R: Parameters of the seawater carbonate system

carbb {seacarb} | R Documentation

## Parameters of the seawater carbonate system

### Description

Returns parameters of the seawater carbonate system.

### Usage

    carbb(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", badd=0, warn="y")

### Arguments

`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
`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
`S` | Salinity
`T` | Temperature in degrees Celsius
`Patm` | Surface atmospheric pressure in atm, default is 1 atm
`P` | Hydrostatic pressure in bar (surface = 0)
`Pt` | Concentration of total phosphate in mol/kg; set to 0 if NA
`Sit` | Concentration of total silicate in mol/kg; set to 0 if NA
`k1k2` | "l" for using K1 and K2 from Lueker et al. (2000), "m06" from Millero et al. (2006), "m10" from Millero (2010) and "r" from Roy et al. (1993). "x" is the default flag; the default value is then "l", except if T is outside the range 2 to 35oC and/or S is outside the range 19 to 43. In these cases, the default value is "w14".
`kf` | "pf" for using Kf from Perez and Fraga (1987) and "dg" for using Kf from Dickson and Riley (1979 in Dickson and Goyet, 1994). "x" is the default flag; the default value is then "pf", except if T is outside the range 9 to 33oC and/or S is outside the range 10 to 40. In these cases, the default is "dg".
`ks` | "d" for using Ks from Dickson (1990) and "k" for using Ks from Khoo et al. (1977), default is "d"
`pHscale` | "T" for the total scale, "F" for the free scale and "SWS" for using the seawater scale, default is "T" (total scale)
`b` | Concentration of total boron. "l10" for the Lee et al. (2010) formulation or "u74" for the Uppstrom (1974) formulation, default is "u74"
`gas` | used to indicate the convention for INPUT pCO2, i.e., when it is an input variable (flags 21 to 25): "insitu" indicates it is referenced to in situ pressure and in situ temperature; "potential" indicates it is referenced to 1 atm pressure and potential temperature; and "standard" indicates it is referenced to 1 atm pressure and in situ temperature. All three options should give identical results at surface pressure. This option is not used when pCO2 is not an input variable (flags 1 to 15). The default is "potential".
`badd` | Amount of boron added in mol/kg.
`warn` | "y" to show warnings when T or S go beyond the valid range for constants; "n" to supress warnings. The default is "y".

### Details

The Lueker et al. (2000) constants for K1 and K2, the Perez and Fraga (1987) constant for Kf and the Dickson (1990) constant for Ks are recommended by Dickson et al. (2007). It is, however, critical to consider that each formulation is only valid for specific ranges of temperature and salinity:

For K1 and K2:

- Roy et al. (1993): S ranging between 5 and 45 and T ranging between 0 and 45oC.

- Lueker et al. (2000): S ranging between 19 and 43 and T ranging between 2 and 35oC.

- Millero et al. (2006): S ranging between 0.1 and 50 and T ranging between 1 and 50oC.

- Millero (2010): S ranging between 1 and 50 and T ranging between 0 and 50oC. Millero (2010) provides a K1 and K2 formulation for the seawater, total and free pH scales. Therefore, when this method is used and if P=0, K1 and K2 are computed with the formulation corresponding to the pH scale given in the flag "pHscale".

For Kf:

- Perez and Fraga (1987): S ranging between 10 and 40 and T ranging between 9 and 33oC.

- Dickson and Riley (1979 in Dickson and Goyet, 1994): S ranging between 0 and 45 and T ranging between 0 and 45oC.

For Ks:

- Dickson (1990): S ranging between 5 and 45 and T ranging between 0 and 45oC.

- Khoo et al. (1977): S ranging between 20 and 45 and T ranging between 5 and 40oC.

The arguments can be given as a unique number or as vectors. If the lengths of the vectors are different, the longer vector is retained and only the first value of the other vectors is used. It is recommended to use either vectors with the same dimension or one vector for one argument and numbers for the other arguments.

Pressure corrections and pH scale:

- For K0, the pressure correction term of Weiss (1974) is used.

- For K1, K2, pK1, pK2, pK3, Kw, Kb, Khs and Ksi, the pressure correction was applied on the seawater scale. Hence, if needed, 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 Riley (1979 in Dickson and Goyet, 1994) 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).

