hab: Calculate Shannon diversity of all transitions.
In LandscapeDynamics/ITmetrics: R functions for calculating IT statistics

Description Usage Arguments Details Value Author(s) References Examples

Calculate measures of transition diversity using the Shannon index. Note that the formulas are conditional to omit zero probability values from the calculation.

hab(jd)

jd

A matrix indicating the joint distribution across all interactions of X and Y in the form:

p(x,y)		Y
	0.06	0.06	0.06	...
X	0.14	0.14	0.14	...
	0.12	0.12	0.14	...
	...	...	...	...

Element-wise multiply matrix jd by logarithm base 2 jd and sum.

∑ -p(x_i,y_j) * log2 p(x_i,y_j) = -p(1,1) * log2 p(1,1) + -p(1,2) * log2 p(1,2) + … + -p(i,j) * log2 p(i,j)

Returns a value indicating the Shannon diversity of all transitions.

Bjorn J. Brooks, Lars Y. Pomara, Danny C. Lee

PAPER TITLE.

data(transitions)             # Load example data
b <- brkpts(transitions$phenofr, # Find 10 probabilistically
            10)                  #  equivalent breakpoints
m <- xt(transitions,          # Make transition matrix
        fr.col=2, to.col=3,
        cnt.col=4, brk=b)
jd <- jpmf(m)                 # Joint distribution
hab(jd)                       # Shannon diversity