enaFlow: Analyses of Ecological Networks

In enaR: Tools for Ecological Network Analysis

Description

Performs the primary throughflow analysis developed for input-output systems. It returns a vector of throughflows, the input and output oriented matrices for "direct flow intensities" and "integral flow intensities", and a set of flow based network statistics.

Usage

enaFlow(x, zero.na = TRUE, balance.override = FALSE)

Arguments

x	a network object. This includes all weighted flows into and out of each node.
zero.na	LOGICAL: should NA values be converted to zeros.
balance.override	Flow analysis assumes the network model is at steady-state (inputs = outputs). Setting balance.override = TRUE allows the function to be run on unbalanced models.

Value

T	vector of node throughflows total amount of energy-matter flowing into or out of each node
G	matrix of the output oriented direct flow intensities
GP	matrix of the input oriented direct flow intensities
N	matrix of the ouput oriented integral (boundary+direct+indirect) flow intensities
NP	matrix of the input oriented integral flow intensities
TCC	matrix of total contribution coefficients (Szyrmer & Ulanowicz 1987). The elements of TCC indicate the fraction of total output of i which reaches j
TDC	matrix of total dependency coefficients (Szyrmer & Ulanowicz 1987). The elements of TDC indicate the fraction j's total consuption which passes through i
ns	vector of flow based network statistics. These include "Boundary" the total input into or output from the system, "TST" the total system throughflow, "TSTp" total system throughPUT,"APL" is the network aggradation TST/Boundary which is also called average path length, "FCI" (Finn Cycling Index) is a metric of the amount of cycling in a system, "BFI" is the boundary flow intensity Boundary/TST, "DFI" is the direct flow intensity Direct/TST, "IFI" is the indirect flow intensity Indirect/TST, "ID.F" is the realized indirect to direct flow intensity, "ID.F.I" is the input idealized indirect flow intensity, "id.F.O"is the output idealized indirect flow intensity, "HMG.I" is the input network homogenization, "HMG.O" is the output network homogenization, "AMP.I" is the strong measure of input network amplifiation, "AMP.O" is the strong measure of output network amplification, "mode0.F" is the boundary flow - flow that reaches a compartment from across the system boundary, "mode1.F" is internal first passage flow, "mode2.F" is cycled flow, "mode3.F" is the dissipative eqivalent to mode2, and "mode4.F" is the dissipative equivalent ot mode0.

Author(s)

Matthew K. Lau Stuart R. Borrett

References

Borrett, S. R., Freeze, M. A., 2011. Reconnecting environs to their environment. Ecol. Model. 222, 2393-2403.

Fath, B. D., Borrett, S. R. 2006. A Matlab function for Network Environ Analysis. Environ. Model. Softw. 21, 375-405.

Fath, B. D., Patten, B. C., 1999. Review of the foundations of network environ analysis. Ecosystems 2, 167-179.

Finn, J. T., 1976. Measures of ecosystem structure and function derived from analysis of flows. J. Theor. Biol. 56, 363-380.

Patten, B.C. Higashi, M., Burns, T. P. 1990. Trophic dynamics in ecosystem networks: significance of cycles and storage. Ecol. Model. 51, 1-28.

Schramski, J. R., Kazanci, C., Tollner, E. W., 2011. Network environ theory, simulation and EcoNet 2.0. Environ. Model. Softw. 26, 419-428.

Szyrmer, J., Ulanowicz, R. E., 1987. "Total Flows in Ecosystems". Ecol. Mod. 35:123-136.

Ulanowicz, R.E., 2004. Quantitative methods for ecological network analysis. Comput. Biol. Chem. 28, 321-33

Ulanowicz, R.E., Holt, R.D., Barfield, M., 2014. Limits on ecosystem trophic complexity: insights from ecological network analysis. Ecology Letters 17:127-136.

See Also

read.scor,read.wand,enaStorage,enaUtility

Examples

data(troModels)
F = enaFlow(troModels[[6]])  # completes the full analysis
F$ns  # returns just the network statisics

enaR documentation built on May 1, 2019, 10:54 p.m.