enaR: An R package for Ecosystem Network Analysis

Methods in Ecology and Evolution

Volumn 5, Issue 11, 2014, Pages 1206-1213

  Borrett, Stuart R ^a,b   Lau, Matthew K ^c,d  

^a UNIVERSITY OF NORTH CAROLINA WILMINGTON   (United States)

^b DUKE UNIVERSITY   (United States)

^c NORTHERN ARIZONA UNIVERSITY   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

Ascendency; Ecopath; Ecosystem; Food web; Input output analysis; Network analysis; Network environ analysis; NETWRK; Open source software; WAND

Indexed keywords

EID: 84913583607     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12282     Document Type: Article

References (74)

1. Allesina, S. & Bondavalli, C. (2003) Steady state of ecosystem flow networks: a comparison between balancing procedures. Ecological Modelling, 165, 221-229.
2. Allesina, S. & Bondavalli, C. (2004) Wand: an ecological network analysis user-friendly tool. Environmental Modelling & Software, 19, 337-340.
3. Allesina, S., Bodini, A. & Bondavalli, C. (2005) Ecological subsystems via graph theory: the role of strongly connected components. Oikos, 110, 164-176.
4. Baird, D. & Ulanowicz, R.E. (1989) The seasonal dynamics of the Chesapeake Bay ecosystem. Ecological Monographs, 59, 329-364.
5. Barabási, A.L. (2012) The network takeover. Nature Physics, 8, 14-16.
6. Bodini, A. & Bondavalli, C. (2002) Towards a sustainable use of water resources: a whole-ecosystem approach using network analysis. International Journal of Environmental Pollution, 18, 463-485.
7. Bodini, A., Bondavalli, C. & Allesina, S. (2012) Cities as ecosystems: growth, development and implications for sustainability. Ecological Modelling, 245, 185-198.
8. Bondavalli, C. & Ulanowicz, R.E. (1999) Unexpected effects of predators upon their prey: the case of the American alligator. Ecosystems, 2, 49-63.
9. Borgatti, S.P. & Foster, P.C. (2003) The network paradigm in organizational research: a review and typology. Journal of Management, 29, 991-1013.
10. Borrett, S.R. (2013) Throughflow centrality is a global indicator of the functional importance of species in ecosystems. Ecological Indicators, 32, 182-196.
11. Borrett, S.R. & Salas, A.K. (2010) Evidence for resource homogenization in 50 trophic ecosystem networks. Ecological Modelling, 221, 1710-1716.
12. Borrett, S.R., Fath, B.D. & Patten, B.C. (2007) Functional integration of ecological networks through pathway proliferation. Journal of Theoretical Biology, 245, 98-111.
13. Borrett, S.R., Whipple, S.J. & Patten, B.C. (2010) Rapid development of indirect effects in ecological networks. Oikos, 119, 1136-1148.
14. Borrett, S.R., Christian, R.R. & Ulanowicz, R.E. (2012) Network ecology. Encyclopedia of Environmetrics, 2nd edn. (eds A.H. El-Shaarawi & W.W. Piegorsch ), pp. 1767-1772. John Wiley & Sons, New York.
15. Borrett, S.R., Moody, J. & Edelmann, A. (2014) The rise of network ecology: maps of the topic diversity and scientific collaboration. Ecological Modelling. doi: 10.1016/j.ecolmodel.2014.02.019.
16. Brandes, U., Kenis, P. & Wagner, D. (2003) Communicating centrality in policy network drawings. IEEE Transactions on Visualization and Computer Graphics, 9, 241-253.
17. Butts, C. (2008a) network: a package for managing relational data in R. Journal of Statistical Software, 24, 1-36.
18. Butts, C. (2008b) Social network analysis with sna. Journal of Statistical Software, 24, 1-51.
19. Chen, S. & Chen, B. (2012) Network environ perspective for urban metabolism and carbon emissions: a case study of Vienna, Austria. Environmental Science & Technology, 46, 4498-4506.
20. Christensen, V. (1995) Ecosystem maturity-towards quantification. Ecological Modelling, 77, 3-32.
21. Christensen, V. & Walters, C.J. (2004) Ecopath with Ecosim: methods, capabilities and limitations. Ecological Modelling, 172, 109-139.
22. Christian, R.R. & Thomas, C.R. (2003) Network analysis of nitrogen inputs and cycling in the Neuse River Estuary, North Carolina, USA. Estuaries, 26, 815-828.
23. Christian, R.R., Fores, E., Comin, F., Viaroli, P., Naldi, M. & Ferrari, I. (1996) Nitrogen cycling networks of coastal ecosystems: influence of trophic status and primary producer form. Ecological Modelling, 87, 111-129.
