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Copy pathFig.5_data_mod_new_FINALE.R
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Fig.5_data_mod_new_FINALE.R
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setwd('C:/Users/Ginevra/Desktop/ULTIME_hgII___/Centrale_NOme')
setwd('C:/Users/gi/Desktop/nuoveMEt/Lamb/L6')
#Output/FOsfati/CALIBRATO_inorganico/Centrale_nme')
medie_hg_pM<-c(1.86,2.127058824,1.7675,1.902,2.056666667,3.0875,2.810909091,3.714,3.713684211)
medie_mehg_pM<-c(0.116285714,0.1408125,0.120611111,0.108857143,0.157888889,0.767916667,0.551913043,0.751090909,0.737428571)
sd1<-c(0.4911890,0.6179782,0.5060026,0.5832838,0.6269617,0.7147727,0.5266774,0.3722066,0.4352804)
sd2<-c(0.036545471,0.034533498,0.034428338,0.035267684,0.083861152,0.170347104,0.149375644,0.130289388,0.095633974)
prof<-c(11.4525,13.3275,14.715,15.41,15.92,16.41,16.83,17.14,17.25)
#Leggi model output
hg<-read.csv("Dissolved_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(hg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
str(hg)
hgT<-read.csv("Total_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(hgT)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
solids<-read.csv("Total_Solids.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(solids)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
Phg<-read.csv("Total_Sorbed_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(Phg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
DOChg<-read.csv("DOC_Sorbed_Divalent_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(DOChg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
mehg<-read.csv("Dissolved_Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(mehg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
DOCmehg<-read.csv("DOC_Sorbed_Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(DOCmehg)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
hg0<-read.csv("Elemental_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(hg0)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
dhg0<-read.csv("Dissolved_Elemental_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(dhg0)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
DOChg0<-read.csv("DOC_Sorbed_Elemental_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(DOChg0)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
mehgT<-read.csv("Methyl_Hg.csv", header=FALSE, skip = 1,sep = ",", dec=".")
names(mehgT)<-c("Time", "Oxic1","Oxic2", "CIL", "Oxycline","Suboxic1", "Suboxic2",
"Anoxic","Anoxic2","Anoxic3","Sed1","Sed2")
# dati utimo anno
fine_hgT<-hgT[1957:1968,]
fine_hg<- hg [1957:1968,]
fine_Phg<- Phg [1957:1968,]
fine_DOChg<- DOChg [1957:1968,]
fine_DOCmehg<- DOCmehg [1957:1968,]
fine_mehg<- mehg [1957:1968,]
fine_hg0<- hg0 [1957:1968,]
fine_mehgT<- mehgT [1957:1968,]
fine_solids<- solids [1957:1968,]
hgII_pM<-(hg+DOChg0+DOChg)/200.59*1000
tail(hgII_pM,3)
mehg_pM_<-(mehg+DOCmehg)/215*1000
