display.untb {untb} | R Documentation |
Animation of neutral ecological drift
Description
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()
|
Author(s)
Robin K. S. Hankin
References
S. P. Hubbell 2001. “The Unified Neutral Theory of Biodiversity”.
Princeton University Press.
Examples
data(butterflies)
display.untb(start=butterflies,prob=0, gens=1e2)
[Package
untb version 1.7-7-1
Index]