skeleSim: Genetic Simulation Engine

Share:

A shiny interface and supporting tools to guide users in choosing appropriate simulations, setting parameters, calculating summary genetic statistics, and organizing data output, all within the R environment. In addition to supporting existing forward and reverse-time simulators, new simulators can be integrated into the environment relatively easily.

Author
Eric Archer [aut], Michelle DePrenger-Levin [aut], Sean Hoban [aut], Libby Liggins [aut], Christian Parobek [aut], Allan Strand [aut, cre]
Date of publication
2016-09-15 00:19:30
Maintainer
Allan Strand <stranda@gmail.com>
License
GPL-2
Version
0.9.5
URLs

View on CRAN

Man pages

analysis.funcs
Analysis functions for skeleSim parameter objects
fastsimcoal.params-class
fastsimcoal Parameters Class
fsc.loadScenario
Load skeleSim scenario parameters for fastsimcoal
fsc.run
Run fastsimcoal
fsc.scenarioCheck
Check parameters for fastsimcoal
fsc.write
Write fastsimcoal files
getGammaMutRates
Get a Vector of Randomly Chosen Mutation Rates
rmetasim.classes
rmetasim Parameters Class
rms.convert
Extract genetic data from landscape object
rms.init.landscape
Initialize a landscape object
rms.init.landscape.func
Initialize a landscape object
rms.run
Run rmetasim
rms.scenarioCheck
Check parameters for rmetasim
rms.write
Write metasim file
runSim
Run simulation
skeleSim.checks
Check all simulation parameters
skeleSim.classes
skeleSim Parameters Class
skeleSimGUI
GUI for skeleSim system
skeleSim.internals
SkeleSim internal functions
skeleSim-package
Genetic simulation engine

