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seacarb

Carbonate chemistry with R

In 2003, Aurélien Proye and I put together seacarb, an R package that calculates various parameters of the carbonate system in seawater. The package was subsequently upgraded. In 2008, a new version (2.0) was built with the assistance of Héloïse Lavigne. Five additional functions were included to assist the design of perturbation experiments to investigate ocean acidification and other functions were revised in order to strictly follow the "Guide to best practices for ocean CO2 measurements" (Dickson et al., 2007). Seacarb uses equations mostly from the following sources:

  • Dickson A. G., Sabine C. L. & Christian J. R., 2007. Guide to best practices for ocean CO2 measurements. PICES Special Publication 3:1-191.
  • DOE, 1994. Handbook of methods for the analysis of the various parameters of the carbon dioxide system in sea water; version 2. Dickson, A. G. and Goyet, C., editors. ORNL/CDIAC-74, 1994.
  • Frankignoulle M., 1994. A complete set of buffer factors for acid/base CO2 system in seawater. Journal of Marine Systems 5: 111-118.
  • Orr J. C., Epitalon J.-M., Dickson A. G. & Gattuso J.-P., 2018. Routine uncertainty propagation for the marine carbon dioxide system. Marine Chemistry 207:84-107.
  • Zeebe R. E. & Wolf-Gladrow D. A., 2001. CO2 in seawater: equilibrium, kinetics, isotopes. Amsterdam: Elsevier, 346 pp.

A portion of the code has been adapted, with permission from the authors, from the Matlab files mentioned above. I am grateful to Richard Zeebe and Dieter Wolf-Gladrow for that. Héloïse Lavigne contributed a lot to seacarb in 2008 and 2009; this was critical to the launch of version 2.0 and subsequent updates. Portions of code and/or corrections have also been contributed by Jean-Marie Epitalon (2004, 2018), Bernard Gentili (2006), Karline Soetaert (2007) and Jim Orr (2007, 2010, 2018). Jean-Marie Epitalon considerably improved the code, leading to much faster calculations in version 3.0.

Orr et al. (2015) assessed seacarb together with other packages which calculate the seawater carbonate chemistry. In 2018, option to calculate uncertainty propagation was added (Orr et al., 2018).

This program is provided free under the GNU General Public License (GNU GPL). It will be improved using the comments that I will receive. If you are new to R, please check the manuals and FAQs available on the R-project web site to get information on how to install R and the seacarb package on your system. Please only report and comment on seacarb, not on general problems related to R.

Briefly, after installing R and if you have an Internet connection, here is the simplest way to install seacarb:

  • Launch R
  • To install seacarb (to be done only once), type the following command: install.packages("seacarb")
  • To load the seacarb package into memory in order to use it (to be done each time R is launched), type the following command: library(seacarb)

The seacarb package can be downloaded from the Comprehensive R Archive Network (CRAN; see link below). The documentation is included in the package and is accessible using standard R commands. Please give due credit to the publications mentioned above and cite seacarb as follows:

Gattuso J.-P., Epitalon J.-M., Lavigne H. & Orr J., 2021. seacarb: seawater carbonate chemistry. R package version 3.3.0. http://CRAN.R-project.org/package=seacarb

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Version

Install

install.packages('seacarb')

Monthly Downloads

1,285

Version

3.3.3

License

GPL (>= 2)

Last Published

February 15th, 2024

Functions in seacarb (3.3.3)

K1

First dissociation constant of carbonic acid (mol/kg)
Kspa

Solubility product of aragonite (mol/kg)
Ksi

Dissociation constant of Si(OH)4
Kn

Dissociation constant of ammonium (mol/kg)
Pcorrect

Pressure correction of equilibrium constants
Ks

Stability constant of hydrogen sulfate (mol/kg)
sir

Parameters of the seawater carbonate system including the substrate-inhibitor-ratio (SIR)
Pcoeffs

