Returns an estimate of the fundamental biodiversity number

Returns a maximum likelihood estimate for the fundamental biodiversity number \(\theta\) (function optimal.theta()) or the probability of mutation (function optimal.prob()) and optionally return information about the likely error

Usage

optimal.prob(x,  interval=NULL, N=NULL, like=NULL, ...)
optimal.theta(x, interval=NULL, N=NULL, like=NULL, ...)

Arguments

x: Ecosystem vector or species count table
interval: Bracketing interval for probability of mutation to be passed to the optimization routine (here optimize()). Default of NULL means to use a wide interval. Note that this argument is interpreted as an interval of \(\theta\) for both optimal.prob() and optimal.theta().
N: Integer; the number of parametric resampled estimates to give. Default of NULL means to return just the maximum likelihood estimate
like: Units of likelihood to calculate credible interval. Edwards recommends using 2
...: Further arguments passed to optimize()

Note

The fundamental biodiversity parameter \(\theta\) is \(2\nu J\), where \(\nu\) is the probability of mutation (ie, as estimated by optimal.prob()), and \(J\) is the size of the ecosystem.

For the general case of dispersal limitation, see functions etienne() and optimal.params().

Author

Robin K. S. Hankin

Examples

data(butterflies)
optimal.prob(butterflies)
#> [1] 0.01328401
optimal.theta(butterflies)
#> [1] 9.989579