PathInd {NetIndices} | R Documentation |
Calculates the direct and indirect pathways in a network, i.e. the total system cycled throughflow, Finn's cycling index and average pathlength,...
Based on Finn(1980) (and not Finn (1976))
PathInd(Flow=NULL, Tij=t(Flow), Import=NULL, Export=NULL)
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).
|
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.
A list with the following items:
TSTC |
total system cycled throughflow. |
TSTS |
non-cycled throughflow. |
FCI |
Finn's cycling index (1980). |
FCIb |
revised Finn's cycling index, sensu Allesina and Ulanowicz, 2004. |
APL |
average pathlength, also known as Network Aggradation (Sum of APLc and APLs in Latham 2006). |
Karline Soetaert <k.soetaert@nioo.knaw.nl>, Julius Kipyegon Kones<jkones@uonbi.ac.ke>
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.
Allesina and Ulanowicz, 2004. Cycling in ecological netowrks: Finn's index revisited. Computational Biology and Chemistry 28, 227-233.
# 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")))