pedAgree (version 0.0.1.0)

R package for demographically realistic pedigree generation using individual based simulations

Installation

devtools::install_github("squidgroup/pedAgree")
library(pedAgree)

Use

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.

Pedigree Size

• Integer: 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)

Demography

• 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)

Mating System

• 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.