Comparison of ten packages that compute ocean carbonate chemistry

Biogeosciences

Volumn 12, Issue 5, 2015, Pages 1483-1510

  Orr, J C ^a   Epitalon, J M ^b   Gattuso, J P ^c,d  

^a DIF   (France)

^b Geoscientific Programming Services   (France)

^c LABORATOIRE D OCÉANOGRAPHIE DE VILLEFRANCHE   (France)

^d SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONATE SYSTEM; CHEMISTRY; DATA SET; OCEAN; SENSITIVITY ANALYSIS; SURFACE AREA; THERMODYNAMICS;

EID: 84924351723     PISSN: 17264170     EISSN: 17264189     Source Type: Journal    
DOI: 10.5194/bg-12-1483-2015     Document Type: Article

References (66)

1. Antonov, J. I., Seidov, D., Boyer, T. P., Locarnini, R. A., Mishonov, A. V., Garcia, H. E., Baranova, O. K., Zweng, M. M., and Johnson, D. R.: World Ocean Atlas 2009, Volume 2: Salinity, edited by: Levitus, S., Atlas NESDIS 69, NOAA, US Government Printing Office, Washington DC, 184 pp., 2010.
2. Byrne, R. H. and Yao, W.: Procedures for measurement of carbonate ion concentrations in seawater by direct spectrophotometric observations of Pb (II) complexation, Mar. Chem., 112, 128-135, 2008.
3. Cai, W.-J. and Wang, Y.: The chemistry, fluxes, and sources of carbon dioxide in the estuarine waters of the Satilla and Altamaha Rivers, Georgia, Limnol. Oceanogr., 43, 657-668, 1998.
4. Culberson, C. and Pytkowicz, R. M.: Effect of pressure on carbonic acid, boric acid and the pH in seawater, Limnol. Oceanogr., 13, 403-417, 1968.
5. - in synthetic seawater from 273.15 to 318.15 K, Chemical Thermodynamics, 22, 113-127, 1990a.
6. Dickson, A. G.: Thermodynamics of the dissociation of boric acid in synthetic seawater from 273.15 to 318.15 K, Deep-Sea Res., 37, 755-766, 1990b.
7. Dickson, A. G.: The carbon dioxide system in seawater: equilibrium chemistry and measurements, in: Guide to Best Practices for Ocean Acidification Research and Data Reporting, edited by: Riebesell, U., Fabry, V. J., Hansson, L., and Gattuso, J.-P., Publications Office of the European Union, 17-40, 2010.
8. Dickson, A. G. and Goyet, C.: Handbook of methods for the analysis of the various parameters of the carbon dioxide system in seawater; version 2, ORNL/CDIAC-74, ORNL, 1994.
9. Dickson, A. G. and Millero, F.: A comparison of the equilibrium constants for the dissociation of carbonic acid in seawater media, Deep-Sea Res., 34, 1733-1743, 1987.
10. Dickson, A. G. and Riley, J. P.: The effect of analytical error on the evaluation of the components of the aquatic carbon-dioxide system, Mar. Chem., 6, 77-85, 1978.
11. W, Mar. Chem., 7, 89-99, 1979.
12. 2 measurements, PICES Special Publication 3, 191 pp., 2007.
13. Easley, R. A., Patsavas, M. C., Byrne, R. H., Liu, X., Feely, R. A., and Mathis, J. T.: Spectrophotometric Measurement of Calcium Carbonate Saturation States in Seawater, Environ. Sci. Technol., 47, 1468-1477, 2013.
14. 2 system in seawater, J. Marine Syst., 5, 111-118, 1994.
15. Garcia, H. E., Locarnini, R. A., Boyer, T. P., Antonov, J. I., Zweng, M. M., Baranova, O. K., and Johnson, D. R.: World Ocean Atlas 2009, Volume 4: Nutrients (Phosphate, Nitrate, Silicate), edited by: Levitus, S., Atlas NESDIS 71, NOAA, US Government Printing Office, Washington DC, 398 pp., 2010.
16. Gattuso, J.-P. and Hansson, L. (Eds.): Ocean Acidification, Oxford Univ. Press, Oxford, UK, 408 pp., 2011.
17. Gattuso, J.-P. and Lavigne, H.: Technical Note: Approaches and software tools to investigate the impact of ocean acidification, Biogeosciences, 6, 2121-2133, doi:10.5194/bg-6-2121-2009, 2009.
18. Gattuso, J.-P., Epitalon, J.-M. and Lavigne, H. : seacarb: seawater carbonate chemistry with R. R package version 3.0.6, The Comprehensive R Archive Network, http://CRAN.R-project.org/package=seacarb (last access: 24 February 2015), 2015.
19. Goyet, C. and Poisson, A.: New determination of carbonic acid dissociation constants in seawater as a function of temperature and salinity, Deep-Sea Res., 36, 1635-1654, 1989.
20. Hansson, I.: A new set of acidity constants for carbonic acid and boric acid in sea water, Deep-Sea Res., 20, 461-478, 1973a.
