sra: Selection Response Analysis
Version 0.1.1

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sra")

Popular man pages

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...
sraMinuslogL: Calculation of the likelihood of time series (internal...
sraStartingvalues: Provides reasonable starting values for sra model fit...
See all...

All man pages Function index File listing

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...

Functions

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

Files

NAMESPACE
R
R/sraCanalization.R
R/logLik.srafit.R
R/sraAutoreg.R
R/sraPlotMean.R
R/sraAutoregLog.R
R/sraAutoregHeritTimeseries.R
R/sraPlotlegend.R
R/sraSelection.R
R/sraStartingvalues.R
R/confint.srafit.R
R/sraTimeseries.R
R/sraAutoregEvolvTimeseries.R
R/sraDrift.R
R/sraAutoregTsMinuslogL.log.R
R/sraMakeObject.R
R/BIC.srafit.R
R/sraMinuslogL.log.R
R/sraFormatlegend.R
R/sraCstvar.R
R/sraPlotMeanResid.R
R/sraPlotVar.R
R/sraAutoregTsMinuslogL.R
R/sraMinuslogL.R
R/vcov.srafit.R
R/AIC.srafit.R
R/sraDirepistasis.R
R/sraAutoregTimeseries.R
R/sraPlotVarResid.R
R/sraAutoregHerit.R
R/sraMutation.R
R/sraData.R
R/sraEpiTimeseries.R
R/coef.srafit.R
R/sraAutoregEvolv.R
R/plot.srafit.R
R/sraCanalizationOpt.R
MD5
DESCRIPTION
man
man/sraStartingvalues.Rd
man/sraAutoregTimeseries.Rd
man/D_methods.srafit.Rd
man/sraMinuslogL.Rd
man/B_sraAutoreg.Rd
man/sraData.Rd
man/sraMakeObject.Rd
man/C_sraMechanistic.Rd
man/A-sra-package.Rd
man/E_plot.srafit.Rd
sra documentation built on May 19, 2017, 10:50 a.m.

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