Package NetIndices, network indices and food web descriptors in R

R package NetIndices is designed to estimate the most common network indices. It has been created to accompany the following article [14]: Kones, J.K., Soetaert, K., van Oevelen, D. and J.Owino (2009). Are network indices robust indicators of food web functioning? a Monte Carlo approach. Ecological Modelling, 220: 370-382. http://dx.doi.org/10.1016/j.ecolmodel.2008.10.012 Please use this reference to cite package NetIndices in publications. In this vignette we first deal with conventions adopted, after which network functions are briefly discussed. The formulations for all network indices are represented in several tables. This table is more complete than the one in the article.

[1]  Stefano Allesina,et al.  Cycling in ecological networks: Finn's index revisited , 2004, Comput. Biol. Chem..

[2]  Robert E. ULANOWlCZ,et al.  Symmetrical overhead in flow networks , 1990 .

[3]  Bernard C. Patten,et al.  PATH ANALYSIS OF A RESERVOIR ECOSYSTEM MODEL , 1982 .

[4]  R. Ulanowicz An hypothesis on the development of natural communities. , 1980, Journal of theoretical biology.

[5]  R. Mulholland,et al.  Ecological stability: an information theory viewpoint. , 1976, Journal of theoretical biology.

[6]  Raymond L. Lindeman The trophic-dynamic aspect of ecology , 1942 .

[7]  Robert W. Bosserman,et al.  17 – Propagation of Cause in Ecosystems , 1976 .

[8]  Karline Soetaert,et al.  Are network indices robust indicators of food web functioning? A Monte Carlo approach , 2009 .

[9]  Bernard C. Patten,et al.  Dominance of Indirect Causality in Ecosystems , 1989, The American Naturalist.

[10]  E. Scully,et al.  Quantifying constraint to assess development in ecological networks , 2002 .

[11]  Bernard C. Patten,et al.  System Theory of the Ecological Niche , 1981, The American Naturalist.

[12]  John H. Lawton,et al.  ARE FOOD WEBS DIVIDED INTO COMPARTMENTS , 1980 .

[13]  Robert E. Ulanowicz,et al.  Quantitative methods for ecological network analysi , 2004, Comput. Biol. Chem..

[14]  Robert E. Ulanowicz,et al.  Growth and Development , 1987, Springer New York.

[15]  S. Jørgensen,et al.  Movement rules for individual-based models of stream fish , 1999 .

[16]  Robert E. Ulanowicz,et al.  Quantifying the complexity of flow networks: How many roles are there? , 2003, Complex..

[17]  Luke G. Latham Network flow analysis algorithms , 2006 .

[18]  B. C. Patten,et al.  Review of the Foundations of Network Environ Analysis , 1999, Ecosystems.

[19]  J. Finn,et al.  Measures of ecosystem structure and function derived from analysis of flows. , 1976, Journal of theoretical biology.

[20]  MARK R. GARDNER,et al.  Connectance of Large Dynamic (Cybernetic) Systems: Critical Values for Stability , 1970, Nature.

[21]  Villy Christensen,et al.  ECOPATH II − a software for balancing steady-state ecosystem models and calculating network characteristics , 1992 .

[22]  R. Gallager Information Theory and Reliable Communication , 1968 .

[23]  John G. Field,et al.  The Need to Analyze Ecological Networks , 1989 .

[24]  Hironori Hirata,et al.  Information theoretical analysis of ecological networks , 1984 .

[25]  Brian D. Fath,et al.  Quantifying resource homogenization using network flow analysis , 1999 .

[26]  Brian D. Fath,et al.  Network synergism: Emergence of positive relations in ecological systems , 1998 .

[27]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[28]  Bernard C. Patten,et al.  Modified cycling index for ecological applications , 1984 .

[29]  Brian D. Fath,et al.  Network analysis applied to large-scale cyber-ecosystems , 2004 .

[30]  Bernard C. Patten,et al.  Energy, emergy and environs , 1992 .

[31]  John T. Finn,et al.  Flow analysis of models of the Hubbard Brook Ecosystem. , 1980 .