tail(mehg_pM_,3)
mehgT_pM<-mehgT/215*1000
tail(mehg_pM_,3)/tail(mehgT_pM,3)*100
B_Phg<- fine_hgT - (fine_DOChg+fine_hg+fine_mehgT+fine_hg0)
B_Phg$Oxic1
fine_Phg$Oxic1
#medie layer
layer_hg <-c(layer1<-mean(fine_hg$Oxic1),
layer2<-mean(fine_hg$Oxic2),
layer3<-mean(fine_hg$CIL),
layer4<-mean(fine_hg$Oxycline),
layer5<-mean(fine_hg$Suboxic1),
layer6<-mean(fine_hg$Suboxic2),
layer7<-mean(fine_hg$Anoxic),
layer8<-mean(fine_hg$Anoxic2),
layer9<-mean(fine_hg$Anoxic3))
layer_hgT <-c(layer1<-mean(fine_hgT$Oxic1),
layer2<-mean(fine_hgT$Oxic2),
layer3<-mean(fine_hgT$CIL),
layer4<-mean(fine_hgT$Oxycline),
layer5<-mean(fine_hgT$Suboxic1),
layer6<-mean(fine_hgT$Suboxic2),
layer7<-mean(fine_hgT$Anoxic),
layer8<-mean(fine_hgT$Anoxic2),
layer9<-mean(fine_hgT$Anoxic3))
layer_mehg <-c(layer1<-mean(fine_mehg$Oxic1),
layer2<-mean(fine_mehg$Oxic2),
layer3<-mean(fine_mehg$CIL),
layer4<-mean(fine_mehg$Oxycline),
layer5<-mean(fine_mehg$Suboxic1),
layer6<-mean(fine_mehg$Suboxic2),
layer7<-mean(fine_mehg$Anoxic),
layer8<-mean(fine_mehg$Anoxic2),
layer9<-mean(fine_mehg$Anoxic3))
layer_mehgT <-c(layer1<-mean(fine_mehgT$Oxic1),
layer2<-mean(fine_mehgT$Oxic2),
layer3<-mean(fine_mehgT$CIL),
layer4<-mean(fine_mehgT$Oxycline),
layer5<-mean(fine_mehgT$Suboxic1),
layer6<-mean(fine_mehgT$Suboxic2),
layer7<-mean(fine_mehgT$Anoxic),
layer8<-mean(fine_mehgT$Anoxic2),
layer9<-mean(fine_mehgT$Anoxic3))
layer_mehgT22 <-data.frame(layer1<- fine_mehgT$Oxic1[1],
layer2<- fine_mehgT$Oxic2[1],
layer3<- fine_mehgT$CIL[1],
layer4<- fine_mehgT$Oxycline[1],
layer5<- fine_mehgT$Suboxic1[1],
layer6<- fine_mehgT$Suboxic2[1],
layer7<- fine_mehgT$Anoxic,
layer8<- fine_mehgT$Anoxic2,
layer9<- fine_mehgT$Anoxic3)
layer_mehgT22<-t(layer_mehgT22)
names(layer_mehgT22)<-c('ol1','ol2','cil','oxy','sol','uaol1',
'uaol2','daol','bbl')
str(layer_mehgT22)
layer_Phg <-c(layer1<-mean(fine_Phg$Oxic1),
layer2<-mean(fine_Phg$Oxic2),
layer3<-mean(fine_Phg$CIL),
layer4<-mean(fine_Phg$Oxycline),
layer5<-mean(fine_Phg$Suboxic1),
layer6<-mean(fine_Phg$Suboxic2),
layer7<-mean(fine_Phg$Anoxic),
layer8<-mean(fine_Phg$Anoxic2),
layer9<-mean(fine_Phg$Anoxic3))
layer_DOChg <-c(layer1<-mean(fine_DOChg$Oxic1),
layer2<-mean(fine_DOChg$Oxic2),
layer3<-mean(fine_DOChg$CIL),
layer4<-mean(fine_DOChg$Oxycline),
layer5<-mean(fine_DOChg$Suboxic1),
layer6<-mean(fine_DOChg$Suboxic2),
layer7<-mean(fine_DOChg$Anoxic),
layer8<-mean(fine_DOChg$Anoxic2),
layer9<-mean(fine_DOChg$Anoxic3))
layer_DOCmehg <-c(layer1<-mean(fine_DOCmehg$Oxic1),
layer2<-mean(fine_DOCmehg$Oxic2),
layer3<-mean(fine_DOCmehg$CIL),
layer4<-mean(fine_DOCmehg$Oxycline),
layer5<-mean(fine_DOCmehg$Suboxic1),
layer6<-mean(fine_DOCmehg$Suboxic2),
layer7<-mean(fine_DOCmehg$Anoxic),
layer8<-mean(fine_DOCmehg$Anoxic2),
layer9<-mean(fine_DOCmehg$Anoxic3))
layer_hg0 <-c(layer1<-mean(fine_hg0$Oxic1),
layer2<-mean(fine_hg0$Oxic2),
layer3<-mean(fine_hg0$CIL),
layer4<-mean(fine_hg0$Oxycline),
