getspe: Specificity
In ESM: Ecological Specificity Measures

Description Usage Arguments Details Value References Examples

View source: R/functions.r

Returns a vector containing the specificity of each organism

1 2	getspe(mat,measure=pdi,normal='whole',...)

`mat`	A matrix giving the performance of each organism on each resource, with organisms as rows
`measure`	The index of specificity to use. See details, defaults to `pdi`.
`normal`	The method to normalize the matrix. Defaults to `whole`, can be set to `species`.
`...`	Additional arguments to be passed to `measure`

Values of measure can be : rr, the classical resource range; ssi, the species specialization index; pdi (default), the Paired Differences Index; hs, Shannon's entropy.

normal is the way to normalize the performance value within the matrix. Defaults to whole, which means that the matrix is divided by its maximal value. Can be set to species, so that the maximal value of each species is set to 1. The performances of the measures were not evaluated with this method of normalization, and it will result in a overestimation of the specificity.

A vector with the specificity of each organism. Uses names if the matrix has such property.

For PDI, and this package, cite : Poisot, T, Canard E, Mouquet N & 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.

 
# Read an interaction matrix
MAT <- 'http://www.nceas.ucsb.edu/interactionweb/data/host_parasite/text_matrices/mcgregor_p.txt'
mat <- t(read.table(MAT))
# Returns host range
getspe(mat)