sra: Selection Response Analysis

This package (sra) provides a set of tools to analyse artificial-selection response datasets. The data typically feature for several generations the average value of a trait in a population, the variance of the trait, the population size and the average value of the parents that were chosen to breed. Sra implements two families of models aiming at describing the dynamics of the genetic architecture of the trait during the selection response. The first family relies on purely descriptive (phenomenological) models, based on an autoregressive framework. The second family provides different mechanistic models, accounting e.g. for inbreeding, mutations, genetic and environmental canalization, or epistasis. The parameters underlying the dynamics of the time series are estimated by maximum likelihood. The sra package thus provides (i) a wrapper for the R functions mle() and optim() aiming at fitting in a convenient way a predetermined set of models, and (ii) some functions to plot and analyze the output of the models.

Author
Arnaud Le Rouzic <lerouzic@legs.cnrs-gif.fr>
Date of publication
2015-01-08 18:21:13
Maintainer
Arnaud Le Rouzic <lerouzic@legs.cnrs-gif.fr>
License
GPL-2
Version
0.1.1

View on CRAN

Man pages

A-sra-package
Selection Response Analysis: a R package
B_sraAutoreg
Descriptive models of artificial-selection responses:...
C_sraMechanistic
Descriptive models of artificial-selection responses:...
D_methods.srafit
Overloaded functions for "srafit" objects
E_plot.srafit
Plotting "srafit" objects
sraAutoregTimeseries
Expected dynamics for different SRA models (internal...
sraData
Generates an object of class "sradata", necessary to run the...
sraMakeObject
Creates an object of class "srafit" (internal function)
sraMinuslogL
Calculation of the likelihood of time series (internal...
sraStartingvalues
Provides reasonable starting values for sra model fit...

Files in this package

sra
sra/NAMESPACE
sra/R
sra/R/sraCanalization.R
sra/R/logLik.srafit.R
sra/R/sraAutoreg.R
sra/R/sraPlotMean.R
sra/R/sraAutoregLog.R
sra/R/sraAutoregHeritTimeseries.R
sra/R/sraPlotlegend.R
sra/R/sraSelection.R
sra/R/sraStartingvalues.R
sra/R/confint.srafit.R
sra/R/sraTimeseries.R
sra/R/sraAutoregEvolvTimeseries.R
sra/R/sraDrift.R
sra/R/sraAutoregTsMinuslogL.log.R
sra/R/sraMakeObject.R
sra/R/BIC.srafit.R
sra/R/sraMinuslogL.log.R
sra/R/sraFormatlegend.R
sra/R/sraCstvar.R
sra/R/sraPlotMeanResid.R
sra/R/sraPlotVar.R
sra/R/sraAutoregTsMinuslogL.R
sra/R/sraMinuslogL.R
sra/R/vcov.srafit.R
sra/R/AIC.srafit.R
sra/R/sraDirepistasis.R
sra/R/sraAutoregTimeseries.R
sra/R/sraPlotVarResid.R
sra/R/sraAutoregHerit.R
sra/R/sraMutation.R
sra/R/sraData.R
sra/R/sraEpiTimeseries.R
sra/R/coef.srafit.R
sra/R/sraAutoregEvolv.R
sra/R/plot.srafit.R
sra/R/sraCanalizationOpt.R
sra/MD5
sra/DESCRIPTION
sra/man
sra/man/sraStartingvalues.Rd
sra/man/sraAutoregTimeseries.Rd
sra/man/D_methods.srafit.Rd
sra/man/sraMinuslogL.Rd
sra/man/B_sraAutoreg.Rd
sra/man/sraData.Rd
sra/man/sraMakeObject.Rd
sra/man/C_sraMechanistic.Rd
sra/man/A-sra-package.Rd
sra/man/E_plot.srafit.Rd