NetIndices (version 1.4.4.1)

EnvInd: 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.

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.

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.

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

# NOT RUN {
# 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)
# }