simulate: Simulate Spread of Gene for Altruism
In homerhanumat/simaltruist: Altruistic Behavior in Animal Populations

Description Usage Arguments Value Note Examples

View source: R/simulate.R

Simulate Spread of Gene for Altruism

simulate(initial_pop = list(m0 = 90, m1 = 0, m2 = 10, f0 = 90, f1 = 0, f2 =
  10), average_litter_size = 5, birth_rate_natural = 0.05,
  death_rate_natural = 0, prob_attack = 0.2, warner_death_prob = 0.4,
  nonwarner_death_prob = 0.2, hider_death_prob = 0, sim_gens = 2,
  capacity = 2000, mating_behavior = NULL, culling_behavior = NULL,
  attack_behavior = NULL, relationship_method = c("matrix", "graph",
  "none"), graph = TRUE)

`initial_pop`	List comprised of six named elements: m0 initial number of males with 0 altruist alleles; m1 initial number of males with 1 altruist allele; m2 initial number of males with 2 altruist alleles; f0 initial number of females with 0 altruist alleles; f1 initial number of females with 1 altruist allele; f2 initial number of females with 2 altruist alleles.
`average_litter_size`	Mean size of a litter.
`birth_rate_natural`	Birth rate for the population.
`death_rate_natural`	Death rate for a size-zero population. Rises linearly to `birth_rate_natrual` as populaiion approaches `capacity`.
`prob_attack`	The probability of a predator attack in any given generation.
`warner_death_prob`	Probability that an individual who warns others during an attack will be killed.
`nonwarner_death_prob`	Probability of death for an individual who does not warn others but who was not forewarned by a warner.
`hider_death_prob`	Probability of death during an attack for an individual who accepts a warning.
`sim_gens`	Number of generations to simulate.
`capacity`	Carrying capacity of the population.
`mating_behavior`	Custom function to govern how eligible partners form couples.
`culling_behavior`	Custom function to determine death probabilities of individuals at the culling stage..
`attack_behavior`	Custom function to govern behavior of warners when population is under attack.
`relationship_method`	One of `"matrix"`, `"graph"` and `"none"`. Defaults to `"matrix"`. Use `"none"` only if no relationships (other than mother and father id) need to be tracked.
`graph`	If `TRUE`, provides a graph of the total per-capita warner alleles in population over the generations.

A data frame with information on the population at each generation. Each row describes the population at the end of a single birth-death-attack cycle. Variables are:

populationSize: total population
males: total number of males
males0: number of males with no alleles for altruism
males1: number of males with one allele for altruism
males2: number of males with two alleles for altruism
females: total number of females
females0: number of females with no alleles for altruism
females1: number of females with one allele for altruism
females2: number of females with two alleles for altruism

For details on mating_behavior, mating_behavior and attack_behavior consult the package documentation.

## Not run: 
# use defaults, get a graph:
pop <- simulate(sim_gens = 400)
# attacks are infrequent, and it's dangerous to warn:
pop <- simulate(sim_gens = 200,
                warner_death_prob = 0.8,
                attack_prob = 0.05)
# use an alternative mating function exported by package:
pop <- simulate(sim_gens = 200,
                warner_death_prob = 0.8,
                mating_behavior = list(
                  fn = sexualSelection,
                  args = list(
                    matrix(
                      c(1, 5, 10, 1, 1, 1, 10, 5, 1),
                      nrow = 3,
                      ncol = 3))))

## End(Not run)