EvoRAG-internal functions are not typically called by the user
● Data Source:
CranContrib
● Keywords:
● Alias: MScorrection_MSwithin, find.mle.sister, simulation.analysis, sisterContinuous_logSpace, sisterContinuous_logSpace_profile_CI
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starting.values
(Package: EvoRAG) :
returns the null starting values used in model.test.sisters
returns the null starting values used in model.test.sisters
● Data Source:
CranContrib
● Keywords: Brownian Motion, Ornstein Uhlenbeck
● Alias: starting.values
●
0 images
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expectation.time
(Package: EvoRAG) :
calculate the expected (i.e. mean) Euclidean distances through time given a rate of evolution, Beta.
calculate the expected (i.e. mean) Euclidean distances through time given a rate of evolution, Beta.
● Data Source:
CranContrib
● Keywords: Expectation
● Alias: expectation.time
●
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model.test.sisters
(Package: EvoRAG) :
Fit evolutionary models for continuous trait data
Takes a dataset of continuous trait values for a series of sister pairs (e.g. sister species) with known ages of divergence and finds the maximum likelihood fits under a series of evolutionary models.
● Data Source:
CranContrib
● Keywords: Brownian Motion, Ornstein Ulhembeck
● Alias: model.test.sisters
●
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Profile.like.CI
(Package: EvoRAG) :
Estimate confidence intervals using profile likelihood
profile likelihood is used to estimate 95
● Data Source:
CranContrib
● Keywords:
● Alias: Profile.like.CI
●
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plotGradient.ci
(Package: EvoRAG) :
Plot evolutionary rates and their confidence regions across a gradient
Takes the output from bootstrap.test for the BM_linear model and plots how evolutionary rates and their confidence regions change across the gradient.
● Data Source:
CranContrib
● Keywords: confidence interval, plot
● Alias: plotGradient.ci
●
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expectation.gradient
(Package: EvoRAG) :
calculate the expected (i.e. mean) Euclidean distances for a gradient model
For models where evolutionary rate (Beta) or constraint (alpha) vary across a gradient, calculate the expected (i.e. mean) Euclidean distances at each point across the gradient after a given amount of time.
● Data Source:
CranContrib
● Keywords: Expectation
● Alias: expectation.gradient
●
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sim.sisters
(Package: EvoRAG) :
simulate Euclidean distances for sister pair data under 10 evolutionary models
simulate Euclidean distances for sister pair data under 10 evolutionary models
● Data Source:
CranContrib
● Keywords: Brownian Motion, Ornstein Uhlenbeck, Simulation
● Alias: sim.sisters
●
2 images
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parameter.reestimation
(Package: EvoRAG) :
uses simulation to determine robustness of parameter estimates under a model
uses simulation to determine robustness of parameter estimates under a model
● Data Source:
CranContrib
● Keywords: Simulation, parameter re-estimation
● Alias: parameter.reestimation
●
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power.test
(Package: EvoRAG) :
performs a simulation based analysis of statistical power
performs a simulation based analysis of statistical power
● Data Source:
CranContrib
● Keywords: Simulation, Statistical power, Type II error
● Alias: power.test
●
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