PathInd {NetIndices}R Documentation

Pathway analysis

Description

Calculates the direct and indirect pathways in a network, i.e. the total system cycled throughflow, Finn's cycling index and average pathlength,...

Base on Finn(1980) (and not Finn (1976))

Usage

PathInd(Flow=NULL, Tij=t(Flow), Import=NULL, Export=NULL)

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)

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:

TSTC Total system cycled throughflow
TSTS Non-cycled throughflow
FCI Finn's cycling index (1980)
APL Average pathlength, also known as Network Aggradation (Sum of APLc and APLs in Latham 2006)

Author(s)

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

References

Finn JT. 1980. Flow analysis of models of the Hubbard Brook ecosystem. Ecology 61: 562-571.
Patten BC, Higashi M. 1984. Modified cycling index for ecological applications. Ecological Modelling 25: 69-83.
Patten BC, Bosserman RW, Finn JT, Cale WG. 1976. Propagation of cause in ecosystems. Patten BC, editor. Systems Analysis and Simulation in Ecology, vol. 4. Academic Press, New York. p457-579.

Examples

# The takapoto atoll network
PathInd(Takapoto,Import ="CO2",
        Export=c("CO2","Sedimentation","Grazing"))
        # Conesprings is the example set 1a from Latham 2006.
as.data.frame(PathInd(Tij=Conesprings,Import="Inflows",
    Export=c("Export","Dissipation")))

[Package NetIndices version 1.2 Index]