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selac

Model by O'Meara, Beaulieu, Chai, and Gilchrist for SELection on Amino acids and/or Codons

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Version

Install

install.packages('selac')

Monthly Downloads

2

Version

1.7.5

License

GPL

Maintainer

Jeremy Beaulieu

Last Published

June 18th, 2020

Functions in selac (1.7.5)

GetMarginalAllGenes

Get marginal reconstruction all genes
SelonOptimize

Optimize parameters under the SELON model
SelonHMMOptimize

Optimize parameters under the HMM SELON model
GetAdequateManyReps

Parallel model adequacy test
SelonSimulator

Simulate DNA under the SELON model
PlotEquilbriumCodonDistribution

Function to plot a distribution of frequencies of codons given a 3d array of equilibrium frequency matrices
selon example

Example archosaur dataset
PlotExpectedFitness

Function to plot a distribution of fitnesses based on codon equilibrium freqs
GetAdequateSelac

Model adequacy simulation
GetSelacSiteLikelihoods

Calculate site likelihoods under SelAC
NucSimulator

Simulate DNA under General-Time Reversible model
GetPartitionOrder

Get data partiion order
SelacSimulator

Simulate DNA under the SELAC model
SelacHMMSimulator

Simulate DNA under the SELAC model
SelacOptimize

Efficient optimization of the SELAC model
SelacSimulatorEvolvingRates

Simulate DNA under the SELAC model and evolving rates
GetSelacPhiCat

Phi rate category information under SELAC+gamma
selac example

Example yeast dataset
PlotPerAAFitness

Function to plot a distribution of fitnesses W or selection coefficients S for a given optimal aa and other terms.
PlotGeneSiteInfo

Function to plot info by site in a gene
PlotMutationFitnessSpectra

Plot fitness of mutations, weighted by frequency of those mutations
SelacHMMOptimize

Efficient optimization of a Hidden Markov SELAC model
internal

Internal functions
Index matrix

Example datasets
GetFunctionality

Calculate functionality