Coefficients used for pressure-correcting the equilibrium constants
Om

Carbonate saturation state for magnesian calcites
Kw

Ion product of water (mol2/kg2)
Kspc

Solubility product of calcite (mol/kg)
bjerrum

Bjerrum plot
buffer

Buffer parameters of the seawater carbonate system
buffesm

Buffer capacities of the seawater carbonate system from Egleston et al. (2010), corrected and enhanced
alkalinity

Example data file for function at
amp

pH value of the AMP buffer
bor

Total boron concentration (mol/kg)
sir_b

Parameters of the seawater carbonate system with boron addition, including the substrate-inhibitor-ratio (SIR)
buffergen

Buffer factors of the seawater carbonate system as defined by Hagens and Middelburg (2016)
carb

Parameters of the seawater carbonate system
sir_full

Parameters of the seawater carbonate system including the substrate-inhibitor-ratio (SIR) - extension of carb
eos2teos_chem

Convert temperature and salinity from EOS-80 to TEOS-10
derivnum

Numerical derivatives of seawater carbonate system variables
carbfull

Parameters of the seawater carbonate system - extension of carb
fH

Total activity coefficient for H+
f2pCO2

Converts the CO2 fugacity to CO2 partial pressure
fCO2insi

fCO2 at in situ temperature
eos2teos_geo

Convert temperature and salinity from EOS-80 to TEOS-10
carbb

Parameters of the seawater carbonate system with boron addition
errors

Uncertainty propagation for computed marine carbonate system variables
d2p

Converts depth in meters to pressure in dbar
kconv

Conversion factors to change the pH scale of dissociation constants
p2fCO2

Converts pCO2 (partial pressure in CO2) into fCO2 (fugacity of CO2)
oa

Perturbation of the seawater carbonate system
kfg

variable for internal use
pH

Potentiometric pH
p2xCO2

Converts partial pressure of CO2 to mole fraction of CO2
pHconv

Conversion of pH
pCO2insi

pCO2 at in situ temperature
p2d

Converts pressure in dbar to depth in meters
pCa

pCa
pHspec

Calculates pHT from results of spectrophotometric measurements
pgas

pgas
ppH

ppH
pHslope

Slope of the calibration curve of a pH electrode
pHnbs2sws

Converts pH from NBS to SWS scale
pHsws2nbs

Converts pH from SWS to NBS scale
psi

Molar ratio of CO2 released vs CaCO3 precipitated
pmix

pmix
pHinsi

pH at in situ temperature and pressure
rho

Density of seawater (kg/m3)
seacarb_test_P0

Test data file (at P=0) to test the use of the carb function
pTA

pTA
sa2sp_geo

From absolute to practical salinity
seacarb_test_P300

Test data file (at P=300) to test the use of the carb function
sa2sp_chem

From absolute to practical salinity
vapress

Computes vapor pressure of seawater
tris

pH of TRIS buffer
sp2sa_chem

From Practical to absolute salinity
sf_calc

Calculation of calibrated pH for seaFET sensor
sf_calib

Calibration coefficients for seaFET sensor
seaFET

Test seaFET data file
x2pCO2

Converts mole fraction to partial pressure of CO2
speciation

ionic forms as a function of pH
teos2eos_chem

Convert temperature and salinity from TEOS-10 to EOS-80
teos2eos_geo

Convert temperature and salinity from TEOS-10 to EOS-80
sp2sa_geo

From practical to absolute salinity
theta

Potential temperature of seawater
K2p

Second dissociation constant of phosphoric acid (mol/kg)
K2si

Second dissociation constant of Si(OH)4
Kb

Dissociation constant of boric acid (mol/kg)
Khs

Dissociation constant of hydrogen sulfide (mol/kg)
K3p

Third dissociation constant of phosphoric acid (mol/kg)
K1p

First dissociation constant of phosphoric acid (mol/kg)
K0

Henry's constant mol/(kg/atm)
K2

Second dissociation constant of carbonic acid (mol/kg)
Kf

Equilibrium constant of hydrogen fluoride (mol/kg)