multigen: Function to run the simulation
In Rekyt/fdcoexist: Multi-Species Trait-Based Coexistence Model in Discrete time

multigen

R Documentation

Function to run the simulation

Description

Using specified parameters this function run the simulation

Usage

multigen(
  traits,
  trait_weights,
  env,
  time,
  species,
  patches,
  composition,
  A = A,
  B = B,
  d,
  k,
  width,
  H,
  h_fun = "+",
  di_thresh = 24,
  lim_sim_exponent = 2,
  hierar_exponent = 0.5
)

Arguments

`traits`	a species-traits data.frame with species as rownames and traits as numeric columns with names matching `trait_weights` column `trait`
`trait_weights`	data.frame with at least three columns equal to `trait` (giving the name of the concerned traits in `traits` df), `growth_weight` the relative weight of the trait in growth and `compet_weight` the relative weight of the trait in competition.
`env`	a vector of environmental values
`time`	an integer giving the total number of generations
`species`	an integer giving the total number of species to simulate
`patches`	an integer giving the total number of patches to simulate
`composition`	the actual array containing species abundances per site over time, giving the initial populations of each species
`A`	the scalar of inter-specific competition coefficient (see `bevHoltFct()`)
`B`	the scalar for intra-specific competition coefficient by default B = A
`d`	a numeric value between 0 and 1 giving the percentage of dispersal occurring across all patches
`k`	a scalar giving the maximum growth rate in optimal environment
`width`	a numeric giving niche breadth of all species
`H`	a numeric for hierarchical competition such as H/k <= 1
`h_fun`	a function that describes how hierarchical is combined to environmental-based growth (default: `sum()`)
`di_thresh`	dissimilary threshold above which species are considered maximally dissimilar
`lim_sim_exponent`	exponent to use for limiting similarity distances
`hierar_exponent`	exponent to use for hierarchical compet. distances