Selection Models for Amino Acid and/or Codon Evolution

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Documentation for package ‘selac’ version 1.7.5

Help Pages

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
non_zero_pos Example datasets
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
SelacHMMOptimize Efficient optimization of a Hidden Markov SELAC model
SelacHMMSimulator Simulate DNA under 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
SelonHMMOptimize Optimize parameters under the HMM SELON model
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