R: ppH

ppH {seacarb} | R Documentation

## ppH

### Description

Calculates the carbonate chemistry after pH manipulations through addition of acid or base

### Usage

    ppH(flag, sys, var1, var2, pCO2a, vol, N, S=35, T=20, P=0, Pt=0,
    	Sit=0, pHscale="T", k1k2="x", kf="x", ks="d")

### 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
`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. The acid must be fortified with NaCl in order to have the same salinity than seawater.
`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
`k1k2` | "l" for using K1 and K2 from Lueker et al. (2000), "m06" from Millero et al. (2006), "m10" from Millero (2010), "w14" from Waters et al. (2014), 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 Dickon (1990), "k" for using Ks from Khoo et al. (1977), default is "d"
`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

### 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:

`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

### Note

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

### Author(s)

Jean-Pierre Gattuso and Heloise Lavignegattuso@obs-vlfr.fr

### References

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.

Gattuso J.-P. and Lavigne H., 2009 Perturbation experiments to investigate the impact of ocean acidification: approaches and software tools. Biogeosciences 6, 4413-4439.

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.

Waters, J., Millero, F. J., and Woosley, R. J., 2014. Corrigendum to “The free proton concentration scale for seawater pH”, [MARCHE: 149 (2013) 8-22], Marine Chemistry 165, 66-67.

### See Also

`buffer`.

### Examples

    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", ks="d")

    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", ks="d")

[Package seacarb version 3.1.1 Index]