default_params_doc: Documentation for main parameters of the model
In TheoPannetier/comsie: R implementation of a Competitive Radiation model

default_params_doc

R Documentation

Documentation for main parameters of the model

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  comm,
  trait_ind,
  traits_comm,
  island_comm,
  mainland_comm,
  mainland_nb_species,
  mainland_z_sd,
  competition_sd,
  trait_opt,
  carrying_cap_opt,
  carrying_cap_sd,
  growth_rate,
  mutation_sd,
  trait_dist_sp,
  nb_gens,
  fitness_func,
  comrad_tbl
)

Arguments

`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.
`trait_ind`	numeric. Trait value `z` of a focal individual.
`traits_comm`	numeric vector of variable length, the trait values of every individual in the community.
`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
`mainland_nb_species`	integer, the number of species in the island community.
`mainland_z_sd`	standard deviation of the trait distribution of mainland species
`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.
`growth_rate`	numeric `>= 0`, the baseline growth rate. Generations being discrete, high values will cause chaos.
`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.
`nb_gens`	integer, how many generations should the simulation be run for?
`fitness_func,`	the name of the function used to compute fitness.
`comrad_tbl`	a tibble containing the output of a `comrad` simulation, as produced by `run_simulation()` or read by `comrad::read_comrad_tbl()`.