layer5<-mean(fine_hg0$Suboxic1),
layer6<-mean(fine_hg0$Suboxic2),
layer7<-mean(fine_hg0$Anoxic),
layer8<-mean(fine_hg0$Anoxic2),
layer9<-mean(fine_hg0$Anoxic3))
concentrazioni<-cbind(layer_hg,layer_DOChg, layer_Phg, layer_hgT,
layer_hg0, layer_mehg, layer_DOCmehg, layer_mehgT)
layer_hgT_pm<-layer_hgT/200.59*1000
disshg<-(layer_hg+layer_DOChg+layer_hg0)
dissmehg<-(layer_mehg+layer_DOCmehg)
disshgII_pM<-disshg/200.59*1000
dissMehg_pM<-dissmehg/215*1000
disshg_pM<-(disshgII_pM+dissMehg_pM)
disshg_pM/layer_hgT_pm*100
cor<-cor(disshg_pM,medie_hg_pM)
x1<-medie_hg_pM
y<-prof
cormehg<-cor(dissMehg_pM,medie_mehg_pM)
x2<-medie_mehg_pM
mean(disshg_pM[1:4])
##-----SEDIMENT conc
hgT_fine<-hgT[1957:1968, 1:13]
b<-mean(hgT_fine$Sed1/200.59*1000);b
c<-mean(hgT_fine$Sed2/200.59*1000);c
mehgT_fine<-mehgT[1957:1968, 1:13]
d<-mean(mehgT_fine$Sed1/200.59*1000)
e<-mean(mehgT_fine$Sed2/200.59*1000)
sed_hg_pmol_g<-data.frame(b,c)
names(sed_hg_pmol_g)<-c('surface','subsurface')
sed_mehg_pmol_g<-data.frame(d,e)
names(sed_mehg_pmol_g)<-c('surface','subsurface')
sed_hg_pmol_g
sed_mehg_pmol_g
# ----end sed conc
#setwd("C:/Users/gi/Dropbox/BlackSea2/implementazione/BlackSea_IIDraft/submission_figures")
#----- PLOT----------------
tiff('dato_model_hg_mehg17.tiff', height=25, width=23, units='cm',
compression="lzw", res=300)
par(mfrow=c(1,2),cex.axis=1.2, cex.lab=1.3,
cex.main=1.4, mar=c(4.5,5,1,0))
plot(medie_hg_pM, prof, bty='n',lwd=2, cex=4,
ylim=c(17.5,10.5), lty=1, yaxt='n',xaxt='n',
xlim=c(0, 4), pch=21,
ylab=" ", xlab=" ", type="b",
col="#3288bd00", bg='#41b6c400',main=" ")
abline(h=15.64, lty=2, col='grey60')
abline(h=16.2, lty=2, col='grey60')
par(new=T)
plot(medie_hg_pM, prof, bty='n',lwd=1, cex=4,
ylim=c(17.5,10.5), lty=1, yaxt='n', xaxt='n',
xlim=c(0, 4), pch=21,
ylab=" ", xlab=" ", type="b", col="#5716a2", bg='#5716a244',main=" ")
par(new=TRUE)
segments(x1-sd1,y,x1+sd1,y, col='#5716a2', lwd=1)
epsilon <- 0.12
segments(x1-sd1,y-epsilon,x1-sd1,y+epsilon, col='#5716a2')
segments(x1+sd1,y-epsilon,x1+sd1,y+epsilon, col='#5716a2')
par(new=TRUE)
plot(disshg_pM,prof, type="b",pch=23, lwd=1,cex=4, yaxt='n',
ylim=c(17.5,10.5), bty='n', xlim=c(0, 4), lty=3,
xlab=" ", col="#b3db25", bg='#b3db2577', cex.axis=1.8,
ylab='')
yy<-c(11,12,13,14,15,16,17)
#axis(side=2, at = yy, col="black", line=.50, cex.axis=1.8)
y2<-c(10.5,11.5,12.5,13.5,14.5,15.5,
16.5,17, 17.5)
y1<-c(11,12,13,14,15,16,17)
axis(2, at=y1,line=0, col="black", cex.axis=1.6 , las=2)
axis(2, at=y2,line=0,labels=F, col="black" , tck =-.02, cex.axis=1.6)
#axis(2, at=y,line=0, col="black", cex.axis=1.6 )
mtext(expression('Hg'[D]*' (pM)'),side=1,line=3.5, cex=1.6)
mtext(expression(paste(sigma[theta]*' (kg m'^-3*')')), 2, line=3.2,at=13.5,
col="black", cex=1.6)
p<-c(21,23)
#legend(4,11, pch=p,legend=c("Observations",
# 'Model'),
# col=c("#5716a2", '#b3db25'),
# pt.bg=c('#5716a255','#b3db2577'))
#text(3,15,"OM=7*10^5 /n silt=2.
