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Species traits, with or without phylogenetic signal

Source: R/traits.R
species_traits.Rd

Environmental optima evolve by Brownian motion with Pagel's lambda and are rescaled to optima_range (or, with uniform_optima = TRUE, replaced by ranks with evenly spaced values on that range, so that only their arrangement on the tree depends on the tree). Niche breadths are drawn from a normal distribution truncated at zero, and maximum growth rates from a uniform distribution. Either can carry phylogenetic signal: the values are then assigned to species by the ranks of a Brownian-motion trait, which keeps their marginal distribution.

Usage

species_traits(
  species,
  lambda = 1,
  optima_range = c(0, 100),
  uniform_optima = FALSE,
  sigma_mean = 10,
  sigma_sd = 10,
  rmax_range = c(2, 8),
  sigma_signal = FALSE,
  rmax_signal = FALSE
)

Arguments

species

A phylo tree, or the number of species for traits without phylogenetic structure.

lambda

Pagel's lambda of the optima (0 = no signal, 1 = Brownian motion). Ignored when species is a number.

optima_range

Range of the optima.

uniform_optima

Give the optima evenly spaced values by rank?

sigma_mean, sigma_sd

Mean and standard deviation of the normal distribution (truncated at zero) of niche breadths.

rmax_range

Range of the uniform distribution of maximum growth rates.

sigma_signal, rmax_signal

Should niche breadth or maximum growth rate carry phylogenetic signal (Brownian motion)?

Value

Data frame with columns optimum, sigma and r_max, one row per species, with species names as row names.

Examples

set.seed(1)
tr <- treeshapesim::sim_tree_shape(10)
species_traits(tr, lambda = 1, sigma_signal = TRUE)
#>        optimum     sigma    r_max
#> t1   81.014935  5.218499 4.731647
#> t2   87.432733  9.461950 4.460504
#> t3   99.189329 14.179416 6.865221
#> t4  100.000000  8.972123 5.629600
#> t5   54.609559  5.850054 5.928344
#> t6    0.000000  9.406866 4.119184
#> t7   29.662989  6.057100 3.621561
#> t8   38.305851 23.586796 7.956104
#> t9   35.050894 13.876716 5.800960
#> t10   5.656532 21.000254 3.279249
species_traits(5)
#>       optimum      sigma    r_max
#> sp1  29.94562  0.6590237 2.382851
#> sp2 100.00000 12.9144624 4.012925
#> sp3  41.12514  5.5670813 6.342356
#> sp4   0.00000 10.0110535 4.025692
#> sp5  45.81600 10.7434132 5.782485