Files in christianparobek/skeleSim

Genetic Simulation Engine

.Rbuildignore

.gitignore

.travis.yml

Archive/NESCent.code/DNAbin2gtypes.R Archive/NESCent.code/README.md Archive/NESCent.code/StopLoop.Rmd Archive/NESCent.code/analyze.onerep.R Archive/NESCent.code/check.megalist.R Archive/NESCent.code/example_plots.pdf Archive/NESCent.code/genind.metadata.getter.R

Archive/NESCent.code/megalist-freq.rda

Archive/NESCent.code/megalist-seq.rda

Archive/NESCent.code/mig.matrix.R Archive/NESCent.code/new.mainparam.list.R Archive/NESCent.code/old fastsimcoal code/fastsimcoal.skeleSim.R Archive/NESCent.code/old fastsimcoal code/fastsimcoal.skeleSim.read.R Archive/NESCent.code/old fastsimcoal code/fastsimcoal.skeleSim.run.R Archive/NESCent.code/old fastsimcoal code/fastsimcoal.test.R Archive/NESCent.code/old fastsimcoal code/set.fastsimcoal.params.R Archive/NESCent.code/old fastsimcoal code/sim.wrap.fastsimcoal.R Archive/NESCent.code/plot_all_stats.R Archive/NESCent.code/rmetasim/rmetasim.sim.wrap.R Archive/NESCent.code/rmetasim/set.specparams.rmetasim.R Archive/NESCent.code/set.commonparams.R Archive/NESCent.code/set.scenarios.R Archive/NESCent.code/sim.iterator.R Archive/NESCent.code/skeleSim.R Archive/NESCent.code/skelesim.sumstats.table.R Archive/NESCent.code/tictocTest.R Archive/NIMBioS.code/Analysis_working_codeBits_MEDL.R

Archive/NIMBioS.code/StopLoop.html

Archive/NIMBioS.code/StopLoop.md Archive/NIMBioS.code/StopLoopBackup.Rmd Archive/NIMBioS.code/analysis_funcs.R Archive/NIMBioS.code/fastsimcoal.skeleSim.R

Archive/NIMBioS.code/fastsimcoal/.gitignore

Archive/NIMBioS.code/fastsimcoal/fsc.classes.R Archive/NIMBioS.code/fastsimcoal/fsc.read.R Archive/NIMBioS.code/fastsimcoal/fsc.run.R Archive/NIMBioS.code/fastsimcoal/fsc.scenarioCheck.R Archive/NIMBioS.code/fastsimcoal/fsc.set.params.R Archive/NIMBioS.code/fastsimcoal/fsc.write.R Archive/NIMBioS.code/fastsimcoal/readme.md Archive/NIMBioS.code/fastsimcoal/test hist ev check.R Archive/NIMBioS.code/multigene sapply example.R Archive/NIMBioS.code/plot.all.stats.R Archive/NIMBioS.code/rmetasim.skeleSim.R Archive/NIMBioS.code/rmetasim/readme.md Archive/NIMBioS.code/rmetasim/rmetasim2adegenet.R Archive/NIMBioS.code/rmetasim/rms.classes.R Archive/NIMBioS.code/rmetasim/rms.convert.R Archive/NIMBioS.code/rmetasim/rms.init.landscape.R Archive/NIMBioS.code/rmetasim/rms.run.R Archive/NIMBioS.code/rmetasim/rms.scenarioCheck.R Archive/NIMBioS.code/shiny/help.md Archive/NIMBioS.code/shiny/server.R Archive/NIMBioS.code/shiny/ui.R Archive/NIMBioS.code/shinySim_v2/help.md Archive/NIMBioS.code/shinySim_v2/server.R

