GenInd {NetIndices}

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

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.

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
(GI<- GenInd(Takapoto, Import = "CO2",
             Export = c("CO2", "Sedimentation", "Grazing")))
as.data.frame(GI)  

# a simple system
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"))
)