R package for demographically realistic pedigree generation using individual based simulations
devtools::install_github("squidgroup/pedAgree")
library(pedAgree)
Just one function exported at the moment simulate_pedigree(). This takes a bunch of parameters (many can be sex specific), to generate stochastic pedigrees via individual based simulations.
- years: Number of time steps/synchronous reproductive events
- n_females: Starting number of breeding females
- constant_pop: Should there be stochastic variation in population size? (Logical)
- afr: Age at first reproduction
- p_breed: Probability that a female breeds. Can be sex-specific if entered as a vector of length 2 (female,male)
- fecundity: Mean number of juveniles a female produces each year.
- fixed_fecundity: Is fecundity fixed or drawn from a Poisson distribution? (Logical)
- juv_surv: Probability of juveniles surviving until local recruitment, where recruitment is defined as having genetic offspring. Can be sex-specific if entered as a vector of length 2 (female,male)
- adult_surv: Probability of survival of adults across years. Can be sex-specific if entered as a vector of length 2 (female,male)
- immigration:: Yearly immigration rate, as a proportion of starting number of females (n_females). Can be sex-specific if entered as a vector of length 2 (female,male)
- p_polyandry: Probability that a female mates with multiple males.
- p_sire: Probability that 'social' male sires all offspring. Conditional on p_polyandry being >0
- p_retain: Probability that social partnership is retained across years.