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. International journal of systems science 15 (3): 261-270

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 1.3 Index]