GenInd {NetIndices}R Documentation

General network indices

Description

Calculates general network indices such as system throughputs, link density, connectance,... of a network

Usage

GenInd(Flow=NULL, Tij=t(Flow), 
  Import=NULL, Export=NULL, tol=0)

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)
tol Flows that are smaller or equal to tol are assumed to be absent

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 that contains:

N Number of compartments, excluding the externals
T.. Total System Throughput
TST Total System Throughflow
Lint Number of Internal links
Ltot Total number of links
LD Link Density
C Connectance (internal)
Tijbar Average Link Weight
TSTbar Average Compartment Throughflow
Cbar Compartmentalization, [0,1], the degree of connectedness of subsystems within a network

Author(s)

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

References

Latham LG. 2006. Network flow analysis algorithms. Ecological Modelling 192: 586-600.
Hirata H, Ulanowicz RE. 1984. Informational theoretical analysis of ecological networks. The American Naturalist 133: 288-302.
Pimm SL, Lawton JH. 1980. Are food webs divided into compartments? Journal of Animal Ecology 49: 879-898.

Examples

# The takapoto atoll network
(GI<- GenInd(Takapoto,Import ="CO2",
             Export=c("CO2","Sedimentation","Grazing")))
as.data.frame(GI)  
as.data.frame(GenInd(diag(5)))

# Conesprings is the example set 1a from Latham 2006.
as.data.frame(GenInd(Tij=Conesprings,Import="Inflows",
       Export=c("Export","Dissipation")))

[Package NetIndices version 1.2 Index]