Animation of neutral ecological drift

Displays an ongoing simulation of neutral ecological drift using nice colours and a simple animation technique. Does not work as intended in RStudio: use base R

Usage

display.untb(start, gens=100, prob.of.mutate = 0, cex=3, individually
= TRUE, ask = FALSE, flash = FALSE, delay = 0, cols=NULL, ...)

Arguments

start

Starting ecosystem; coerced to class census. Usually, pass an object of class count; see examples. To start with a monoculture of size 10, use start=rep(1,10) and to start with a system of maximal diversity (ie all singletons), use start=1:10

gens

Number of generations to simulate

prob.of.mutate

Probability of mutation. The default of zero corresponds to \(\theta=0\) and this means that any ecosystem will eventually become a monoculture (it is particularly instructive to watch this happen, especially with a starting ecosystem of maximal diversity\(\mbox{---}\)but be warned, this can take a long time, especially for ecosystems with a large number of individuals). Nonzero values mean that a nontrivial dominance-diversity curve will eventuate, although this too can take a long time to happen. Try a nonzero value of prob.of.mutate with monoculture start (use individually=FALSE for such experiments)

cex

The size of the dots used for plotting, defaulting to 3

individually

Boolean, with default TRUE meaning that a timestep means the death of a single individual and the simultaneous birth of a new individual; and FALSE meaning that a timestep refers to every individual in the system

ask

Boolean, with default FALSE meaning to display the generations autonomously, and TRUE meaning to wait for the user to hit the “return” before proceeding

flash

Boolean, with TRUE meaning to indicate the site of a death/birth with a flashing ring; and default FALSE meaning to omit the flashing ring. Use TRUE for pedagogic purposes, possibly with ask set to TRUE, or a nonzero delay. This option only kicks in if individually is TRUE

delay

Time delay between generations in seconds; meaningful whatever the value of flash and individually

cols

A vector of colours with default NULL meaning to choose them randomly. Useful for printing stills from a movie

...

Further arguments passed to plot() and points()

References

S. P. Hubbell 2001. “The Unified Neutral Theory of Biodiversity”. Princeton University Press.

Author

Robin K. S. Hankin

Examples

data(butterflies)
display.untb(start=butterflies,prob=0, gens=1e2)