text(3.2,12,'OL', cex=1.6, font=2)
text(3.5,15.9,'SOL', cex=1.6, font=2)
# --- PLOT Mehg----------------------mehg
#mar=c(4.5,4,1,0)
#win.graph() mar=c(4.5,4,1,0) ylim=c(17.5,10.5),
#dev.new(width=12, height=4)
par(mar=c(4.5,.5,1,5), cex.axis=1.2, cex.lab=1.3, cex.main=1.4 )
plot(medie_mehg_pM, prof, bty='n',lwd=1.3, cex=4,
ylim=c(17.5,10.5), lty=1,
xlim=c(0, 1), pch=22,yaxt='n',xaxt='n',
ylab=" ", xlab=" ", type="b", col="#c51b7d00", main=" ")
#plot(layer_Pmehg*20 ,prof, type="b",pch=23, lwd=1.3,cex=1.3,
# ylim=c(17.3,10.9), bty='n', xlim=c(0,1),lty=3,
# xlab="MeHg concentrations (pM)", col='#103513', bg='#10351322', ylab=expression(paste(sigma[theta]*' (kg/m'^3*')')),
# main=expression(paste("MeHg vertical profiles /n along the water column")))
par(new=T)
plot(medie_mehg_pM, prof, bty='n',lwd=1.3, cex=4,
ylim=c(17.5,10.5), lty=1, yaxt='n',xaxt='n',
xlim=c(0, 1), pch=21,
ylab=" ", xlab=" ", type="b", col="#5716a2",bg='#5716a255', main=" ")
abline(h=15.64, lty=2, col='grey60')
abline(h=16.2, lty=2, col='grey60')
segments(x2-sd2,y,x2+sd2,y, col='#5716a2', lwd=1)
epsilon <- 0.12
segments(x2-sd2,y-epsilon,x2-sd2,y+epsilon, col='#5716a2')
segments(x2+sd2,y-epsilon,x2+sd2,y+epsilon, col='#5716a2')
par(new=TRUE)
plot(dissMehg_pM, prof, type="b",pch=23, lwd=1.3,cex=4,cex.axis=1.8,
ylim=c(17.5,10.5), bty='n', xlim=c(0,1), lty=2,
xlab=" ", col="#b3db25", yaxt='n',xaxt='n',
bg='#b3db2577', ylab='', main='')
#mtext(expression(paste(sigma[theta]*' (kg/m'^3*')')),
# 2, line=2.5 ,at=14,col="black", cex=1.2)
p<-c(21,23)
legend(.3,11, pch=p,legend=c("Observations",
'Model'),pt.cex=2,
col=c("#5716a2", '#b3db25'),
pt.bg=c('#5716a255','#b3db2577'), cex=1.5)
text(.1,16.6,'AOL', cex=1.6, font=2)
at=c(0,0.1,.3,.5,.7,.9)
atx=c(0.2,.4,.6,.8,1)
axis(1, at = at, labels = F ,tick=T, cex.axis=1.8)
axis(1, at = atx, labels = atx,tick=T, cex.axis=1.8)
mtext(expression('MeHg'[D]*' (pM)'),side=1,line=3.5, cex=1.6)
#aty<-c(,11.5, 12.5, 13.5, 14.5, 15.5, 16.5, 17.5)
y1<-c( 10.5, 12.05, 14.25, 15.285, 15.64, 16.2, 16.6, 17.04, 17.35)
why<-c(0, 20, 40, 55, 75, 100, 280, 460, 2000)
axis(4, at = y1, labels = why, tick = TRUE, cex.axis=1.5, las=2)
mtext('depth (m)', at=13.5, side=4,line=3.2, cex=1.6)
dev.off()
sed_hg_pmol_g
sed_mehg_pmol_g/ sed_hg_pmol_g*100 # % of Mehg sed
disshg_pM$Sed1
disshg_pM_upper<-disshg_pM
sed_hg_pmol_g_upper<-sed_hg_pmol_g
s3<-c(disshg_pM_upper, sed_hg_pmol_g_upper$surface)
dati<-c(1.86,2.127058824,1.7675,1.902,2.056,3.0875,2.81090,3.714,3.7137,798.06)
#setwd("C:/Users/gi/Dropbox/BlackSea2/implementazione/new_sim0")
#sim_hgII<-data.frame(s1, s2, s3, dati)
#write.table(sim_hgII, file='sim_hgII_out.txt')
#sub_met<-data.frame(dissMehg_pM_O1, dissMehg_pM_O2, dissMehg_pM_O3)
# names(sub_met)<-c('s1','s2','s3')
#setwd("C:/Users/gi/Dropbox/BlackSeA3/implementazione/new_sim0/_met")
# write.table(sub_met, file='sub_met_mehg_out.txt')
# Root Mean Squared Error
rmse <- function(error)
{
sqrt(mean(error^2))}
# Function that returns Mean Absolute Error
mae <- function(error)
{
mean(abs(error))
}
error<-medie_hg_pM-disshg_pM# Example of invocation of functions
rmse(error)
rmse <- function(error)
{
sqrt(mean(error^2))}
# Function that returns Mean Absolute Error
mae <- function(error)
{
mean(abs(error))
}
error<-medie_mehg_pM-dissMehg_pM# Example of invocation of functions
RMSE<-rmse(error)
rel_error<-error/medie_mehg_pM*100 # Example of invocation of functions
rmse(error)
error_hg<-medie_hg_pM-disshg_pM# Example of invocation of functions
RMSE_hg<-rmse(error_hg)
hgT_surf_sed<-sed_hg_pmol_g$surface + sed_mehg_pmol_g$surface
hgT_subs_sed<-sed_hg_pmol_g$subsurface + sed_mehg_pmol_g$subsurface
model_out<-cbind(disshg_pM,dissMehg_pM,-rel_error,
RMSE, RMSE_hg,hgT_surf_sed,hgT_subs_sed )
write.table(model_out,file='mod_out.txt')
sed_hg_pmol_g