Competition matrix

Intraspecific coefficients are 1 and interspecific coefficients lie in [0, inter_max), all multiplied by scale. With the default scale of 0.05, as in Thompson et al. (2020), a species alone at its optimum with r_max = 5 reaches an equilibrium of (5 - 1) / 0.05 = 80 individuals, and inter_max is the strength of interspecific relative to intraspecific competition. The matrix is symmetric.

Usage

competition_matrix(
  species,
  type = c("none", "random", "phylo"),
  inter_max = 0.1,
  scale = 0.05
)

Arguments

species

A phylo tree, or the number of species (not for type = "phylo").

type

Type of interspecific competition.

inter_max

Maximum interspecific coefficient, relative to intraspecific competition.

scale

Multiplier of all coefficients.

Value

Square matrix: element [j, k] is the effect of species k on species j.

Details

• "none": no interspecific competition.

• "random": interspecific coefficients drawn from U(0, inter_max).

• "phylo": the same uniform values, assigned to pairs of species by rank of phylogenetic similarity (1 - d / max(d), with d the patristic distance), so that close relatives compete more strongly while the distribution of coefficients stays the same as with "random".

Examples

set.seed(1)
tr <- treeshapesim::sim_tree_shape(5)
round(competition_matrix(tr, "phylo", inter_max = 0.5), 3)
#>       t1    t2    t3    t4    t5
#> t1 0.050 0.023 0.003 0.016 0.012
#> t2 0.023 0.050 0.007 0.005 0.010
#> t3 0.003 0.007 0.050 0.019 0.018
#> t4 0.016 0.005 0.019 0.050 0.025
#> t5 0.012 0.010 0.018 0.025 0.050