "fluxwcdet_wcamm" "fluxomni_wcamm" "fluxcarn_wcamm"
#[124] "fluxpfishlar_wcamm" "fluxdfishlar_wcamm" "fluxpfish_wcamm"
#[127] "fluxmfish_wcamm" "fluxdfish_wcamm" "fluxbenthslar_wcamm"
#[130] "fluxbenthclar_wcamm" "fluxbenths_wcamm" "fluxbenthc_wcamm"
#[133] "fluxbird_wcamm" "fluxseal_wcamm" "fluxceta_wcamm"
#[136] "fluxxdet_sedamm" "fluxxRdet_sedamm" "fluxwcamm_wcnit"
#[139] "fluxsednit_wcnit" "fluxsedamm_sednit" "fluxxdet_wcdet"
#[142] "fluxkelpdebris_wcdet" "fluxcorp_wcdet" "fluxphyt_wcdet"
#[145] "fluxomni_wcdet" "fluxcarn_wcdet" "fluxpfishlar_wcdet"
#[148] "fluxdfishlar_wcdet" "fluxpfish_wcdet" "fluxmfish_wcdet"
#[151] "fluxdfish_wcdet" "fluxbenthslar_wcdet" "fluxbenthclar_wcdet"
#[154] "fluxbenths_wcdet" "fluxbenthc_wcdet" "fluxbird_wcdet"
#[157] "fluxseal_wcdet" "fluxceta_wcdet" "fluxwcdet_xdet"
#[160] "fluxcorp_xdet" "fluxbenths_xdet" "fluxbenthc_xdet"
#[163] "fluxxdet_xRdet" "fluxkelpdebris_xRdet" "fluxcorp_xRdet"
#[166] "fluxkelp_kelpdebris" "fluxdisc_corp" "fluxpfish_corp"
#[169] "fluxmfish_corp" "fluxdfish_corp" "fluxbenths_corp"
#[172] "fluxbenthc_corp" "fluxbird_corp" "fluxseal_corp"
#[175] "fluxceta_corp" "fluxwcamm_kelp" "fluxwcnit_kelp"
#[178] "fluxwcamm_phyt_o" "fluxwcamm_phyt_i" "fluxwcnit_phyt_o"
#[181] "fluxwcnit_phyt_i" "fluxwcdet_omni" "fluxphyt_omni"
#[184] "fluxbenthslar_omni" "fluxbenthclar_omni" "fluxomni_carn"
#[187] "fluxpfishlar_carn" "fluxdfishlar_carn" "fluxbenthslar_carn"
#[190] "fluxbenthclar_carn" "fluxomni_pfishlar" "fluxbenthslar_pfishlar"
#[193] "fluxbenthclar_pfishlar" "fluxomni_dfishlar" "fluxbenthslar_dfishlar"
#[196] "fluxbenthclar_dfishlar" "fluxomni_pfish" "fluxcarn_pfish"
#[199] "fluxpfishlar_pfish" "fluxdfishlar_pfish" "fluxbenthslar_pfish"
#[202] "fluxbenthclar_pfish" "fluxomni_mfish" "fluxcarn_mfish"
#[205] "fluxpfishlar_mfish" "fluxdfishlar_mfish" "fluxbenthslar_mfish"
#[208] "fluxbenthclar_mfish" "fluxcorp_dfish" "fluxdisc_dfish"
#[211] "fluxcarn_dfish" "fluxpfishlar_dfish" "fluxdfishlar_dfish"
#[214] "fluxpfish_dfish" "fluxmfish_dfish" "fluxdfish_dfish"
#[217] "fluxbenths_dfish" "fluxbenthc_dfish" "fluxwcdet_benthslar"
#[220] "fluxphyt_benthslar" "fluxwcdet_benthclar" "fluxphyt_benthclar"
#[223] "fluxwcdet_benths" "fluxxdet_benths" "fluxxRdet_benths"
#[226] "fluxphyt_benths" "fluxkelp_benthc" "fluxkelpdebris_benthc"
#[229] "fluxcorp_benthc" "fluxbenths_benthc" "fluxcorp_bird"
#[232] "fluxdisc_bird" "fluxcarn_bird" "fluxpfish_bird"
#[235] "fluxmfish_bird" "fluxdfish_bird" "fluxbenths_bird"
#[238] "fluxbenthc_bird" "fluxcorp_seal" "fluxdisc_seal"
#[241] "fluxcarn_seal" "fluxpfish_seal" "fluxmfish_seal"
#[244] "fluxdfish_seal" "fluxbenths_seal" "fluxbenthc_seal"
#[247] "fluxbird_seal" "fluxdisc_ceta" "fluxomni_ceta"
#[250] "fluxcarn_ceta" "fluxpfish_ceta" "fluxmfish_ceta"
#[253] "fluxdfish_ceta" "fluxbenths_ceta" "fluxbenthc_ceta"
#[256] "fluxbird_ceta" "fluxseal_ceta" "Bs_spawn"
#[259] "Bs_recruit" "Bc_spawn" "Bc_recruit"
#[262] "Pfish_spawn" "Pfish_recruit" "Dfish_spawn"
#[265] "Dfish_recruit" "fluxwcnit_Ngas" "fluxsednit_Ngas"
#[268] "fluxkelpdebris_beachexport" "fluxAMMoutflow_o" "fluxNIToutflow_o"
#[271] "fluxAMMoutflow_i" "fluxNIToutflow_i" "fluxPHYToutflow_o"
#[274] "fluxDEToutflow_o" "fluxPHYToutflow_i" "fluxDEToutflow_i"
#[277] "mfish_emigration" "fluxsedboundary_o" "fluxsedboundary_i"
#[280] "fluxAMMinflow_o" "fluxNITinflow_o" "fluxAMMinflow_i"
#[283] "fluxNITinflow_i" "fluxPHYTinflow_o" "fluxDETinflow_o"
#[286] "fluxPHYTinflow_i" "fluxDETinflow_i" "mfish_imigration"
#[289] "atmosAMMinput_o" "atmosNITinput_o" "atmosAMMinput_i"
#[292] "atmosNITinput_i" "rivAMMinflow" "rivNITinflow"
#[295] "rivPARTinflow" "DINflux_i_o" "DINflux_o_i"
