Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software R

Environmental Modelling and Software

Volumn 32, Issue , 2012, Pages 49-60

  Soetaert, Karline ^a   Meysman, Filip ^a  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

Author keywords

Model; Open source; R; Reactive transport; Software

Indexed keywords

3D MODELS; AQUATIC ECOSYSTEM; BIOGEOCHEMICAL MODELS; BIOLOGICAL TRANSFORMATION; BREAK THROUGH CURVE; ESTUARINE SEDIMENTS; EXPERIMENTAL SETUP; FLAT SURFACES; FLOWTHROUGH; GEOCHEMICAL REACTION; HOTSPOTS; MODELING PACKAGES; MULTIPLE TIMESCALES; NATURAL COMPOUNDS; NATURAL ENVIRONMENTS; OPEN SOURCE SOFTWARE; OPEN SOURCES; ORDERS OF MAGNITUDE; OXYGEN DYNAMICS; PHYSICAL PROCESS; POPULAR PLATFORM; R; REACTIVE COMPONENTS; REACTIVE TRACER; REACTIVE TRANSPORT; REACTIVE TRANSPORT MODELING; REACTIVE TRANSPORT MODELS; SIMPLE GEOMETRIES; SMALL STREAMS; SOLUTION METHODS; SPATIAL SCALE; SPHERICAL BODY; SULFATE REDUCTION; TEMPORAL SCALE; THREE-DIMENSIONAL DOMAIN; UPPER LAYER; WATER COLUMNS;

ADSORPTION; ANOXIC SEDIMENTS; CHEMICAL COMPOUNDS; COMPUTER OPERATING SYSTEMS; COMPUTER SOFTWARE; CURVE FITTING; DYNAMICS; GROUNDWATER; MODELS; REACTION RATES; RIVERS; SEDIMENTOLOGY;

THREE DIMENSIONAL;

ADSORPTION; ADVECTION; AGGREGATE; AQUATIC ECOSYSTEM; BIOTRANSFORMATION; BREAKTHROUGH CURVE; DISPERSION; GEOMETRY; SOFTWARE;

EID: 84857370432     PISSN: 13648152     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.envsoft.2011.08.011     Document Type: Article

References (53)

