# Copyright (C) 2020 Kimberlee Baldry
#
# This file is part of seacarb.
#
# Seacarb is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.
#
# Seacarb is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with seacarb; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#
sir <- function(flag, var1, var2, S = 35, T = 25, Patm = 1, P = 0,
Pt = 0, Sit = 0, k1k2 = "x", kf = "x", ks = "d", pHscale = "T",
b = "u74", gas = "potential", warn = "y", eos = "eos80",
long = 1e+20, lat = 1e+20){
Carb_out = carb(flag, var1, var2, S , T , Patm , P ,
Pt, Sit , k1k2 , kf , ks , pHscale ,
b , gas , warn , eos ,
long , lat )
### pH conversions
# carb allows multiple pH scale inputs
# set up flag vectors
free_flag <- NA
total_flag <- NA
sws_flag <- NA
for(ph in 1:length(pHscale)){
if(pHscale[ph] == "F"){
free_flag[ph] <- NA
total_flag[ph] <- 2
sws_flag[ph] <- 6
}
if(pHscale[ph] == "T"){
free_flag[ph] <- 4
total_flag[ph] <- NA
sws_flag[ph] <- 3
}
if(pHscale[ph] == "SWS"){
free_flag[ph] <- 5
total_flag[ph] <- 1
sws_flag[ph] <- NA
}}
pH_f <- Carb_out$pH
pH_t <- Carb_out$pH
pH_sws <- Carb_out$pH
#identify those that need conversion
idx_f <- is.finite(free_flag)
idx_t <- is.finite(total_flag)
idx_sws <- is.finite(sws_flag)
#convert only those not in scale
if(length(which(idx_f)) != 0){pH_f[idx_f] = pHconv(flag = free_flag[idx_f], pH=Carb_out$pH[idx_f], S=Carb_out$S[idx_f], T=Carb_out$T[idx_f], P=Carb_out$P[idx_f], ks = ks)}
if(length(which(idx_t)) != 0){pH_t[idx_t] = pHconv(flag = total_flag[idx_t], pH=Carb_out$pH[idx_t], S=Carb_out$S[idx_t], T=Carb_out$T[idx_t], P=Carb_out$P[idx_t], ks = ks)}
if(length(which(idx_sws)) != 0){pH_sws[idx_sws] = pHconv(flag = sws_flag[idx_sws], pH=Carb_out$pH[idx_sws], S=Carb_out$S[idx_sws], T=Carb_out$T[idx_sws], P=Carb_out$P[idx_sws], ks = ks)}
### calculate H ions on different scales
H_f <- (10^(-pH_f)*1000000) * 1000 / rho(S=Carb_out$S, T=Carb_out$T, P=Carb_out$P) #mol/L to mol/kg (devide by kg/L)
H_t <- (10^(-pH_t)*1000000) * 1000 / rho(S=Carb_out$S, T=Carb_out$T, P=Carb_out$P) #mol/L to mol/kg (devide by kg/L)
H_sws <- (10^(-pH_sws)*1000000) * 1000 / rho(S=Carb_out$S, T=Carb_out$T, P=Carb_out$P) #mol/L to mol/kg (devide by kg/L)
### SIR calculation
sir <- (Carb_out$HCO3) / H_f
### output
RES <- data.frame(flag, Carb_out$S, Carb_out$T, Carb_out$Patm, Carb_out$P, Carb_out$pH, Carb_out$CO2, Carb_out$fCO2, Carb_out$pCO2,
Carb_out$fCO2pot, Carb_out$pCO2pot, Carb_out$fCO2insitu, Carb_out$pCO2insitu, Carb_out$HCO3, Carb_out$CO3,
Carb_out$DIC, Carb_out$ALK, Carb_out$OmegaAragonite, Carb_out$OmegaCalcite, sir, H_f,H_t,H_sws,pH_f,pH_sws,pH_t)
names(RES) <- c("flag", "S", "T", "Patm", "P", "pH", "CO2",
"fCO2", "pCO2", "fCO2pot", "pCO2pot", "fCO2insitu", "pCO2insitu",
"HCO3", "CO3", "DIC", "ALK", "OmegaAragonite", "OmegaCalcite","SIR","H_free","H_sws","H_t","pH_free","pH_sws","pH_t")
return(RES)
}
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