phylocomr (version 0.3.4)

ph_ecovolve: ecovolve

Description

Ecovolve generates a phylogeny via a random birth and death process, generates a traits file with five randomly evolving, in-dependent traits, and a sample file with a single sample unit (‘alive’) containing all extant members of the phylogeny.

Usage

ph_ecovolve(
  speciation = 0.05,
  extinction = 0.01,
  time_units = 100,
  out_mode = 3,
  prob_env = "3211000000",
  extant_lineages = FALSE,
  only_extant = FALSE,
  taper_change = NULL,
  competition = FALSE
)

Value

a list with three elements:

• phylogeny - a phylogeny as a newick string. In the case of out_mode = 2 gives a Lineage Through Time data.frame instead of a newick phylogeny

• sample - a data.frame with three columns, "sample" (all "alive"), "abundance" (all 1's), "name" (the species code). In the case of out_mode = 2 gives an empty data.frame

• traits - a data.frame with first column with spcies code ("name"), then 5 randomly evolved and independent traits. In the case of out_mode = 2 gives an empty data.frame

Arguments

speciation

(numeric) Probability of speciation per unit time. Default: 0.05

extinction

(numeric) Probability of extinction per unit time. Default: 0.01

time_units

(integer) Time units to simulate over. Default: 100

out_mode

(integer) Output mode (2 = LTT; 3 = newick). Default: 3

prob_env

(character) Probability envelope for character change. must be a string of 10 integers. Default: 3211000000

extant_lineages

(logical) Stop simulation after this number of extant lineages. Default: FALSE

only_extant

(logical) Output phylogeny pruned only for extant taxa. Default: FALSE

taper_change

(numeric/integer) Taper character change by e^(-time/F). This produces more conservatism in traits (see Kraft et al., 2007). Default: NULL, not passed

competition

(logical) Simulate competition, with trait proximity increasing extinction. Default: FALSE

Clean up

Two files, "ecovolve.sample" and "ecovolve.traits" are written to the current working directory when this function runs - we read these files in, then delete the files via unlink

Failure behavior

Function occasionally fails with error "call to 'ecovolve' failed with status 8. only 1 taxon; > 1 required" - this just means that only 1 taxon was created in the random process, so the function can't proceed

Examples

if (FALSE) {
# ph_ecovolve(speciation = 0.05)
# ph_ecovolve(speciation = 0.1)
# ph_ecovolve(extinction = 0.005)
# ph_ecovolve(time_units = 50)
# ph_ecovolve(out_mode = 2)
# ph_ecovolve(extant_lineages = TRUE)
# ph_ecovolve(extant_lineages = FALSE)
# ph_ecovolve(only_extant = FALSE)
# ph_ecovolve(only_extant = TRUE, speciation = 0.1)
# ph_ecovolve(taper_change = 2)
# ph_ecovolve(taper_change = 10)
# ph_ecovolve(taper_change = 500)

if (requireNamespace("ape")) {
  # library(ape)
  # x <- ph_ecovolve(speciation = 0.05)
  # plot(read.tree(text = x$phylogeny))
}

}