intrinsicModels: Intrinsic Character Evolution Models
In bomeara/treevo: Using ABC to Understand Trait Evolution
intrinsicModels R Documentation
Intrinsic Character Evolution Models
Description
Functions describing various models of 'intrinsic' evolution (i.e. evolutionary processes intrinsic to the evolving
lineage, independent of other evolving lineages (competitors, predators, etc).
Usage
nullIntrinsic(params, states, timefrompresent)
brownianIntrinsic(params, states, timefrompresent)
boundaryIntrinsic(params, states, timefrompresent)
boundaryMinIntrinsic(params, states, timefrompresent)
boundaryMaxIntrinsic(params, states, timefrompresent)
autoregressiveIntrinsic(params, states, timefrompresent)
maxBoundaryAutoregressiveIntrinsic(params, states, timefrompresent)
minBoundaryAutoregressiveIntrinsic(params, states, timefrompresent)
autoregressiveIntrinsicTimeSlices(params, states, timefrompresent)
autoregressiveIntrinsicTimeSlicesConstantMean(params, states, timefrompresent)
autoregressiveIntrinsicTimeSlicesConstantSigma(params, states, timefrompresent)
Arguments
params
A vector containing input parameters for the given model (see Description below on what parameters).
states
Vector of current trait values for a taxon. May be multiple 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 intrinsic models are:
nullIntrinsic describes a model of no intrinsic character change.
It has no parameters, really.
brownianIntrinsic describes a model of intrinsic character evolution via
Brownian motion. The input parameters for this model are:
boundaryIntrinsic with parameters params = sigma
boundaryIntrinsic describes a model of intrinsic character evolution where character
change is restricted above a minimum and below a maximum threshold.
The input parameters for this model are:
boundaryMinIntrinsic with parameters params = sigma, minimum, maximum
boundaryMinIntrinsic describes a model of intrinsic character evolution where character
change is restricted above a minimum threshold.
The input parameters for this model are:
boundaryMinIntrinsic with parameters params = sigma, minimum
autoregressiveIntrinsic describes a model of intrinsic character evolution.
New character values are generated after one time step via a discrete-time OU process.
The input parameters for this model are:
autoregressiveIntrinsic with
params = sigma (sigma), attractor (character mean), attraction (alpha)
minBoundaryAutoregressiveIntrinsic describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with a minimum bound.
The input parameters for this model are:
MinBoundaryAutoregressiveIntrinsic with parameters params = sigma (sigma), attractor
(character mean), attraction (alpha), minimum
autoregressiveIntrinsicTimeSlices describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with differing means, sigma, and attraction over time.
In the various TimeSlices models, time threshold units are in time before present
(i.e., 65 could be 65 MYA). The last time threshold should be 0.
The input parameters for this model are:
autoregressiveIntrinsicTimeSlices with parameters params = sd-1 (sigma-1),
attractor-1 (character mean-1), attraction-1 (alpha-1), time threshold-1,
sd-2 (sigma-2), attractor-2 (character mean-2), attraction-2 (alpha-2), time
threshold-2
autoregressiveIntrinsicTimeSlicesConstantMean describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with differing sigma and attraction over time
The input parameters for this model are:
autoregressiveIntrinsicTimeSlicesConstantMean with parameters params = sd-1
(sigma-1), attraction-1 (alpha-1), time threshold-1, sd-2 (sigma-2),
attraction-2 (alpha-2), time threshold-2, attractor (character mean)
autoregressiveIntrinsicTimeSlicesConstantSigma describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with differing means and attraction over time.
The input parameters for this model are:
autoregressiveIntrinsicTimeSlicesConstantSigma with parameters params = sigma (sigma),
attractor-1 (character mean-1), attraction-1 (alpha-1), time threshold-1,
attractor-2 (character mean-2), attraction-2 (alpha-2), time threshold-2
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
Another intrinsic model with multiple optima is described at multiOptimaIntrinsic.
Extrinsic models are described at abcmodels.extrinsic.
Examples
set.seed(1)
# Examples of simulations with various intrinsic models (and null extrinsic model)
tree <- rcoal(20)
# get realistic edge lengths
tree$edge.length <- tree$edge.length*20
#Simple Brownian motion Intrinsic Model
char <- doSimulation(
phy = tree,
intrinsicFn = brownianIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01),
extrinsicValues = c(0),
generation.time = 100000)
# Simple model with BM, but a minimum bound at 0, max bound at 15
char <- doSimulation(
phy = tree,
intrinsicFn = boundaryIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01, 0, 15),
extrinsicValues = c(0),
generation.time = 100000)
# Autoregressive (Ornstein-Uhlenbeck) model
# with minimum bound at 0
char <- doSimulation(
phy = tree,
intrinsicFn = minBoundaryAutoregressiveIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01, 3, 0.1, 0),
extrinsicValues = c(0),
generation.time = 100000)
# Autoregressive (Ornstein-Uhlenbeck) model
# with max bound at 1
char <- doSimulation(
phy = tree,
intrinsicFn = maxBoundaryAutoregressiveIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01, 3, 0.1, 1),
extrinsicValues = c(0),
generation.time = 100000)
bomeara/treevo documentation built on Aug. 19, 2023, 6:52 p.m.