Files in this package

skeleSim
skeleSim/inst
skeleSim/inst/shiny
skeleSim/inst/shiny/skeleSimShinyGUI
skeleSim/inst/shiny/skeleSimShinyGUI/ui.R
skeleSim/inst/shiny/skeleSimShinyGUI/server.R
skeleSim/inst/shiny/skeleSimShinyGUI/update-ui.R
skeleSim/inst/shiny/skeleSimShinyGUI/utils.R
skeleSim/inst/shiny/skeleSimShinyGUI/debug.R
skeleSim/inst/shiny/skeleSimShinyGUI/vizfuncs.R
skeleSim/inst/shiny/skeleSimShinyGUI/simcoal-server.R
skeleSim/inst/shiny/skeleSimShinyGUI/saveParams.R
skeleSim/inst/shiny/skeleSimShinyGUI/vizServer.R
skeleSim/inst/shiny/skeleSimShinyGUI/mig.matrix.R
skeleSim/inst/shiny/skeleSimShinyGUI/simcoal-history.R
skeleSim/inst/shiny/skeleSimShinyGUI/serverInit.R
skeleSim/inst/shiny/skeleSimShinyGUI/modules
skeleSim/inst/shiny/skeleSimShinyGUI/modules/matrixInputs.R
skeleSim/inst/shiny/skeleSimShinyGUI/modules/tableinput.R
skeleSim/inst/shiny/skeleSimShinyGUI/README.md
skeleSim/inst/shiny/skeleSimShinyGUI/intro-questions-server.R
skeleSim/inst/shiny/skeleSimShinyGUI/vizAbstract.R
skeleSim/inst/shiny/skeleSimShinyGUI/test.ssClass.rdata
skeleSim/inst/shiny/skeleSimShinyGUI/scenarios-server.R
skeleSim/inst/shiny/skeleSimShinyGUI/serverplots.R
skeleSim/inst/shiny/skeleSimShinyGUI/sanity-checks.R
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/rmetasim-loci.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/help-questions.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/lefkovitch.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/help-migration.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/help-history.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/file-ops.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/simulations.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/load-params.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/skelesim-general-help.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/save-params.md
skeleSim/inst/shiny/skeleSimShinyGUI/helpfiles/rmetasim-alleles.md
skeleSim/inst/shiny/skeleSimShinyGUI/rmetasim-server.R
skeleSim/inst/shiny/skeleSimShinyGUI/runSim.R
skeleSim/inst/shiny/skeleSimShinyGUI/make-skelesim-class.R
skeleSim/inst/shiny/skeleSimShinyGUI/loadParams.R
skeleSim/inst/shiny/skeleSimShinyGUI/visualize.R
skeleSim/inst/shiny/skeleSimShinyGUI/global.R
skeleSim/inst/tableinput
skeleSim/inst/tableinput/tableinput.js
skeleSim/inst/tableinput/tableinput.css
skeleSim/inst/doc
skeleSim/inst/doc/Forecasting.R
skeleSim/inst/doc/SampleSize.Rmd
skeleSim/inst/doc/SampleSize.html
skeleSim/inst/doc/Installing.Rmd
skeleSim/inst/doc/Simulating.html
skeleSim/inst/doc/Simulating.R
skeleSim/inst/doc/Installing.html
skeleSim/inst/doc/Installing.R
skeleSim/inst/doc/Simulating.Rmd
skeleSim/inst/doc/Forecasting.Rmd
skeleSim/inst/doc/Forecasting.html
skeleSim/inst/doc/SampleSize.R
skeleSim/NAMESPACE
skeleSim/R
skeleSim/R/rms.internals.R
skeleSim/R/fsc.loadScenario.R
skeleSim/R/rms.init.landscape.R
skeleSim/R/fsc.classes.R
skeleSim/R/skeleSim.classes.R
skeleSim/R/rms.classes.R
skeleSim/R/rms.scenarioCheck.R
skeleSim/R/skeleSim.checks.R
skeleSim/R/rms.run.R
skeleSim/R/fsc.scenarioCheck.R
skeleSim/R/analysis.funcs.R
skeleSim/R/skeleSim-package.R
skeleSim/R/fsc.run.R
skeleSim/R/rms.convert.R
skeleSim/R/getGammaMutRates.R
skeleSim/R/rms.init.land.function.R
skeleSim/R/runSim.R
skeleSim/R/skeleSim.internals.R
skeleSim/R/skeleSimGUI.R
skeleSim/vignettes
skeleSim/vignettes/SampleSize.Rmd
skeleSim/vignettes/SampleSizeImages
skeleSim/vignettes/SampleSizeImages/screen6_loci.JPG
skeleSim/vignettes/SampleSizeImages/screen2_GenConf.JPG
skeleSim/vignettes/SampleSizeImages/screen7_simcoal_history.JPG
skeleSim/vignettes/SampleSizeImages/screen5_migr_rates.JPG
skeleSim/vignettes/SampleSizeImages/screen3_ScenConf.JPG
skeleSim/vignettes/Choosemetasim.png
skeleSim/vignettes/Installing.Rmd
skeleSim/vignettes/obsvdheterozygosity.png
skeleSim/vignettes/ScenarioConf_PopChar.png
skeleSim/vignettes/ForecastImages
skeleSim/vignettes/ForecastImages/screen1_Actions.png
skeleSim/vignettes/ForecastImages/screen8_ssClass.png
skeleSim/vignettes/ForecastImages/screen4_Migr_rate.png
skeleSim/vignettes/ForecastImages/RmetasimLocus.png
skeleSim/vignettes/ForecastImages/screen2_Gen_Conf.png
skeleSim/vignettes/ForecastImages/screen6_Metasim_pop_matrices.png
skeleSim/vignettes/ForecastImages/screen5_Loc_Mut_rate.png
skeleSim/vignettes/ForecastImages/screen3_Pop_Samp_Sizes.png
skeleSim/vignettes/ForecastImages/screen9_Scen2_diff_migr.png
skeleSim/vignettes/ForecastImages/screen7_Metasim_allele_freq.png
skeleSim/vignettes/ScenarioConf_LocChar.png
skeleSim/vignettes/Simulating.Rmd
skeleSim/vignettes/Choosermetasim2.png
skeleSim/vignettes/Forecasting.Rmd
skeleSim/README.md
skeleSim/MD5
skeleSim/build
skeleSim/build/vignette.rds
skeleSim/DESCRIPTION
skeleSim/man
skeleSim/man/skeleSimGUI.Rd
skeleSim/man/rms.init.landscape.func.Rd
skeleSim/man/rms.init.landscape.Rd
skeleSim/man/rms.scenarioCheck.Rd
skeleSim/man/getGammaMutRates.Rd
skeleSim/man/rms.write.Rd
skeleSim/man/fsc.scenarioCheck.Rd
skeleSim/man/rms.convert.Rd
skeleSim/man/fsc.run.Rd
skeleSim/man/fsc.write.Rd
skeleSim/man/rms.run.Rd
skeleSim/man/analysis.funcs.Rd
skeleSim/man/fsc.loadScenario.Rd
skeleSim/man/rmetasim.classes.Rd
skeleSim/man/fastsimcoal.params-class.Rd
skeleSim/man/skeleSim.checks.Rd
skeleSim/man/skeleSim-package.Rd
skeleSim/man/skeleSim.internals.Rd
skeleSim/man/runSim.Rd
skeleSim/man/skeleSim.classes.Rd