### Value

The function returns a data frame containing the following columns:

`S` | Salinity
`T` | Temperature in degrees Celsius
`Patm` | Surface atmospheric pressure in atm
`P` | Hydrostatic pressure in bar
`pH` | pH
`CO2` | CO2 concentration (mol/kg)
`pCO2` | "standard" pCO2, CO2 partial pressure computed at in situ temperature and atmospheric pressure (μatm)
`fCO2` | "standard" fCO2, CO2 fugacity computed at in situ temperature and atmospheric pressure (μatm)
`pCO2pot` | "potential" pCO2, CO2 partial pressure computed at potential temperature and atmospheric pressure (μatm)
`fCO2pot` | "potential" fCO2, CO2 fugacity computed at potential temperature and atmospheric pressure (μatm)
`pCO2insitu` | "in situ" pCO2, CO2 partial pressure computed at in situ temperature and total pressure (atm + hydrostatic) (μatm)
`fCO2insitu` | "in situ" fCO2, CO2 fugacity computed at in situ temperature and total pressure (atm + hydrostatic) (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

### Note

Warning: pCO2 estimates below 100 m are subject to considerable uncertainty. See Weiss (1974) and Orr et al. (2015)

### Author(s)

Heloise Lavigne, James Orr and Jean-Pierre Gattuso gattuso@obs-vlfr.fr

### References

Dickson A. G. and Riley J. P., 1979 The estimation of acid dissociation constants in seawater media from potentiometric titrations with strong base. I. The ionic product of water. Marine Chemistry 7, 89-99.

Dickson A. G., 1990 Standard potential of the reaction: AgCI(s) + 1/2H2(g) = Ag(s) + HCI(aq), and the standard acidity constant of the ion HSO4 in synthetic sea water from 273.15 to 318.15 K. Journal of Chemical Thermodynamics 22, 113-127.

Dickson A. G., Sabine C. L. and Christian J. R., 2007 Guide to best practices for ocean CO2 measurements. PICES Special Publication 3, 1-191.

Khoo H. K., Ramette R. W., Culberson C. H. and Bates R. G., 1977 Determination of Hydrogen ion concentration in seawater from 5 to 40oC: standard potentials at salinities from 20 to 45. Analytical Chemistry 49, 29-34.

Lee K., Tae-Wook K., Byrne R.H., Millero F.J., Feely R.A. and Liu Y-M, 2010 The universal ratio of the boron to chlorinity for the North Pacific and North Atlantoc oceans. Geochimica et Cosmochimica Acta 74 1801-1811.

Lueker T. J., Dickson A. G. and Keeling C. D., 2000 Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: validation based on laboratory measurements of CO2 in gas and seawater at equilibrium. Marine Chemistry 70 105-119.

Millero F. J., 1995. Thermodynamics of the carbon dioxide system in the oceans. Geochimica Cosmochimica Acta 59: 661-677.

Millero F. J., 2010. Carbonate constant for estuarine waters. Marine and Freshwater Research 61: 139-142.

Millero F. J., Graham T. B., Huang F., Bustos-Serrano H. and Pierrot D., 2006. Dissociation constants of carbonic acid in seawater as a function of salinity and temperature. Marine Chemistry 100, 80-84.

Orr J. C., Epitalon J.-M. and Gattuso J.-P., 2015. Comparison of seven packages that compute ocean carbonate chemistry. Biogeosciences 12, 1483-1510.

Perez F. F. and Fraga F., 1987 Association constant of fluoride and hydrogen ions in seawater. Marine Chemistry 21, 161-168.

Roy R. N., Roy L. N., Vogel K. M., Porter-Moore C., Pearson T., Good C. E., Millero F. J. and Campbell D. M., 1993. The dissociation constants of carbonic acid in seawater at salinities 5 to 45 and temperatures 0 to 45oC. Marine Chemistry 44, 249-267.

Uppstrom L.R., 1974 The boron/chlorinity ratio of the deep-sea water from the Pacific Ocean. Deep-Sea Research I 21 161-162.

Weiss, R. F., 1974. Carbon dioxide in water and seawater: the solubility of a non-ideal gas, Mar. Chem., 2, 203-215.

Weiss, R. F. and Price, B. A., 1980. Nitrous oxide solubility in water and seawater, Marine Chemistry, 8, 347-359.

Zeebe R. E. and Wolf-Gladrow D. A., 2001 CO2 in seawater: equilibrium, kinetics, isotopes. Amsterdam: Elsevier, 346 pp.

### Examples

    ## With a couple of variables
    carbb(flag=8, var1=8.2, var2=0.00234, S=35, T=25, P=0, Patm=1.0, Pt=0, Sit=0,
    	pHscale="T", kf="pf", k1k2="l", ks="d", b="u74", badd=0)

[Package seacarb version 3.1.1 Index]