#[298] "PARTflux_i_o" "PARTflux_o_i" "activemigpelfish_i_o"
#[301] "activemigmigfish_i_o" "activemigdemfish_i_o" "activemigbird_i_o"
#[304] "activemigseal_i_o" "activemigceta_i_o" "activemigpelfish_o_i"
#[307] "activemigmigfish_o_i" "activemigdemfish_o_i" "activemigbird_o_i"
#[310] "activemigseal_o_i" "activemigceta_o_i" "vertnitflux"
#[313] "horiznitflux" "landp_o" "landd_quota_o"
#[316] "landd_nonquota_o" "landm_o" "landsb_o"
#[319] "landcb_o" "landcz_o" "landbd_o"
#[322] "landsl_o" "landct_o" "discpel_o"
#[325] "discdem_quota_o" "discdem_nonquota_o" "discmig_o"
#[328] "discsb_o" "disccb_o" "disccz_o"
#[331] "discbd_o" "discsl_o" "discct_o"
#[334] "landp_i" "landd_quota_i" "landd_nonquota_i"
#[337] "landm_i" "landsb_i" "landcb_i"
#[340] "landcz_i" "landbd_i" "landsl_i"
#[343] "landct_i" "landkp_i" "discpel_i"
#[346] "discdem_quota_i" "discdem_nonquota_i" "discmig_i"
#[349] "discsb_i" "disccb_i" "disccz_i"
#[352] "discbd_i" "discsl_i" "discct_i"
#[355] "disckp_i" "offalpel_o" "offaldem_quota_o"
#[358] "offaldem_nonquota_o" "offalmig_o" "offalsb_o"
#[361] "offalcb_o" "offalcz_o" "offalbd_o"
#[364] "offalsl_o" "offalct_o" "offalpel_i"
#[367] "offaldem_quota_i" "offaldem_nonquota_i" "offalmig_i"
#[370] "offalsb_i" "offalcb_i" "offalcz_i"
#[373] "offalbd_i" "offalsl_i" "offalct_i"
#[376] "offalkp_i" "omninetprod_o" "omninetprod_i"
#[379] "carnnetprod_o" "carnnetprod_i" "pfishlarnetprod_o"
#[382] "pfishlarnetprod_i" "dfishlarnetprod_o" "dfishlarnetprod_i"
#[385] "pfishnetprod_o" "pfishnetprod_i" "mfishnetprod_o"
#[388] "mfishnetprod_i" "dfishnetprod_o" "dfishnetprod_i"
#[391] "benthslarnetprod_o" "benthslarnetprod_i" "benthclarnetprod_o"
#[394] "benthclarnetprod_i" "benthsnetprod_o" "benthsnetprod_i"
#[397] "benthcnetprod_o" "benthcnetprod_i" "birdnetprod_o"
#[400] "birdnetprod_i" "sealnetprod_o" "sealnetprod_i"
#[403] "cetanetprod_o" "cetanetprod_i" "totalN"
#[406] "totalN_o" "totalN_i" "x_detritus"
#[409] "x_detritus_o" "x_detritus_i" "corpse"
#[412] "corpse_o" "corpse_i" "x_ammonia"
#[415] "x_ammonia_o" "x_ammonia_i" "x_nitrate"
#[418] "x_nitrate_o" "x_nitrate_i" "s_detritus"
#[421] "s_ammonia" "s_nitrate" "s_phyt"
#[424] "benthslar" "benthclar" "benths"
#[427] "benthc" "discard" "omni"
#[430] "carn" "fishp" "fishd"
#[433] "fishm" "bird" "seal"
#[436] "ceta" "fishplar" "fishdlar"
#[439] "PNP" "netpprod" "fluxwcamm_phyt"
#[442] "fluxwcnit_phyt" "phytgrossprod" "omnigrossprod"
#[445] "carngrossprod" "pfishlargrossprod" "dfishlargrossprod"
#[448] "pfishgrossprod" "mfishgrossprod" "dfishgrossprod"
#[451] "benthslargrossprod" "benthclargrossprod" "benthsgrossprod"
#[454] "benthcgrossprod" "birdgrossprod" "sealgrossprod"
#[457] "cetagrossprod" "omninetprod" "carnnetprod"
#[460] "pfishlarnetprod" "dfishlarnetprod" "pfishnetprod"
#[463] "mfishnetprod" "dfishnetprod" "benthslarnetprod"
#[466] "benthclarnetprod" "benthsnetprod" "benthcnetprod"
#[469] "birdnetprod" "sealnetprod" "cetanetprod"
#[472] "wcdenitrif" "seddenitrif" "fluxsedboundary"
#[475] "DIN_NET_flux_o_i" "PART_NET_flux_o_i" "NET_activemigpelfish_o_i"
#[478] "NET_activemigmigfish_o_i" "NET_activemigdemfish_o_i" "NET_activemigbird_o_i"
#[481] "NET_activemigseal_o_i" "NET_activemigceta_o_i" "NET_mfish_ext_o"
#[484] "fluxDINinflow" "fluxDINoutflow" "fluxPARTinflow"
#[487] "fluxPARToutflow" "atmosDINinput" "rivDINinflow"
#[490] "landp" "landd" "landd_o"
#[493] "landd_i" "landd_quota" "landd_nonquota"
#[496] "landm" "landsb" "landcb"
#[499] "landcz" "landbd" "landsl"
#[502] "landct" "discpel" "discdem"
#[505] "discdem_o" "discdem_i" "discdem_quota"
#[508] "discdem_nonquota" "discmig" "discsb"
#[511] "disccb" "disccz" "discbd"
