skeleSim: Genetic Simulation Engine

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.

Install the latest version of this package by entering the following in R:
install.packages("skeleSim")
AuthorEric Archer [aut], Michelle DePrenger-Levin [aut], Sean Hoban [aut], Libby Liggins [aut], Christian Parobek [aut], Allan Strand [aut, cre]
Date of publication2016-09-15 00:19:30
MaintainerAllan Strand <stranda@gmail.com>
LicenseGPL-2
Version0.9.5
https:://github.com/christianparobek/skelesim

View on CRAN

Functions

analyses.check Man page
analysisFunc Man page
analysis.funcs Man page
calcChordDist Man page
currentLabel Man page
currentScenario Man page
fastsimcoal.params Man page
fastsimcoal.params-class Man page
formatOverallStats Man page
fsc.histEvCheck Man page
fsc.histEvConverges Man page
fsc.loadScenario Man page
fsc.run Man page
fsc.scenarioCheck Man page
fsc.write Man page
gen.scenario.check Man page
getGammaMutRates Man page
globalAnalysis Man page
hapSmryFunc Man page
loadResultsMatrix Man page
locusAnalysisGenotypes Man page
locusAnalysisHaplotypes Man page
non.scenario.check Man page
overall.check Man page
pairwiseAnalysis Man page
rmetasim.params-class Man page
rms.convert Man page
rms.init.landscape Man page
rms.init.landscape.func Man page
rms.run Man page
rms.scenarioCheck Man page
rms.write Man page
runSim Man page
scenario.params Man page
scenario.params-class Man page
skeleSim Man page
skeleSim.checks Man page
skeleSim.classes Man page
skeleSimGUI Man page
skeleSim.internals Man page
skeleSim-package Man page
skeleSim.params Man page
skeleSim.params-class Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.