plot.count

0th

Percentile

Abundance curves

Plot the ranked abundance curve

Keywords
math
Usage
# S3 method for count
plot(x, uncertainty = FALSE, expectation = FALSE, theta = NULL, n = 10, ...)
# S3 method for 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

Fundamenal 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.

Aliases
  • plot.count
  • plot.census
Examples
# NOT RUN {
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))

# }
Documentation reproduced from package untb, version 1.7-4, License: GPL

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