#[514] "discsl" "discct" "offalpel"
#[517] "offaldem" "offaldem_o" "offaldem_i"
#[520] "offaldem_quota" "offaldem_nonquota" "offalmig"
#[523] "offalsb" "offalcb" "offalcz"
#[526] "offalbd" "offalsl" "offalct"
#[529] "shallowprop" "depth_si" "depth_so"
#[532] "depth_d" "area_s0" "area_s1"
#[535] "area_s2" "area_s3" "area_d0"
#[538] "area_d1" "area_d2" "area_d3"
#[541] "depth_s1" "depth_s2" "depth_s3"
#[544] "depth_d1" "depth_d2" "depth_d3"
#[547] "poros_s1" "poros_s2" "poros_s3"
#[550] "poros_d1" "poros_d2" "poros_d3"
#[553] "iteration" "likelihood" "dummy"
creds<-c(0.005,0.25,0.5,0.75,0.995) # This can be any lenth of vector in any order. All values must be between 0 and 1
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Build_Cred_Timeseries_Fluxes<-function(VtoPid,areaid,thikid,io,creds,varname){
#io = 0 means offshore
#io = 1 means inshore
#io = 2 means whole domain
rownamesvec<-rep(NA,(length(creds)+1))
for(kkk in 1:(length(creds)+1)){
if(kkk==1) rownamesvec[kkk]<-paste(varname,"-maxlik",sep="")
if(kkk>1) rownamesvec[kkk]<-paste(varname,"-",creds[kkk-1],sep="")
}
Resultdata<-data.frame(rep(NA,(length(creds)+1)))
for(kkk in 1:360){
Resultdata[,kkk+1]<-(rep(NA,(length(creds)+1)))
}
names(Resultdata)<-seq(0,360)
row.names(Resultdata)<-rownamesvec
template<-data.frame(newlastyearstore$time)
names(template)<-"time"
if(io==2) template$VtoP<-newlastyearstore[,VtoPid]
if(io==1) template$VtoP<-newlastyearstore[,VtoPid]/(newlastyearstore[,areaid]*newlastyearstore[,thikid])
if(io==0) template$VtoP<-newlastyearstore[,VtoPid]/((1-newlastyearstore[,areaid])*newlastyearstore[,thikid])
template$iteration<-newlastyearstore$iteration
template$likelihood<-newlastyearstore$likelihood
for(ii in 0:360){
Resultdata[1,ii+1]<-template$VtoP[which(template$time==ii&template$iteration==1)]
modresvector<-template$VtoP[which(template$time==ii)]
likevector<-template$likelihood[which(template$time==ii)]
#message("\n","Processing ",varname," data")
credvals<-GetCredInt(modresvector,likevector,creds,var=varname,plotgraph=FALSE)
Resultdata[2:(length(credvals)+1),ii+1]<-credvals
}
return(Resultdata)
}
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# CONVERT CUMULATIVE FLUX COLUMNS INTO DAILY FLUXES
#Find the number of runs that were stored
n_datasets<-nrow(lastyearstore)/361
newlastyearstore<-data.frame(lastyearstore$time)
names(newlastyearstore)<-"time"
newlastyearstore$dummy<-1
newlastyearstore$iteration<-lastyearstore$iteration
newlastyearstore$likelihood<-lastyearstore$likelihood
newlastyearstore$shallowprop<-lastyearstore$shallowprop
tempset<-rep(0,361)
#################################################
col2proc<-477 # Pelagic fish migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-478 # Migratory fish migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-479 # Demersal fish migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-480 # Bird migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-481 # Seal migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
col2proc<-482 # Cetacean migrations
v2proc<-lastyearstore[,col2proc]
newcol<-(ncol(newlastyearstore)+1)
newnames<-c(names(newlastyearstore),names(lastyearstore)[col2proc])
newlastyearstore[,newcol]<-0
names(newlastyearstore)<-newnames
for(jjjj in 1:n_datasets){
tempset[1:360]<-v2proc[((jjjj-1)*361+1+(1)):(jjjj*361)]
tempset[361] <-v2proc[(jjjj*361)] + v2proc[((jjjj-1)*361+1+(1))] - v2proc[((jjjj-1)*361+1)]
newlastyearstore[((jjjj-1)*361+1):(jjjj*361),newcol] <- tempset - v2proc[((jjjj-1)*361+1):(jjjj*361)]
}
################################################################
newlastyearstore$NET_activemigpelfish_o_i_propbiom <- newlastyearstore$NET_activemigpelfish_o_i/(lastyearstore$fishp_o+lastyearstore$fishp_i)