21. Hansson, I.: The determination of dissociation constants of carbonic acid in synthetic sea water in the salinity range of 20-40 ‰ and temperature range of 5-30°C, Acta Chemica Scandanavia, 27, 931-944, 1973b.
22. Hofmann, A. F., Soetaert, K., Middelburg, J. J., and Meysman, F. J.: AquaEnv: An Aquatic Acid-Base Modelling Environment in: R. Aquatic Geochemistry, 16, 507-546, 2010.
23. Hoppe, C. J. M., Langer, G., Rokitta, S. D., Wolf-Gladrow, D. A., and Rost, B.: Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies, Biogeosciences, 9, 2401-2405, doi:10.5194/bg-9-2401-2012, 2012.
24. 2 Equilibrium Calculations Using Excel Version 2, University of Otago, New Zealand, available at: http://neon.otago.ac.nz/research/mfc/people/keith-hunter/software/swco2/ (last access: 24 February 2015), 2007.
25. Key, R. M., Sabine., C. L., Lee, K., Wanninkhof, R., Bullister, J., Feely, R. A., Millero, F. J., Mordy, C., and Peng, T.-H.: A Global Ocean carbon climatology: results from Global Data Analysis Project (GLODAP), Global Biogeochem. Cy., 18, GB4031, doi:10.1029/2004GB002247, 2004.
26. Khoo, K. H., Ramette, R. W., Culberson, C. H., and Bates, R. G.: Determination of hydrogen ion concentrations in seawater from 5 to 40 °C: standard potentials at salinities from 20 to 45 ‰, Anal. Chem., 49, 29-34, 1977.
27. Kroeker, K. J., Kordas, R. L., Crim, R., Hendriks, I. E., Ramajo, L., Singh, G. S., Duarte, C. M., and Gattuso, J.-P.: Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming, Glob. Change Biol., 19, 156-159, 2013.
28. Lee, K., Kim, T.-W., Byrne, R. H., Millero, F. J., Feely, R. A., and Liu, Y.-M.: The universal ratio of boron to chlorinity for the North Pacific and North Atlantic oceans, Geochim. Cosmochim. Ac., 74, 1801-1811, doi:10.1016/j.gca.2009.12.027, 2010.
29. 2 System Calculations, ORNL/CDIAC-105, Carbon Dioxide Inf. Anal. Cent., Oak Ridge Natl. Lab., Oak Ridge, Tenn., 38 pp., 1998.
30. Locarnini, R., Mishonov, A., Antonov, J., Boyer, T., Garcia, H., Baranova, O., Zweng, M., and Johnson, D.: World Ocean Atlas 2009, Volume 1: Temperature, edited by: Levitus, S., Atlas NESDIS 68, NOAA, US Government Printing Office, Washington DC, 184 pp., 2010.
31. 2 in gas and seawater at equilibrium, Mar. Chem., 70, 105-119, 2000.
32. Martz, T. R., Jannasch, H. W., and Johnson, K. S.: Determination of carbonate ion concentration and inner sphere carbonate ion pairs in seawater by ultraviolet spectrophotometric titration, Mar. Chem., 115, 145-154, 2009.
33. Mehrbach, C., Culberson, C. H., Hawley, J. E., and Pytkowicz, R. M.: Measurement of the apparent dissociation constants of carbonic acid in seawater at atmospheric pressure, Limnol. Oceanogr., 18, 897-907, 1973.
34. Millero, F. J.: The thermodynamics of the carbonate system in seawater, Geochim. Cosmochim. Ac., 43, 1651-1661, 1979.
35. Millero, F. J.: Influence of pressure on chemical processes in the sea, in: Chemical Oceanography, edited by: Riley, J. P. and Chester, R., 1-88, Academic Press, New York, 1983.
36. Millero, F. J.: Thermodynamics of the carbon dioxide system in the oceans, Geochim. Cosmochim. Ac., 59, 661-677, 1995.
37. Millero, F. J.: The marine inorganic carbon cycle, Chem. Rev., 107, 308-341, 2007.
38. Millero, F. J.: Carbonate constants for estuarine waters, Mar. Freshwater Res., 61, 139-142, doi:10.1071/MF09254, 2010.
39. Millero, F. J., Graham, T. B., Huang, F., Bustos-Serrano, H., and Pierrot, D.: Dissociation constants of carbonic acid in seawater, Mar. Chem., 100, 80-94, doi:10.1016/j.marchem.2005.12.001, 2006.
40. 2 for the dissociation of carbonic acid in seawater, Geochim. Cosmochim. Ac., 66, 2529-2540, 2002.
41. Morris, A. and Riley, J.: The bromide/chlorinity and sulphate/chlorinity ratio in sea water, Deep-Sea Res., 13, 699-705, 1966.
42. Mosley, L. M., Peake, B. M., and Hunter, K. A.: Modelling of pH and inorganic carbon speciation in estuaries using the composition of the river and seawater end members, Environ. Modell. Softw., 25, 1658-1663, 2010.
