draw_comm_next_gen: Draw a new community from the current one
In TheoPannetier/comsie: R implementation of a Competitive Radiation model

draw_comm_next_gen

R Documentation

Draw a new community from the current one

Description

From the trait values of the current community, compute the fitness, draw offspring, apply mutations and resolve speciation events.

Usage

draw_comm_next_gen(
  island_comm,
  mainland_comm,
  growth_rate = comrad::default_growth_rate(),
  competition_sd = comrad::default_competition_sd(),
  trait_opt = comrad::default_trait_opt(),
  carrying_cap_opt = comrad::default_carrying_cap_opt(),
  carrying_cap_sd = comrad::default_carrying_cap_sd(),
  mutation_sd = comrad::default_mutation_sd(),
  trait_dist_sp = comrad::default_trait_dist_sp(),
  brute_force_opt = "none",
  used_species_names
)

Arguments

`island_comm`	a tibble with one row per individual in the community and three columns: `z` contains (numeric) traits values `species` contains species names (characters) `ancestral_species` contains ancestral species names (characters) `founder` (characters), the mainland species that this species' clade originates from.
`mainland_comm`	a tibble defining what species exist in the mainland and their trait distribution. One row per species, three columns: `species`, (character) the name of the species `mean_z`, (numeric) mean value of the trait for that species `z_sd`, (numeric) standard deviation of the trait for that species
`growth_rate`	numeric `>= 0`, the baseline growth rate. Generations being discrete, high values will cause chaos.
`competition_sd`	numeric `>= 0`.Parameter σ_{α} of the competition coefficient. Modulates the the strength of competition between two individuals given their distance in trait space.
`trait_opt`	numeric. The optimal trait value, z_{opt}. `get_carrying_cap(trait_opt) = carrying_cap_opt`.
`carrying_cap_opt`	numeric, value of the carrying capacity at `trait_opt`
`carrying_cap_sd`	numeric `>= 0`. Parameter σ_K of the carrying capacity. Modulates how fast the carrying capacity decays when moving away from the optimal trait value.
`mutation_sd`	numeric `>= 0`, the standard deviation of the normal distrbution from which mutations are drawn.
`trait_dist_sp`	numeric, the minimal trait distance between two clusters of individuals triggering speciation.
`brute_force_opt`	a string specifying which brute force option to use to speed up the calculation of competition coefficients. Defaults to "none". Other options are "omp", for multithreading with OpenMP, "simd" for single instruction, multiple data (SIMD) via the C++ library `xsimd`; and "simd_omp" for both.