ppH {seacarb} | R Documentation |
Calculates the carbonate chemistry after pH manipulations through addition of acid or base
ppH(flag, sys, var1, var2, pCO2a, vol, N, S=35, T=20, P=0, Pt=0, Sit=0, pHscale="T", k1k2="l", kf="pf")
flag |
Select the couple of variables available. The flags which can be used are:
flag = 1 pH and CO2 given flag = 2 CO2 and HCO3 given flag = 3 CO2 and CO3 given flag = 4 CO2 and ALK given flag = 5 CO2 and DIC given flag = 6 pH and HCO3 given flag = 7 pH and CO3 given flag = 8 pH and ALK given flag = 9 pH and DIC given flag = 10 HCO3 and CO3 given flag = 11 HCO3 and ALK given flag = 12 HCO3 and DIC given flag = 13 CO3 and ALK given flag = 14 CO3 and DIC given flag = 15 ALK and DIC given flag = 21 pCO2 and pH given flag = 22 pCO2 and HCO3 given flag = 23 pCO2 and CO3 given flag = 24 pCO2 and ALK given flag = 25 pCO2 and DIC given |
sys |
0 if the manipulation is carried out in a system closed to the atmosphere or 1 if its is carried out in a system open to the atmosphere |
var1 |
Value of the first variable in mol/kg, except for pH and for pCO2 in μatm |
var2 |
Value of the second variable in mol/kg, except for pH |
pCO2a |
CO2 partial pressure in the atmosphere pCO2 in μatm. It is only used in systems open to the atmosphere (i.e. when sys=1) |
vol |
Volume of acid or base added in liter. By convention, it is given a negative sign for acid additions and a positive sign for base additions |
N |
Normality of the acid or base in mol/kg |
S |
Salinity |
T |
Temperature in degrees Celsius |
P |
Hydrostatic pressure in bar (surface = 0) |
Pt |
Concentration of total phosphate in mol/kg |
Sit |
Concentration of total silicate in mol/kg |
pHscale |
choice of pH scale: "T" for using the total scale, "F" for using the free scale and "SWS" for using the seawater scale, default is total scale |
k1k2 |
"l" for using K1 and K2 from Lueker et al. and "r" for using K1 and K2 from Roy and al. , default is "l" |
kf |
"pf" for using Kf from Perez and Fraga (1987) and "dg" for using Kf from Dickson and Goyet (1979), default is "pf" |
This function does not take into account the effect of dilution on salinity is not taken into account (i.e; it is assumed that the salinity change is minor or that the acid added has the same salinity as the sample).
Pressure corrections and pH scale: For K1, K2, pK1, pK2, pK3, Kw, Kb, Khs and Ksi, the pressure correction was applied on the seawater scale. Hence, values were first transformed from the total scale to the seawater scale, the pressure correction applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS). For Kf, the pressure correction was applied on the free scale. The formulation of Dickson and Goyet (1979) provides Kf on the free scale but that of Perez and Fraga (1987) provides it on the total scale. Hence, in that case, Kf was first transformed from the total scale to the free scale. With both formulations, the pressure correction was applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS). For Ks, the pressure correction was applied on the free scale. The pressure correction was applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS). For Kn, The pressure correction was applied on the seawater scale. The pressure correction was applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS).
The function returns a data frame containing the following columns:
comment |
The initial or final state water |
S |
Salinity |
T |
Temperature in degrees Celsius |
P |
Pressure in bar |
pH |
pH |
CO2 |
CO2 concentration (mol/kg) |
pCO2 |
pCO2, CO2 partial pressure (μatm) |
fCO2 |
fCO2, CO2 fugacity (μatm) |
HCO3 |
HCO3 concentration (mol/kg) |
CO3 |
CO3 concentration (mol/kg) |
DIC |
DIC concentration (mol/kg) |
ALK |
ALK, total alkalinity (mol/kg) |
OmegaAragonite |
Omega aragonite, aragonite saturation state |
OmegaCalcite |
Omega calcite, calcite saturation state |
Jean-Pierre Gattuso gattuso@obs-vlfr.fr
Gattuso J.-P. and Lavigne H, 2009. Perturbation experiments to investigate the impact of ocean acidification: approaches and software tools. Biogeosciences 6, 4413-4439.
ppH(flag=24, sys=0, var1=384, var2=2302e-6, pCO2a=384, vol=-12e-3, N=0.01, S=34.3, T=16, P=0, pHscale="T", kf="pf", k1k2="l") ppH(flag=24, sys=1, var1=384, var2=2302e-6, pCO2a=384, vol=-12e-3, N=0.01, S=34.3, T=16, P=0, pHscale="T", kf="pf", k1k2="l")