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.

AuthorArnaud Le Rouzic <lerouzic@legs.cnrs-gif.fr>
Date of publication2015-01-08 18:21:13
MaintainerArnaud Le Rouzic <lerouzic@legs.cnrs-gif.fr>
LicenseGPL-2
Version0.1.1

View on CRAN

Functions

AIC.srafit Man page
coef.srafit Man page
confint.srafit Man page
logLik.srafit Man page
plot.srafit Man page
sra Man page
sraAutoreg Man page
sraAutoregEvolv Man page
sraAutoregEvolvTimeseries Man page
sraAutoregHerit Man page
sraAutoregHeritTimeseries Man page
sraAutoregLog Man page
sraAutoregTimeseries Man page
sraAutoregTsMinuslogL Man page
sraAutoregTsMinuslogL.log Man page
sraCanalization Man page
sraCanalizationOpt Man page
sraCstvar Man page
sraData Man page
sraDirepistasis Man page
sraDrift Man page
sraEpiTimeseries Man page
sraFormatlegend Man page
sraMakeObject Man page
sraMinuslogL Man page
sraMinuslogL.log Man page
sraMutation Man page
sra-package Man page
sraPlotlegend Man page
sraPlotMean Man page
sraPlotMeanResid Man page
sraPlotVar Man page
sraPlotVarResid Man page
sraSelection Man page
sraStartingvalues Man page
sraTimeseries Man page
vcov.srafit Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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