skeleSim: Genetic Simulation Engine
Version 0.9.5

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.

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
URL https:://github.com/christianparobek/skelesim
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("skeleSim")

Getting started

Package overview
README.md
Choosing Sample Size
Installing skeleSim
Running a forecasting simulation in skeleSim
Running simulations in skeleSim

Popular man pages

analysis.funcs: Analysis functions for skeleSim parameter objects
fsc.run: Run fastsimcoal
rms.convert: Extract genetic data from landscape object
rms.init.landscape: Initialize a landscape object
runSim: Run simulation
skeleSim.classes: skeleSim Parameters Class
skeleSimGUI: GUI for skeleSim system
See all...

All man pages Function index File listing

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

Functions

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

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
skeleSim documentation built on May 20, 2017, 2:32 a.m.

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

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

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