Package: selac 1.7.5

Jeremy Beaulieu

selac: Selection Models for Amino Acid and/or Codon Evolution

Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. Beaulieu et al (2019) <doi:10.1093/molbev/msy222>.

Authors:Jeremy Beaulieu [aut, cre], JJ Chai [aut], Mike Gilchrist [aut], Cedric Landerer [aut], Graham Derryberry [aut], Brian O'Meara [aut]

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selac.pdf |selac.html✨
selac/json (API)

# Install 'selac' in R:

install.packages('selac', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bomeara/selac/issues

Datasets:

model.fit - Example yeast dataset
model.fit - Example yeast dataset
non_zero_pos - Example datasets
phy - Example yeast dataset
phy - Example yeast dataset
yeast.gene - Example yeast dataset

On CRAN:

2.65 score 1 stars 18 scripts 20 downloads 12 exports 34 dependencies

Last updated 3 years agofrom:cfa135e474. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	OK	Nov 19 2024
R-4.5-linux	OK	Nov 19 2024
R-4.4-win	OK	Nov 19 2024
R-4.4-mac	OK	Nov 19 2024
R-4.3-win	OK	Nov 19 2024
R-4.3-mac	OK	Nov 19 2024

Exports:GetAdequateManyReps GetAdequateSelac GetFunctionality GetMarginalAllGenes GetPartitionOrder GetSelacSiteLikelihoods NucSimulator SelacOptimize SelacSimulator SelacSimulatorEvolvingRates SelonOptimize SelonSimulator

Dependencies:ade4 ape cli cpp11 data.table deSolve digest expm generics GenSA glue igraph lattice lifecycle magrittr MASS Matrix nlme nloptr nnet phangorn pixmap pkgconfig quadprog RColorBrewer Rcpp RcppArmadillo rlang segmented seqinr sp statmod vctrs zoo

Citation

Development and contributors

Readme and manuals

Help Manual

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