generation: Simulate a Single Generation.

In petrelharp/landsim: Simulate Populations on Landscapes

Description

This steps a population forwards by one generation, according to the parameters in a demography object, (which can also be passed in separately; see demography).

Usage

generation(population, demography, N = population$N,
  prob.seed = demography$prob.seed, fecundity = demography$fecundity,
  prob.germination = demography$prob.germination,
  prob.survival = demography$prob.survival,
  pollen.migration = demography$pollen.migration,
  seed.migration = demography$seed.migration,
  genotypes = demography$genotypes, mating = demography$mating,
  death.first = (is.null(demography$death.first) || demography$death.first),
  expected = FALSE, return.everything = FALSE, debug = FALSE, ...)

Arguments

population	A population object, the initial state of the population.
demography	A demography object, containing the below parameters.
N	Optionally, a matrix of the same form as population$N (overrides population$N if present).
prob.seed	Probability of producing seed, per individual.
fecundity	Mean number of seeds produced, per individual, if seeds are produced.
prob.germination	Probability of germination (establishment) per seed.
prob.survival	Probability of survival per already-extant individual.
pollen.migration	A migration object for pollen dispersal.
seed.migration	A migration object for seed dispersal.
genotypes	A character vector of genotypes.
mating	An array giving probabilities for offspring genotypes given parental genotypes.
death.first	If TRUE, germination probability is a function of densities *after* death has taken place.
expected	If TRUE, do no sampling, returning only expected values.
return.everything	If TRUE, returns the number of seeders, amount of pollen, density of seeds, number of germinating seeds, and number of dying individuals.
debug	Do checks for NAs and the like.
...	Additional parameters that will be passed to demographic functions.

Value

A matrix of the same dimensions as population$N, unless return.everything is TRUE, in which case it is a list with entries:

seeders : number of seeding individuals pollen : quantity of pollen produced, by genotype of parent seed.production : quantity of fertilized seeds produced seeds.dispersed : quantity of seeds, post-dispersal germination : number of new seeds that germinate (survive) death : number of previously alive individuals that die

petrelharp/landsim documentation built on May 25, 2019, 2:53 a.m.