Abundance curves — plot.count • untb

Plot the ranked abundance curve

Usage

# S3 method for class 'count'
plot(x, uncertainty = FALSE, expectation = FALSE, theta = NULL, n = 10, ...)
# S3 method for class 'census'
plot(x, uncertainty = FALSE, expectation = FALSE, theta = NULL, n = 10, ...)

Arguments

x: Ecosystem object, coerced to class count
uncertainty: Boolean, with TRUE meaning to show bootstrapped estimates for the species diversity curve, and default FALSE meaning to omit this
expectation: Boolean, with TRUE meaning to plot expected abundances, and default FALSE meaning not to plot them. Warning this option takes a loooong time to run, even for moderate values of \(J\)
theta: Fundamental biodiversity number used if argument uncertainty or expectation are TRUE. Default value of NULL means to use the maximum likelihood estimate returned by function optimal.theta()
n: Number of bootstrapped estimates to plot
...: Extra parameters passed to untb()

Details

Plots a ranked abundance curve, optionally with parametrically resampled datasets showing the uncertainties

Note

If using expectation, it's usually necessary to set ylim and possibly xlim manually.

Author

Robin K. S. Hankin

Examples

data(copepod)
plot(copepod)


data(butterflies)
plot(butterflies,uncertainty=TRUE)


x <- count(c(pigs=1, dogs=1, cats=2, frogs=3, bats=5, slugs=8))
plot(x,expectation=TRUE,ylim=c(0.5,10))