get_diversity_from_transition: Compute the diversity of a transition matrix, that is the...
In Lamarche-Perrin/triversity: Diversity Measures on Multipartite Graphs

Description Usage Arguments Value Examples

get_diversity_from_transition either computes the individual diversity values associated to the rows of the input transition matrix, or the geometric means of these values, optionally weighting them according to the input mean_distribution. This hence allows to compute conditional diversity values associated to a transition matrix.

1 2	get_diversity_from_transition(transition, type = "individual", mean_distribution = NULL, order = NULL, measure = NULL)

`transition`	A matrix of floats in [`0`,`1`], with all lines summing to `1`, giving the transition matrix from which the individual diversity values are computed.
`type`	Either `'individual'`, to separately compute all individual diversities, or `'mean'`, to compute their geometric mean.
`mean_distribution`	(optional, only when `type == 'mean'`) A vector of floats in [`0`,`1`] and summing to `1` giving the probability distribution that is used to weight the diversity values when computing their geometric means. It should hence contain as many values as there are rows in the input `transition`. If not specified, this distribution is assumed uniform.
`order`	A vector of positive floats (possibly including `Inf`) giving the orders of the diversity measures to be computed. If neither `order` nor `measure` is specified, a predefined list of 8 diversity measures is computed.
`measure`	A vector of strings giving the names of the diversity measures to compute. Possible values are `richness`, `entropy`, `herfindahl`, and `bergerparker`.

A matrix (or a vector) of positive floats giving the individual diversity values (or their geometric mean) of the row of the input transition matrix.

transition <- matrix (c (1/3, 1/3, 1/3, 0.9, 0.1, 0), nrow=2, ncol=3, byrow=TRUE)

get_diversity_from_transition (transition, type='individual', order=c(0,Inf), measure='entropy')
get_diversity_from_transition (transition, type='mean')
get_diversity_from_transition (transition, type='mean', mean_distribution=c(1/4,3/4))