43. Mucci, A.: The solubility of calcite and aragonite in seawater at various salinities, temperatures, and one atmosphere total pressure, Am. J. Sc., 283, 780-799, 1983.
44. Munhoven, G.: Mathematics of the total alkalinity-pH equation - pathway to robust and universal solution algorithms: the SolveSAPHE package v1.0.1, Geosci. Model Dev., 6, 1367-1388, doi:10.5194/gmd-6-1367-2013, 2013.
45. Orr, J. C.: Recent and future changes in ocean carbonate chemistry, in: Ocean Acidification, edited by: Gattuso, J.-P., and Hansson, L., chap. 3, 41-66, Oxford Univ. Press, 2011.
46. Orr, J. C. and Epitalon, J.-M.: Improved routines to model the ocean carbonate system: mocsy 1.0, Geosci. Model Dev. Discuss., 7, 2877-2902, doi:10.5194/gmdd-7-2877-2014, 2014.
47. Orr, J. C. and Epitalon, J.-M.: Improved routines to model the ocean carbonate system: mocsy 2.0, Geosci. Model Dev., 8, 485-499, doi:10.5194/gmd-8-485-2015, 2015.
48. Orr, J. C., Najjar, R., Sabine, C. L., and Joos, F.: Abiotic-HOWTO. Internal OCMIP Report, LSCE/CEA Saclay, Gif-sur-Yvette, France, 25 pp., 1999.
49. Orr, J. C., Fabry, V. J., Aumont, O., Bopp, L., Doney, S. C., Feely, R. A., Gnanadesikan, A., Gruber, N., Ishida, A., Joos, F., Key, R. M., Lindsay, K., Maier-Reimer, E., Matear, R., Monfray, P., Mouchet, A., Najjar, R. G., Plattner, G.-K., Rodgers, K. B., Sabine, C. L., Sarmiento, J. L., Schlitzer, R., Slater, R. D., Totterdell, I. J., Weirig, M.-F., Yamanaka, Y., and Yool, A.: Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms, Nature, 437, 681-686, doi:10.1038/nature04095, 2005.
50. Orr, J. C., Epitalon, J.-M., and Gattuso, J.-P.: Comparison of seven packages that compute ocean carbonate chemistry, Biogeosciences Discuss., 11, 5327-5397, doi:10.5194/bgd-11-5327-2014, 2014. 2014.
51. 2 system in seawater for Microsoft Excel/VBA, Wash. State Dept. of Ecology/Brookhaven Nat. Lab., Olympia, WA/Upton, NY, USA, 2007.
52. Perez, F. F. and Fraga, F.: Association constant of fluoride and hydrogen ions in seawater, Mar. Chem., 21, 161-168, 1987.
53. 2 System Calculations, Tech. rep., Carbon Dioxide Inf. Anal. Cent., Oak Ridge Natl. Lab., US DOE, Oak Ridge, Tenn., 2006.
54. Proye, A. and Gattuso, J.-P.: Seacarb, an R package to calculate parameters of the seawater carbonate system, 2003.
55. R Development Core Team: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0, 2012.
56. Riley, J. P.: The occurrence of anomalously high fluoride concentrations in the North Atlantic, Deep-Sea Res., 12, 219-220, 1965.
57. Riley, J. and Tongudai, M.: The major cation/chlorinity ratios in sea water, Chem. Geol., 2, 263-269, 1967.
58. Robbins, L. L., Hansen, M. E., Kleypas, J. A., and Meylan, S. C.: CO2calc: a user-friendly carbon calculator for Windows, Mac OS X, and iOS (iPhone), USGS Open-File Report, 2010-1280, 17, 2010.
59. Roy, R. N., Roy, L. N., Vogel, K. M., Porter-Moore, C., Pearson, T., Good, C. E., Millero, F. J., and Campbell, D. M.: The dissociation constants of carbonic acid in seawater at salinities 5 to 45 and temperatures 0 to 45 °C, Mar. Chem., 44, 249-267, 1993.
60. Sarmiento, J. L., Le Quéré, C., and Pacala, S.: Limiting future atmospheric carbon dioxide, Global Biogeochem. Cy., 9, 121-137, 1995.
61. Schlitzer, R.: Interactive analysis and visualization of geoscience data with Ocean Data View, Comput. Geosci., 28, 1211-1218, 2002.
62. Uppström, L. R.: The Boron/Chlorinity Ratio of Deep-Sea Water from the Pacific Ocean, in: Deep-Sea Research and Oceanographic Abstracts, 21, 161-162, Elsevier, 1974.
63. 2 system calculations, ORNL/CDIAC-105b, Carbon Dioxide Inf. Anal. Cent., Oak Ridge Natl. Lab., US DOE, Oak Ridge, Tenn., 2011.
64. Weiss, R. F.: Carbon dioxide in water and seawater: the solubility of a non-ideal gas, Mar. Chem., 2, 203-215, 1974.
65. Wittmann, A. C. and Pörtner, H.-O.: Sensitivities of extant animal taxa to ocean acidification, Nature Climate Change, 3, 995-1001, 2013.
66. 2 in Seawater: Equilibrium, Kinetics, Isotopes, Elsevier, Amsterdam, 346 pp., 2001.