Selection Models for Amino Acid and/or Codon Evolution

Documentation for package ‘selac’ version 1.7.0

archosaur	Example archosaur dataset
archosaur.phy	Example archosaur dataset
GetAdequateManyReps	Parallel model adequacy test
GetAdequateSelac	Model adequacy simulation
GetFunctionality	Calculate functionality
GetMarginalAllGenes	Get marginal reconstruction all genes
GetPartitionOrder	Get data partiion order
GetSelacPhiCat	Phi rate category information under SELAC+gamma
GetSelacSiteLikelihoods	Calculate site likelihoods under SelAC
model.fit	Example yeast dataset
NucSimulator	Simulate DNA under General-Time Reversible model
phy	Example yeast dataset
PlotEquilbriumCodonDistribution	Function to plot a distribution of frequencies of codons given a 3d array of equilibrium frequency matrices
PlotExpectedFitness	Function to plot a distribution of fitnesses based on codon equilibrium freqs
PlotGeneSiteInfo	Function to plot info by site in a gene
PlotMutationFitnessSpectra	Plot fitness of mutations, weighted by frequency of those mutations
PlotPerAAFitness	Function to plot a distribution of fitnesses W or selection coefficients S for a given optimal aa and other terms.
selac	Efficient optimization of the SELAC model
SelacOptimize	Efficient optimization of the SELAC model
SelacSimulator	Simulate DNA under the SELAC model
SelacSimulatorEvolvingRates	Simulate DNA under the SELAC model and evolving rates
SelonOptimize	Optimize parameters under the SELON model
SelonSimulator	Simulate DNA under the SELON model
uce.model.fit	Example archosaur dataset
yeast	Example yeast dataset
yeast.gene	Example yeast dataset