1. Aller R.C. Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment. Geochimica et Cosmochimica Acta 1980, 44:1955-1965.
2. Andrews F., Croke B.F.W., Jakeman A.J. An open software environment for hydrological model assessment and development. Environmental Modelling & Software 2011, 26:1171-1185.
3. Argent R.M. An overview of model integration for environmental applications - components, frameworks and semantics. Environmental Modelling & Software 2004, 19:219e234.
4. Bencala K.E. Simulation of solute transport in a mountain pool-and-riffle stream with a kinetic mass transfer model for sorption. Water Resources Research 1983, 19:732-738.
5. Bencala K.E., Walters R.A. Simulation of solute transport in a mountain pool-and-riffle stream-A transient storage model. Water Resources Research 1983, 19:718-724.
6. Berg P., Rysgaard S., Thamdrup B. Dynamic modeling of early diagenesis and nutrient cycling. A case study in an Arctic marine sediment. American Journal of Science 2003, 303:905-955.
7. Boudreau B.P. Diagenetic Models and Their Implementation. Modelling Transport and Reactions in Aquatic Sediments 1997, Springer, Berlin.
8. Burchard H., Bolding K., Villarreal M.R. GOTM, a General Ocean Turbulence Model. Theory, Applications and Test Cases 1999, Tech Rep EUR 18745 EN, European Commission.
9. Chapra S.C. Surface Water-quality Modeling 1997, McGraw-Hill, Boston.
10. Fox J. Aspects of the Social Organization and Trajectory of the R project. The R Journal 2010, 1:5-13.
11. Frederiksen M.S., Glud R.N. Oxygen dynamics in the rhizosphere of Zostera marina: a two-dimensional planar optode study. Limnology and Oceanography 2006, 51:1072-1083.
12. Gattuso J.P., Lavigne H. Technical Note: approaches and software tools to investigate the impact of ocean acidification. Biogeosciences 2009, 6:2121-2133.
13. Glud R.N., Stahl H., Berg P., Wenzhofer F., Oguri K., Kitazato H. In situ microscale variation in distribution and consumption of O-2: a case study from a deep ocean margin sediment (Sagami Bay, Japan). Limnology and Oceanography 2009, 54:1-12.
14. Hofmann A.F., Soetaert K., Middelburg J. Present nitrogen and carbon dynamics in the Scheldt estuary using a novel 1-D model. Biogeosciences 2008, 5:981-1006.
15. Hofmann A.F., Soetaert K., Middelburg J.J., Meysman F.J.R. AquaEnv - an Aquatic acid-base modelling Environment in R. Aquatic Geochemistry 2010, 16:507-546.
16. Hundsdorfer W., Verwer J. Numerical Solution of Time-Dependent Advection-Diffusion-Reaction Equations 2003, Springer Series in Computational Mathematics, Springer-Verlag, Berlin.
17. Lancaster J., Hildrew A.G. Characterising in-stream flow refugia. Canadian Journal of Fisheries and Aquatic Sciences 1993, 50:1663-1675.
18. Lichtner P.C. Continuum model for simultaneous chemical reactions and mass transport in hydrothermal systems. Geochimica et Cosmochimica Acta 1985, 49:779-800.
19. Meysman F.J.R., Middelburg J.J., Herman P.M.J., Heip C.H.R. Reactive transport in surface sediments. II. Media: an object-oriented problem-solving environment for early diagenesis. Computers and Geosciences 2003, 29:301-318.
20. Meysman F.J.R., Middelburg J.J., Herman P.M.J., Heip C.H.R. Reactive transport in surface sediments. I. Model complexity and software quality. Computers and Geosciences 2003, 29:291-300.
21. Meysman F.J.R., Galaktionov O.S., Glud R.N., Middelburg J.J. Oxygen penetration around burrows and roots in aquatic sediments. Journal of Marine Research 2010, 68:309-336.
22. Moll A., Radach G. Review of three-dimensional ecological modelling related to the North Sea shelf system - Part 1: models and their results. Progress in Oceanography 2003, 57(2):175-217.
23. Mooij W.M., Trolle D., Jeppensen E., Arhonditsis G., Belolipetsky P.V., Chitamwebwa B.R., Degermendzhy A.G., DeAngelis D.L., De Senerpont Domis L.N., Downing A.S., Elliott J.A., Fragoso C.R., Gaedke U., Genova S.N., Gulati R.D., Hakanson L., Hamilton D.P., Hipsey M.R., 't Hoen J., Hülsmann S., Los F.J., Makler-Pick V., Petzoldt T., Prokopkin I.G., Rinke K., Schep S.A., Tominaga K., Van Dam A.A., Van Nes E.H., Wells S.A., Janse J.H. Challenges and opportunities for integrating lake ecosystem modelling approaches. Aquatic Ecology 2010, 44(3):633-667.
24. Oschlies A., Garcon V. An eddy-permitting coupled physical-biological model of the North Atlantic - 1. Sensitivity to advection numerics and mixed layer physics. Global Biogeochemical Cycles 1999, 13:135-160.