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| intrinsicModels | R Documentation |
Intrinsic Character Evolution Models
Description
Functions describing various models of 'intrinsic' evolution (i.e. evolutionary processes intrinsic to the evolving lineage, independent of other evolving lineages (competitors, predators, etc).
Usage
nullIntrinsic(params, states, timefrompresent)
brownianIntrinsic(params, states, timefrompresent)
boundaryIntrinsic(params, states, timefrompresent)
boundaryMinIntrinsic(params, states, timefrompresent)
boundaryMaxIntrinsic(params, states, timefrompresent)
autoregressiveIntrinsic(params, states, timefrompresent)
maxBoundaryAutoregressiveIntrinsic(params, states, timefrompresent)
minBoundaryAutoregressiveIntrinsic(params, states, timefrompresent)
autoregressiveIntrinsicTimeSlices(params, states, timefrompresent)
autoregressiveIntrinsicTimeSlicesConstantMean(params, states, timefrompresent)
autoregressiveIntrinsicTimeSlicesConstantSigma(params, states, timefrompresent)
Arguments
params |
A vector containing input parameters for the given model (see Description below on what parameters). |
states |
Vector of current trait values for a taxon. May be multiple for some models, but generally expected to be
only a single value. Multivariate |
timefrompresent |
The amount of time from the present - generally ignored except for time-dependent models. |
Details
The following intrinsic models are:
nullIntrinsic describes a model of no intrinsic character change.
It has no parameters, really.
brownianIntrinsic describes a model of intrinsic character evolution via
Brownian motion. The input parameters for this model are:
boundaryIntrinsic with parameters params = sigma
boundaryIntrinsic describes a model of intrinsic character evolution where character
change is restricted above a minimum and below a maximum threshold.
The input parameters for this model are:
boundaryMinIntrinsic with parameters params = sigma, minimum, maximum
boundaryMinIntrinsic describes a model of intrinsic character evolution where character
change is restricted above a minimum threshold.
The input parameters for this model are:
boundaryMinIntrinsic with parameters params = sigma, minimum
autoregressiveIntrinsic describes a model of intrinsic character evolution.
New character values are generated after one time step via a discrete-time OU process.
The input parameters for this model are:
autoregressiveIntrinsic with
params = sigma (sigma), attractor (character mean), attraction (alpha)
minBoundaryAutoregressiveIntrinsic describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with a minimum bound.
The input parameters for this model are:
MinBoundaryAutoregressiveIntrinsic with parameters params = sigma (sigma), attractor
(character mean), attraction (alpha), minimum
autoregressiveIntrinsicTimeSlices describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with differing means, sigma, and attraction over time.
In the various TimeSlices models, time threshold units are in time before present
(i.e., 65 could be 65 MYA). The last time threshold should be 0.
The input parameters for this model are:
autoregressiveIntrinsicTimeSlices with parameters params = sd-1 (sigma-1),
attractor-1 (character mean-1), attraction-1 (alpha-1), time threshold-1,
sd-2 (sigma-2), attractor-2 (character mean-2), attraction-2 (alpha-2), time
threshold-2
autoregressiveIntrinsicTimeSlicesConstantMean describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with differing sigma and attraction over time
The input parameters for this model are:
autoregressiveIntrinsicTimeSlicesConstantMean with parameters params = sd-1
(sigma-1), attraction-1 (alpha-1), time threshold-1, sd-2 (sigma-2),
attraction-2 (alpha-2), time threshold-2, attractor (character mean)
autoregressiveIntrinsicTimeSlicesConstantSigma describes a model of intrinsic character evolution. New
character values are generated after one time step via a discrete-time OU
process with differing means and attraction over time.
The input parameters for this model are:
autoregressiveIntrinsicTimeSlicesConstantSigma with parameters params = sigma (sigma),
attractor-1 (character mean-1), attraction-1 (alpha-1), time threshold-1,
attractor-2 (character mean-2), attraction-2 (alpha-2), time threshold-2
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
Another intrinsic model with multiple optima is described at multiOptimaIntrinsic.
Extrinsic models are described at abcmodels.extrinsic.
Examples
set.seed(1)
# Examples of simulations with various intrinsic models (and null extrinsic model)
tree <- rcoal(20)
# get realistic edge lengths
tree$edge.length <- tree$edge.length*20
#Simple Brownian motion Intrinsic Model
char <- doSimulation(
phy = tree,
intrinsicFn = brownianIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01),
extrinsicValues = c(0),
generation.time = 100000)
# Simple model with BM, but a minimum bound at 0, max bound at 15
char <- doSimulation(
phy = tree,
intrinsicFn = boundaryIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01, 0, 15),
extrinsicValues = c(0),
generation.time = 100000)
# Autoregressive (Ornstein-Uhlenbeck) model
# with minimum bound at 0
char <- doSimulation(
phy = tree,
intrinsicFn = minBoundaryAutoregressiveIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01, 3, 0.1, 0),
extrinsicValues = c(0),
generation.time = 100000)
# Autoregressive (Ornstein-Uhlenbeck) model
# with max bound at 1
char <- doSimulation(
phy = tree,
intrinsicFn = maxBoundaryAutoregressiveIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = c(10), #root state
intrinsicValues = c(0.01, 3, 0.1, 1),
extrinsicValues = c(0),
generation.time = 100000)
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