newlastyearstore$NET_activemigmigfish_o_i_propbiom <- newlastyearstore$NET_activemigmigfish_o_i/(lastyearstore$fishm_o+lastyearstore$fishm_i)
newlastyearstore$NET_activemigdemfish_o_i_propbiom <- newlastyearstore$NET_activemigdemfish_o_i/(lastyearstore$fishd_o+lastyearstore$fishd_i)
newlastyearstore$NET_activemigbird_o_i_propbiom <- newlastyearstore$NET_activemigbird_o_i/(lastyearstore$bird_o+lastyearstore$bird_i)
newlastyearstore$NET_activemigseal_o_i_propbiom <- newlastyearstore$NET_activemigseal_o_i/(lastyearstore$seal_o+lastyearstore$seal_i)
newlastyearstore$NET_activemigceta_o_i_propbiom <- newlastyearstore$NET_activemigceta_o_i/(lastyearstore$ceta_o+lastyearstore$ceta_i)
#################################################
#Pelagic fish migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigpelfish_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Planktivorous_fish_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-Result_data
#Pelagic fish migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigpelfish_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Planktivorous_fish_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#migratory fish migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigmigfish_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Migratory_fish_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#migratory fish migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigmigfish_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Migratory_fish_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Demersal fish migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigdemfish_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Demersal_fish_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Demersal fish migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigdemfish_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Demersal_fish_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Bird migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigbird_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Birds_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Bird migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigbird_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Birds_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Seals migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigseal_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Pinnipeds_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Seals migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigseal_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Pinnipeds_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Cetaceans migrations
VtoPid<-which(names(newlastyearstore)=="NET_activemigceta_o_i")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Cetaceans_offshore_inshore_net_migration"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
#Cetaceans migrations as proportion of whole domain biomass
VtoPid<-which(names(newlastyearstore)=="NET_activemigceta_o_i_propbiom")
areaid<-which(names(lastyearstore)=="dummy")
thikid<-which(names(lastyearstore)=="dummy")
io<-2 #whole domain
varname<-"Cetaceans_off_in_net_migration_propbiom"
Result_data<-Build_Cred_Timeseries_Fluxes(VtoPid,areaid,thikid,io,creds,varname)
Result_data_store<-rbind(Result_data_store,Result_data)
# goes into resultsdir/CredInt/datafile-ident.csv
csvfile <- csvname(credpath, "CredInt_processed_daily_migrations", identifier)
writecsv(Result_data_store, csvfile)
Result_data_store
}
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