25. Pallud C., Meile C., Laverman A.M., Abell J., Van Cappellen P. The use of flow-through sediment reactors in biogeochemical kinetics: Methodology and examples of applications. Marine Chemistry 2007, 106:256-271.
26. Palmieri V., Jose de Carvalho R. Qual2e model for the Corumbatai River. Ecological Modelling 2006, 198:269-275.
27. Papajorgji P. A Plug & play approach for developing environmental models. Environmental Modelling & Software 2005, 20:1353-1357.
28. Parkhurst D.L., Kipp K.L., Engesgaard P., Charlton S.R. PHAST-A Program for Simulating Ground-water Flow, Solute Transport, and Multicomponent Geochemical Reactions 2004, U.S. Geological Survey, Techniques and Methods 6-A8, p. 154.
29. Petzoldt T., Rinke K. Simecol: an object-oriented framework for ecological modeling in R. Journal of Statistical Software 2007, 22(9):1-31.
30. Pietrzak J. The use of TVD limiters for forward-in-time upstream-biased advection schemes in ocean modeling. Monthly Weather Review 1998, 126:812-830.
31. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. Numerical Recipes 2007, Cambridge University Press. third ed.
32. Price W.L. A controlled random search procedure for Global Optimisation. The Computer Journal 1977, 20:367-370.
33. R: a Language and Environment for Statistical Computing 2010, R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria. http://www.r-project.org.
34. Rasmussen E.K., Petersen O.S., Thompson J.R., Flower R.J., Ahmed M.H. Hydrodynamic-ecological model analyses of the water quality of Lake Manzala (Nile Delta, Northern Egypt). Hydrobiologia 2009, 622:195-220.
35. Regnier P., O'Kane J.P., Steefel C.I., Vanderborght J.P. Modeling complex multi-component reactive-transport systems: towards a simulation environment based on the concept of a Knowledge Base. Applied Mathematical Modelling 2002, 26:913-927.
36. Reichert P. AQUASIM - a tool for simulation and data-analysis of aquatic systems. Water Science and Technology 1994, 30(2):21-30.
37. Roychoudhury A.N., Viollier E., Van Cappellen P. A flowthrough reactor for studying biogeochemical reactions in undisturbed aquatic sediments. Applied Geochemistry 1998, 13:269-280.
38. Runkel R.L. One-dimensional Transport with Inflow and Storage (OTIS): A Solute Transport Model for Streams and Rivers 1998, US geological Survey, Denver, Colorado, Water-Resources Investigations Report 98-4018.
39. Runkel R.L. Toward a transport-based analysis of nutrient spiraling and uptake in streams. Limnology Oceanography: Methods 2007, 5:50-62.
40. Soetaert K., Herman P.M.J. A Practical Guide to Ecological Modelling. Using R as a Simulation Platform 2009, Springer.
41. Soetaert K., Petzoldt T. Inverse modelling, sensitivity and Monte Carlo analysis in R using package FME. Journal of Statistical Software 2010, 33(3):1-28.
42. Soetaert K., Herman P.M.J., Middelburg J. A model of early diagenetic processes from the shelf to abyssal depths. Geochimica et Cosmochimica Acta 1996, 60:1019-1040.
43. Soetaert K., Petzoldt T., Setzer R.W. Solving differential equations in R. The R Journal 2010, 2/2:5-15.
44. Soetaert K., Petzoldt T., Setzer R.W. Solving differential equations in R: package deSolve. Journal of Statistical Software 2010, 33(9):1-25.
45. Soetaert K., Petzoldt T., Meysman F.J.R. marelac: Tools for Aquatic Sciences. R Package Version 2.1.1 2010.
46. Stave K.A. Using system dynamics to improve public participation in environmental decisions. System Dynamics Review 2002, 18:139-167.
47. Steefel C.I., DePaolo D.J., Lichtner P.C. Reactive transport modeling: an essential tool and a new research approach for the Earth sciences. Earth and Planetary Science Letters 2005, 240:539-558.
48. Stevens M.H.H. A Primer of Ecology with R 2009, Springer.
49. MATLAB (R) Release 2010a 2010, The Mathworks Inc., (MATLAB is a registed property of The Mathworks Inc). http://www.mathworks.com.
50. van der Lee J., De Windt L., Lagneau V., Goblet P. Module oriented modeling of reactive transport with HYTEC. Computers and Geosciences 2003, 29:265-275.
51. Vanderborght J.P., Wollast R., Loijens M., Regnier P. Application of a transport-reaction model to the estimation of biogas fluxes in the Scheldt estuary. Biogeochemistry 2002, 59:207-237.
52. Wanner O., Reichert P. Mathematical modeling of mixed-culture biofilms. Biotechnology and BioEngineering 1996, 49:172-184.
53. 2 dynamics: Effects of fauna activity. Limnology and Oceanography 2004, 49:1471-1481.