sim_BM_trace_history: Simulate continuous trait evolution tracing lineage history.
In Caetanods/buddPhy: Trait Evolution and Budding Speciation

Description Usage Arguments Details Value

This function simulates continuous traits based on the same lineage history created when using 'sim_BM_budding_exp'. It is useful to simulate under the same lineage history and phylogenetic tree while changing rate parameters or parameter for the decay function. If you don't want to retain a particular lineage history, then please refer to 'sim_BM_budding_exp'.

sim_BM_trace_history(
  sim_BM,
  sigma,
  anc = 0,
  change_rate = 2,
  decay_fn = TRUE,
  jump_size = NA,
  jump_type = "fixed",
  jump_all = FALSE
)

`sim_BM`	output from the 'sim_BM_budding_exp'.
`sigma`	the base rate for the Brownian-motion model.
`anc`	the ancestral state for the trait.
`change_rate`	the rate for an exponential reduction of the rate of trait evolution proportional to lineage-age.
`decay_fn`	TRUE or FALSE. If TRUE, then the rate of trait evolution has a negative (exponential) relationship with lineage-age. If FALSE, then this relationship becomes positive.
`jump_size`	controls the size of the cladogenetic change associated with budding speciation. Setting to NA (default) will turn-off the option of cladogenetic trait changes. If 'jump_type' is "fixed" then 'jump_size' is a proportion of the current trait value. If 'jump_type' is "gaussian", then 'jump_size' is the standard variation of a normal (Gaussian) distribution with mean equal to the current trait value and standard deviation equal to 'jump_size'.
`jump_type`	if the phenotype jump at nodes should be "fixed" or "gaussian". See Details.
`jump_all`	if jumps in the phenotype value should occur in all new lineages or only in new species originated from a mother lineage. See Details.

If 'jump_type' is set to "fixed", then each jump of character value at the node will be an increase or decrease of a fixed proportion of the value at that node. The proportion is controlled with the argument "jump_size". For example, 'jump_size = 0.5' will cause the new lineages to start with an average trait value equal to 50% above or below the current trait value. On the other hand, if 'jump_type' is of type "gaussian", the jump in character state will be sampled from a normal distribution with mean equal to the current trait value and standard deviation (sd) equal to 'jump_size'.

The parameter 'jump_all' controls the concept of new lineage. If set to TRUE, then a branching event which produces a new lineage will be followed by a jump on the phenotype value. For example, if a symmetric speciation event takes place, then both descendants are new lineages and both jump in the morphospace (controlled by the 'jump_size' and 'jump_type' parameters). If set to FALSE, then jumps in the morphospace associated with the origination of a new lineage occurs only if a budding speciation takes place.

A list with the information from the simulation and the states at the tips.

Caetanods/buddPhy documentation built on Oct. 12, 2021, 12:14 p.m.