extrinsicModels: Extrinsic Character Evolution Models

In bomeara/treevo: Using ABC to Understand Trait Evolution

Extrinsic Character Evolution Models

Description

Functions describing various models of 'extrinsic' evolution (i.e. evolutionary processes dependent on factors extrinsic to the evolving lineage, such as environmental change, or other evolving lineages that interact with the lineage in question (competitors, predators, etc).

Usage

nullExtrinsic(params, selfstates, otherstates, timefrompresent)

nearestNeighborDisplacementExtrinsic(
  params,
  selfstates,
  otherstates,
  timefrompresent
)

everyoneDisplacementExtrinsic(params, selfstates, otherstates, timefrompresent)

ExponentiallyDecayingPushExtrinsic(
  params,
  selfstates,
  otherstates,
  timefrompresent
)

Arguments

params	A vector containing input parameters for the given model (see Description below on what parameters).
selfstates	Vector of current trait values for the population of interest. May be multiple for some models, but generally expected to be only a single value. Multivariate TreEvo is not yet supported.
otherstates	Matrix of current trait values for all concurrent taxa/populations other than the one of interest, with one row for each taxon, and a column for each trait. May be multiple states per taxa/populations for some models, but generally expected to be only a single value. Multivariate TreEvo is not yet supported.
timefrompresent	The amount of time from the present - generally ignored except for time-dependent models.

Details

The following extrinsic models are:

nullExtrinsic describes a model of no extrinsic character change. It has no parameters, really.

nearestNeighborDisplacementExtrinsic describes a model of extrinsic trait evolution where character values of a focal taxon depend on the values of closest relatives on the tree (e.g. competitive exclusion). The input parameters for this model are: nearestNeighborDisplacementExtrinsic with parameters params = sigma, springK, maximumForce

everyoneDisplacementExtrinsic describes a model of extrinsic trait evolution where the character values of a focal taxon depend on the values of all co-extant relatives on the simulated tree. The input parameters for this model are: everyoneDisplacementExtrinsic with parameters params = sigma, springK, maximumForce

ExponentiallyDecayingPushExtrinsic describes a model of extrinsic trait evolution where the character values of a focal taxon is 'pushed' away from other taxa with similar values, but the force of that 'push' exponentially decays as lineages diverge and their character values become less similar. The input parameters for this model are: ExponentiallyDecayingPushExtrinsic with parameters params = sigma, maximumForce, halfDistance

Value

A vector of values representing character displacement of that lineage over a single time step.

Author(s)

Brian O'Meara and Barb Banbury

See Also

Intrinsic models are described at intrinsicModels.

Examples

set.seed(1)
# Examples of simulations with various extrinsic models (and null intrinsic model)
tree <- rcoal(20)
# get realistic edge lengths
tree$edge.length <- tree$edge.length*20

#No trait evolution except due to
       # character displacement due to nearest neighbor taxon
char <- doSimulation(
    phy = tree, 
    intrinsicFn = nullIntrinsic, 
    extrinsicFn = nearestNeighborDisplacementExtrinsic, 
    startingValues = c(10), #root state
    intrinsicValues = c(0), 
    extrinsicValues = c(0.1, 0.1, 0.1), 
 generation.time = 100000)

#Similarly, no trait evolution except due to
       # character displacement from all other taxa in the clade
char <- doSimulation(
    phy = tree, 
    intrinsicFn = nullIntrinsic, 
    extrinsicFn = everyoneDisplacementExtrinsic, 
    startingValues = c(10), #root state
    intrinsicValues = c(0), 
    extrinsicValues = c(0.1, 0.1, 0.1), 
    generation.time = 100000)

# A variant where force of character displacement decays exponentially
        # as lineages become more different
char <- doSimulation(
    phy = tree, 
    intrinsicFn = nullIntrinsic, 
    extrinsicFn = ExponentiallyDecayingPushExtrinsic, 
    startingValues = c(10), #root state
    intrinsicValues = c(0), 
    extrinsicValues = c(0.1, 0.1, 2), 
    generation.time = 100000)

bomeara/treevo documentation built on Aug. 19, 2023, 6:52 p.m.