NetIndices (version 1.4.4.1)

GenInd: 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.

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.

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

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

# NOT RUN {
# 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"))
)
# }