future.events: realize future events in quantitative population ethology...

In byandell/ewing: Ewing's Quantitative Population Ethology

realize future events in quantitative population ethology simulation

Description

Steps through future events for community with one or more species. Keeps track of counts by age classes and substrates.

Usage

future.events(
  community,
  ...,
  nstep = 4000,
  species = get.species(community),
  refresh = nstep/20,
  cex = 0.5,
  substrate.plot = TRUE,
  extinct = TRUE,
  timeit = TRUE,
  debugit = FALSE,
  messages = TRUE
)

Arguments

community	object with population data by species
...	additional arguments passed to 'initCount'
nstep	number of steps to perform
species	list of species to simulate
refresh	plot refresh rate
cex	character expansion
substrate.plot	show plots of substrate use
extinct	stop when first specied becomes extinct
timeit	record timing by event
debugit	detailed debug for advanced users
plotit	new plot at each refresh
ggplots	use ggplot if 'TRUE' and 'plotit' is 'TRUE'

Details

This is the main routine for Ewing's Quantitative Population Ethology. It steps through future events for individuals starting with the next minimum future event time.

All individuals have a 'current' stage and are organized into an event queue, which is a triply-linked leftist tree, based on the scheduled time for their next 'future' event. Each species has its own leftist tree, with the tops of those trees identifying the individuals with the closest (in time) next 'future' event. Internal routine 'put.species', in conjuction with 'leftist.update', 'leftist.remove' or 'leftist.birth', modify the leftist trees when there is an individual event update, death (remove) or birth(s), respectfully.

An individual in a species will progress from 'current' to 'future' stage when its event time is at the top of the event queue. The 'fid' points to the row in this table corresponding to the 'future' stage, which would then become the 'current' stage. The code uses numeric 'fid' because it ends up in a vector of other numeric values.

Note that sometimes there are multiple rows with the same 'current' value, which are competing risks. For instance 'future.host' has competing risks from the 'current' stage 'second.3' of becoming 'female' or 'male', while 'future.parasite' has competing risk from the current stage 'adult' to 'feed' or 'ovip'osit, with return lines from 'feed' and 'ovip' to 'adult'. That is, an adult parasite might feed or oviposit, which have different health and population consequences: feeding prolongs life while ovipositing produces new offspring and depletes life.

The 'time' entry is used to schedule the time of the 'future' event. That is, when and individual appears at the top of the event queue.

A plot is created periodically unless plotit=FALSE. If argument 'file' is set to a file name, an external file is written with simulation counts for re-plotting.

Value

List containing the following items:

pop	updated community of species
org	organism information (from init.simulation
temp	temperature and time curve structure
count	simulation counts
cpu	CPU use summary

Author(s)

Brian S. Yandell

References

See www.stat.wisc.edu/~yandell/ewing.

See Also

init.simulation, event.future

Examples

## Not run: 
  init.simulation(mystuff)
## step through 4000 future events
step.mystuff <- future.events(mystuff,4000)
## replot the results
plot.ewing( step.mystuff )
## reprint timing of most recent future.events run
print.timing()
## or of the one you want
print.timing( step.mystuff$timing )
## show temperature information used in simulation
showTemp( step.mystuff$temperature )
## continue on with more future events
step.further <- future.events( step.mystuff,4000 )

## End(Not run)

byandell/ewing documentation built on Jan. 3, 2024, 7:27 p.m.