enaCycle: Full Cycle Analysis of Ecological Networks

In SEELab/enaR: Tools for Ecological Network Analysis

Full Cycle Analysis of Ecological Networks

Description

It performs the full cycle analysis on the network based on the algorithm described in Ulanowicz (1983) and implemented in NETWRK 4.2b. It returns data.frames with details of the simple cycles and nexus, vectors of Cycle distributions and Normalized distribution and matrices of Residual Flows and Aggregated Cycles.

Usage

enaCycle(x)

Arguments

x	a network object. This includes all weighted flows into and out of each node.

Details

The "NODES" in "Table.cycle" are arranged such that the weak arc for the nexus is the arc between the first two nodes of the cycle. This function uses the backtracking procedure for the identification of simple cycles, which are cycles that cross a node only once except the starting node. The backtracking process is a depth-first search algorithm.

In the data.frame "Table.cycle", if the number of cycles in a nexus is more than 50, then a blank line is displayed after 50 cycles of the nexus, followed by the cycles of the next nexus.

The results of the analysis of Feeding Cycles can be obtained as a byproduct of the enaTroAgg function that analyzes the trophic dynamics of a network.

At every multiple of 5000 cycles in a nexus, the program prints an indication for the user to know that it is still running.

Value

Table.cycle	data.frame that presents the details of the simple cycles in the network. It contains "CYCLE" the cycle number, "NEXUS" the nexus number corresponding to the cycle, "NODES" the nodes constituting the cycle
Table.nexus	data.frame that presents the different nexuses characterized by their corresponding weak arcs. It contains "NEXUS" the nexus number, "CYCLES" the number of simple cycles present in that Nexus, "W.arc.From" the starting node of the corresponding weak arc, "W.arc.To" the ending node of the corresponding weak arc and "W.arc.Flow" the flow through that weak arc
CycleDist	vector of the Cycle Distribution that gives the flow cycling in loops of different sizes
NormDist	vector of the Normalized Distribution i.e. the Cycle Distribution normalized by the Total System Throughput of the system
ResidualFlows	matrix of the straight-through (acyclic) flows in the network
AggregatedCycles	matrix of the Aggregated Biogeochemical Cycles in the network
ns	vector of the full cycle analysis based network statistics. These include "NCYCS" the number of simple cycles identified in the network, "NNEX" the number of the disjoint cycles or number of Nexuses detected in the network and "CI" the cycling index of the network.

Author(s)

Pawandeep Singh

References

D.B. 1975. Finding all the elementary circuits of a directed graph. SIAM J. Comput. 4:77–84

Ulanowicz, R.E. 1983. Identifying the structure of cycling in ecosystems. Methematical Biosciences 65:219–237

Ulanowicz, R.E. and Kay, J.J. 1991. A package for the analysis of ecosystem flow networks. Environmental Software 6:131 – 142.

See Also

enaTroAgg

Examples

data(troModels)
cyc6 <- enaCycle(troModels[[6]])
attributes(cyc6)

SEELab/enaR documentation built on April 29, 2023, 8:40 a.m.