GenInd {NetIndices} | R Documentation |
Calculates general network indices such as system throughputs, link density, connectance,... of a network
GenInd(Flow=NULL, Tij=t(Flow), Import=NULL, Export=NULL, tol=0)
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 |
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 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 |
Karline Soetaert <k.soetaert@nioo.knaw.nl>, Julius Kipyegon Kones<jkones@uonbi.ac.ke>
Latham LG. 2006. Network flow analysis algorithms. Ecological Modelling 192: 586-600.
Hirata H, Ulanowicz RE. 1984. Informational theoretical analysis of ecological networks. The American Naturalist 133: 288-302.
Pimm SL, Lawton JH. 1980. Are food webs divided into compartments? Journal of Animal Ecology 49: 879-898.
# 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")))