EnvInd: Environ network indices

In NetIndices: Estimating Network Indices, Including Trophic Structure of Foodwebs in R

Environ network indices

Description

Calculates the indices of homogenization, synergism index, dominance of indirect effects,... of a network.

Usage

EnvInd(Flow = NULL, Tij = t(Flow), Import = NULL, 
       Export = NULL, full = FALSE)

Arguments

Flow	network matrix with Flow[i,j] the flow from i (row) to j (column); component positions in rows and columns must be the same; if present, rownames or columnnames denote the compartment names.
Tij	network matrix where connectance is from column j to row i; component positions in rows and columns must be the same ; if present, rownames or columnnames denote the compartment names.
Import	vector with either the *indices* or the *names* of external compartmens from where flow enters the network; the indices point to the column positions in Tij ( and the row positions in Flow).
Export	vector with either the *indices* or the *names* of external compartmens to where flow leaves the network; the indices point to the row positions in Tij (and the column positions in Flow).
full	if TRUE, also returns matrices.

Details

The mathematical formulation of these indices can be found in the package vignette - vignette("NetIndices").

The PDF can be found in the subdirectory ‘doc’ of the NetIndices package.

Value

A list with the following items:

NAG	Network aggradation = average path length.
HP	Homogenization index.
BC	Synergism.
ID	Dominance of Indirect effects.
MN	Mean of non-dimensional flow-matrix (N).
MG	Mean of direct flow-matrix (G).
CVN	Coefficient of variation of non-dimensional flow-matrix (N).
CVG	Coefficient of variation of direct flow-matrix (G).
U	Only if Full == TRUE: The Utility non-dimensional matrix.
N1	Only if Full == TRUE: The Integral non-dimensional Flow Matrix.
G	Only if Full == TRUE: The Normalized direct flow (or transitive closure) matrix.

Author(s)

Karline Soetaert <[e-mail]>, Julius Kipyegon Kones<[e-mail]>

References

Patten BC, Barber MC, Richardson TH. 1982. Path analysis of a reservoir ecosystem model.

Fath BD, Patten BC. 1999. Review of the foundations of network environ analysis. Ecosystems 2: 167-179.

Fath BD, Patten BC. 1999. Quantifying resource homogenization using network flow analysis. Ecological Modelling 123: 193-205.

Patten BC, Higashi M. 1984. Modified cycling index for ecological applications. Ecological Modelling 25: 69-83.

Higashi M, Patten BC. 1989. Dominance of indirect causality in ecosystems. The American Naturalist 133: 288-302.

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.

Examples

# The takapoto atoll network
EnvInd(Takapoto, Import = "CO2",
         Export = c("CO2", "Sedimentation", "Grazing"))

as.data.frame(
  EnvInd(Tij = Conesprings, Import = "Inflows",
         Export = c("Export", "Dissipation"))
)

EnvInd(Tij = Conesprings, Import = "Inflows",
    Export = c("Export", "Dissipation"), full = TRUE)

NetIndices documentation built on May 11, 2022, 5:09 p.m.