EnvInd {NetIndices}R Documentation

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) matrix

Author(s)

Karline Soetaert <k.soetaert@nioo.knaw.nl>, Julius Kipyegon Kones<jkones@uonbi.ac.ke>

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.

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)

[Package NetIndices version 1.2 Index]