24. Christian, R.R., Baird, D., Luczkovich, J., Johnson, J.C., Scharler, U.M. & Ulanowicz, R.E. (2005) Role of network analysis in comparative ecosystem ecology of estuaries. Aquatic Food Webs: An Ecosystem Approach (eds A. Belgrano, J. Scharler, U.M. Dunne & R. Ulanowicz ), pp. 25-40. Oxford University Press, New York City, New York, USA.
25. Csardi, G. & Nepusz, T. (2006) The igraph software package for complex network research. InterJournal, Complex Systems, 1695.
26. Dame, R.F. & Patten, B.C. (1981) Analysis of energy flows in an intertidal oyster reef. Marine Ecology Progress Series, 5, 115-124.
27. Dixon, P. (2003) VEGAN, a package of R functions for community ecology. Journal of Vegetation Science, 14, 927-930.
28. Dormann, C.F., Gruber, B. & Fründ, J. (2008) Introducing the bipartite package: analysing ecological networks. R News, 8, 8-11.
29. Fann, S.L. & Borrett, S.R. (2012) Environ centrality reveals the tendency of indirect effects to homogenize the functional importance of species in ecosystems. Journal of Theoretical Biology, 294, 74-86.
30. Fath, B.D. (2004) Network analysis applied to large-scale cyber-ecosystems. Ecological Modelling, 171, 329-337.
31. Fath, B.D. & Borrett, S.R. (2006) A Matlab© function for network environ analysis. Environmental Modelling & Software, 21, 375-405.
32. Fath, B.D. & Patten, B.C. (1999) Review of the foundations of network environ analysis. Ecosystems, 2, 167-179.
33. Finn, J.T. (1976) Measures of ecosystem structure and function derived from analysis of flows. Journal of Theoretical Biology, 56, 363-380.
34. Freeman, L.C. (2004) The Development of Social Network Analysis: A Study in the Sociology of Science. Empirical Press, Vancouver.
35. Handcock, M., Hunter, D., Butts, C., Goodreau, S. & Morris, M. (2008) statnet: software tools for the representation, visualization, analysis and simulation of network data. Journal of Statistical Software, 24, 1548.
36. Hannon, B. (1973) The structure of ecosystems. Journal of Theoretical Biology, 41, 535-546.
37. Hines, D.E., Lisa, J.A., Song, B., Tobias, C.R. & Borrett, S.R. (2012) A network model shows the importance of coupled processes in the microbial N cycle in the Cape Fear River estuary. Estuarine, Coastal and Shelf Science, 106, 45-57.
38. Hudson, L.N., Emerson, R., Jenkins, G.B., Layer, K., Ledger, M.E., Pichler, D.E. et al. (2013) Cheddar: analysis and visualisation of ecological communities in R. Methods in Ecology and Evolution, 4, 99-104.
39. Ings, T.C., Montoya, J.M., Bascompte, J., Blüthgen, N., Brown, L., Dormann, C.F. et al. (2009) Review: ecological networks-beyond food webs. Journal of Animal Ecology, 78, 253-269.
40. Jørgensen, S.E., Fath, B.D., Bastianoni, S., Marques, J.C., Müller, F., Nielsen, S., Patten, B.C., Tiezzi, E. & Ulanowicz, R.E. (2007) A New Ecology: Systems Perspective. Elsevier, Amsterdam.
41. Kazanci, C. (2007) EcoNet: a new software for ecological modeling, simulation and network analysis. Ecological Modelling, 208, 3-8.
42. Kones, J.K., Soetaert, K., van Oevelen, D. & Owino, J.O. (2009) Are network indices robust indicators of food web functioning? A Monte Carlo approach. Ecological Modelling, 220, 370-382.
43. Krause, A. (2004) The role of compartments in food-web structure and changes following biological invasions in southeast Lake Michigan. Ph.d., Michigan State University.
44. Lau, M.K., Borrett, S.R. & Hines, D.E. (2013) enaR: tools for ecological network analysis in R. R package version 2.6.
45. Lima, M. (2011) Visual Complexity: Mapping Patterns of Information. Princeton Architectural Press, New York.
46. Matis, J.H. & Patten, B.C. (1981) Environ analysis of linear compartmental systems: the static, time invariant case. Bulletin of the International Statistical Institute, 48, 527-565.
47. Metcalf, C.J.E., McMahon, S.M., Salguero-Gómez, R. & Jongejans, E. (2012) IPMpack: an R package for integral projection models. Methods in Ecology and Evolution, 4, 195-200.
48. Monaco, M.E. & Ulanowicz, R.E. (1997) Comparative ecosystem trophic structure of three us mid-Atlantic estuaries. Marine Ecology Progress Series, 161, 239-254.
