Evolutionary Rates Across Gradients

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Documentation for package ‘EvoRAG’ version 2.0

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EvoRAG-package Evolutionary Rates Across Gradients
bird.pitch example data sets of avian sister pairs with trait data and a gradient
bird.syllables example data sets of avian sister pairs with trait data and a gradient
bootstrap.test Estimate confidence intervals using bootstrap
EvoRAG Evolutionary Rates Across Gradients
expectation.gradient calculate the expected (i.e. mean) Euclidean distances for a gradient model
expectation.time calculate the expected (i.e. mean) Euclidean distances through time given a rate of evolution, Beta.
find.mle.sister internal EvoRAG functions
model.test.sisters Fit evolutionary models for continuous trait data
MScorrection Correct for finite sample size in Euclidean distances given known variances in each sample
MScorrection_MSwithin internal EvoRAG functions
parameter.reestimation uses simulation to determine robustness of parameter estimates under a model
plotGradient.ci Plot evolutionary rates and their confidence regions across a gradient
power.test performs a simulation based analysis of statistical power
Profile.like.CI Estimate confidence intervals using profile likelihood
sim.sisters simulate Euclidean distances for sister pair data under 10 evolutionary models
simulation.analysis internal EvoRAG functions
sisterContinuous likelihood functions for continuous trait evolutionary models
sisterContinuous_logSpace internal EvoRAG functions
sisterContinuous_logSpace_profile_CI internal EvoRAG functions
starting.values returns the null starting values used in model.test.sisters
TypeI.error performs a simulation based analysis of type I error