std.matrix: Read an interaction matrix

In ESM: Ecological Specificity Measures

Description

Returns an interaction matrix normalized to 1

Usage

 
std.matrix(filename,t=FALSE)

Arguments

filename	The file containing the matrix (interaction)
t	Logical to transpose the matrix, FALSE by default

Details

Values of measure can be : hr, the classical host range; ssi, the species specialization index; dfp, the DFP index; shannon, Shannon's entropy; wadfp, the weighted additive DFP.

Value

An interaction matrix

References

For DFP and WADFP, and this package, cite : Poisot, T & Hochberg, M E "..." XXX.

For HS, cite : Schug J, et al. (2005) Promoter features related to tissue specificity as measured by Shannon entropy. Genome biology 6(4):R33

For SSI, cite : Julliard R, Clavel J, Devictor V, Jiguet F, & Couvet D (2006) Spatial segregation of specialists and generalists in bird communities. Ecology Letters 9(11):1237-1244.

Examples

 
# Read an interaction matrix
MAT <- std.matrix('http://www.nceas.ucsb.edu/interactionweb/data/host_parasite/text_matrices/mcgregor_p.txt',t=TRUE)

ESM documentation built on May 2, 2019, 4:51 p.m.