49. Moody, J., McFarland, D. & Bender-deMoll, S. (2005) Dynamic network visualization. The American Journal of Society, 110, 1206-1241.
50. Newman, M. (2003) The structure and function of complex networks. SIAM Review, 45, 167-256.
51. Niquil, N., Chaumillon, E., Johnson, G., Bertin, X., Grami, B., David, V. et al. (2012) The effect of physical drivers on ecosystem indices derived from ecological network analysis: comparison across estuarine ecosystems. Estuarine, Coastal and Shelf Science, 108, 132-143.
52. van Oevelen, D., Soetaert, K., García, R., de Stigter, H.C., Cunha, M.R., Pusceddu, A. & Danovaro, R. (2011) Canyon conditions impact carbon flows in food webs of three sections of the Nazaré canyon. Deep-Sea Research Part II, 58, 2461-2476.
53. Patten, B.C. (1978) Systems approach to the concept of environment. The Ohio Journal of Science, 78, 206-222.
54. Patten, B.C. (1982) Environs: relativistic elementary particles for ecology. The American Naturalist, 119, 179-219.
55. Patten, B.C. (1991) Network ecology: indirect determination of the life-environment relationship in ecosystems. Theoretical Studies of Ecosystems: The Network Perspective (eds M. Higashi & T. Burns ), pp. 288-351. Cambridge University Press, New York.
56. Patten, B.C., Bosserman, R.W., Finn, J.T. & Cale, W.G. (1976) Propagation of Cause in Ecosystems. Systems Analysis and Simulation in Ecology, Vol. IV (ed. B.C. Patten ), pp. 457-579. Academic Press, New York.
57. Proulx, S.R., Promislow, D.E.L. & Phillips, P.C. (2005) Network thinking in ecology and evolution. Trends in Ecology & Evolution, 20, 345-353.
58. Revell, L.J. (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217-223.
59. Salas, A.K. & Borrett, S.R. (2011) Evidence for dominance of indirect effects in 50 trophic ecosystem networks. Ecological Modelling, 222, 1192-1204.
60. Scharler, U. & Fath, B. (2009) Comparing network analysis methodologies for consumer-resource relations at species and ecosystems scales. Ecological Modelling, 220, 3210-3218.
61. Schramski, J.R., Kazanci, C. & Tollner, E.W. (2011) Network environ theory, simulation and EcoNet© 2.0. Environmental Modelling & Software, 26, 419-428.
62. Soetaert, K., Van den Meersche, K. & van Oevelen, D. (2009) limSolve: Solving Linear Inverse Models. R package version 1.5.1. Retrieved from http://cran.r-project.org/web/packages/limSolve/index.html.
63. Ulanowicz, R.E. (1983) Identifying the structure of cycling in ecosystems. Mathematical Biosciences, 65, 219-237.
64. Ulanowicz, R.E. (1986) Growth and Development: Ecosystems Phenomenology. Springer-Verlag, New York.
65. Ulanowicz, R.E. (1997) Ecology, the Ascendent Perspective. Columbia University Press, New York.
66. Ulanowicz, R.E. (2009) A third window, Natural life beyond Newton and Darwin. Templeton Foundation Press, West Conshohocken, Pennsylvania, USA.
67. Ulanowicz, R.E. & Kay, J. (1991) A package for the analysis of ecosystem flow networks. Environmental Software, 6, 131-142.
68. Ulanowicz, R.E. & Kemp, W.M. (1979) Toward canonical trophic aggregations. The American Naturalist, 114, 871-883.
69. Ulanowicz, R.E. & Puccia, C.J. (1990) Mixed trophic impacts in ecosystems. Coenoses, 5, 7-16.
70. Ulanowicz, R.E. & Scharler, U.M. (2008) Least-inference methods for constructing networks of trophic flows. Ecological Modelling, 210, 278-286.
71. Ulanowicz, R.E., Holt, R.D. & Barfield, M. (2014) Limits on ecosystem trophic complexity: insights from ecological network analysis. Ecology Letters, 17, 127-136.
72. Wasserman, S. & Faust, K. (1994) Social Network Analysis: Methods and Applications. Cambridge University Press, Cambridge New York.
73. Whipple, S.J., Borrett, S.R., Patten, B.C., Gattie, D.K., Schramski, J.R. & Bata, S.A. (2007) Indirect effects and distributed control in ecosystems: Comparative network environ analysis of a seven-compartment model of nitrogen flow in the Neuse River Estuary, USA-time series analysis. Ecological Modelling, 206, 1-17.
74. Zhang, Y., Yang, Z.F., Fath, B.D. & Li, S.S. (2010) Ecological network analysis of an urban energy metabolic system: model development, and a case study of four Chinese cities. Ecological Modelling, 221, 1865-1879.