plot.count
From untb v1.7-2
by Robin K S Hankin
Abundance curves
Plot the ranked abundance curve
- Keywords
- math
Usage
"plot"(x, uncertainty = FALSE, expectation = FALSE, theta = NULL, n = 10, ...)
"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 defaultFALSE
meaning to omit this - expectation
- Boolean,
with
TRUE
meaning to plot expected abundances, and defaultFALSE
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
orexpectation
areTRUE
. Default value ofNULL
means to use the maximum likelihood estimate returned by functionoptimal.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.
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))
Community examples
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