Archive/NIMBioS.code/shinySim_v2/server.html

Archive/NIMBioS.code/shinySim_v2/ui.R Archive/NIMBioS.code/shiny_parameters/README.md Archive/NIMBioS.code/shiny_parameters/genparam-server.R Archive/NIMBioS.code/shiny_parameters/global.R Archive/NIMBioS.code/shiny_parameters/helpfiles/help-history.md Archive/NIMBioS.code/shiny_parameters/helpfiles/help-migration.md Archive/NIMBioS.code/shiny_parameters/helpfiles/help-questions.md Archive/NIMBioS.code/shiny_parameters/helpfiles/load-params.md Archive/NIMBioS.code/shiny_parameters/helpfiles/save-params.md Archive/NIMBioS.code/shiny_parameters/intro-questions-server.R Archive/NIMBioS.code/shiny_parameters/loadParams.R Archive/NIMBioS.code/shiny_parameters/make-skelesim-class.R Archive/NIMBioS.code/shiny_parameters/mig.matrix.R Archive/NIMBioS.code/shiny_parameters/renderUI.R Archive/NIMBioS.code/shiny_parameters/runSim.R Archive/NIMBioS.code/shiny_parameters/saveParams.R Archive/NIMBioS.code/shiny_parameters/scenarios-server.R Archive/NIMBioS.code/shiny_parameters/server.R Archive/NIMBioS.code/shiny_parameters/serverInit.R Archive/NIMBioS.code/shiny_parameters/serverplots.R Archive/NIMBioS.code/shiny_parameters/setup.R Archive/NIMBioS.code/shiny_parameters/simcoal-history.R Archive/NIMBioS.code/shiny_parameters/simcoal-server.R

Archive/NIMBioS.code/shiny_parameters/test.ssClass.rdata

Archive/NIMBioS.code/shiny_parameters/ui.R Archive/NIMBioS.code/shiny_parameters/utils.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/global.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/helpfiles/help-history.md Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/helpfiles/help-migration.md Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/helpfiles/help-questions.md Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/intro-questions-server.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/make-skelesim-class.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/mig.matrix.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/paramsLoad.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/paramsSave.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/renderUI.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/scenarios.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/server.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/serverplots.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/setup.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/simRun.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/simcoal-history.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/simcoal-server.R

Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/test.ssClass.rdata

Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/ui.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters/utils.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/genparam-server.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/global.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/helpfiles/help-history.md Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/helpfiles/help-migration.md Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/helpfiles/help-questions.md Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/intro-questions-server.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/make-skelesim-class.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/mig.matrix.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/renderUI.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/runSim.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/saveParams.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/scenarios-server.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/server.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/serverplots.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/setup.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/simcoal-history.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/simcoal-server.R

Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/test.ssClass.rdata

Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/ui.R Archive/NIMBioS.code/shinyparameters.old/shiny_parameters_reactiveValues/utils.R Archive/NIMBioS.code/skeleSim.classes.R Archive/NIMBioS.code/skeleSim.funcs.R Archive/NIMBioS.code/summ.stats.table.R Archive/NIMBioS.code/test.runSim.R

Archive/NIMBioS.code/test.ssClass.rdata

Archive/NIMBioS.code/testRunFastsimcoal.R Archive/NIMBioS.code/testRunMetaSim.R

Archive/doc/DIPnetResultsTemplate.xlsx

Archive/doc/circle.pdf

Archive/doc/new_screens/Tutorial1/screen1_Actions.png

Archive/doc/new_screens/Tutorial1/screen2_Gen_Conf.png

Archive/doc/new_screens/Tutorial1/screen3_Pop_Samp_Sizes.png

Archive/doc/new_screens/Tutorial1/screen4_Migr_rate.png

Archive/doc/new_screens/Tutorial1/screen5_Loc_Mut_rate.png

Archive/doc/new_screens/Tutorial1/screen6_Metasim_pop_matrices.png

Archive/doc/new_screens/Tutorial1/screen7_Metasim_allele_freq.png

Archive/doc/new_screens/Tutorial1/screen8_ssClass.png

Archive/doc/new_screens/Tutorial1/screen9_Scen2_diff_migr.png

Archive/doc/new_screens/Tutorial2/screen2_GenConf.JPG

Archive/doc/new_screens/Tutorial2/screen3_ScenConf.JPG

Archive/doc/new_screens/Tutorial2/screen5_migr_rates.JPG

Archive/doc/new_screens/Tutorial2/screen6_loci.JPG

Archive/doc/new_screens/Tutorial2/screen7_simcoal_history.JPG

Archive/doc/old_screens/action-tab.png

Archive/doc/old_screens/file

Archive/doc/old_screens/general-tab.png

Archive/doc/old_screens/intro-questions.png

Archive/doc/old_screens/rmetasim-1.png

Archive/doc/old_screens/rmetasim-2.png

Archive/doc/old_screens/scenario-1.png

Archive/doc/old_screens/scenario-2.png

Archive/doc/old_screens/scenario-3.png

Archive/doc/old_screens/simcoal1.png

Archive/doc/old_screens/simcoal2.png

Archive/doc/old_screens/simcoal3.png

Archive/doc/shiny-intro-slides.pdf Archive/doc/shiny-intro.pdf Archive/mer_submission.pdf

Archive/sample.data/ssc.fscSEQ.rda

Archive/sample.data/ssc.fscSSR.rda

Archive/sample.data/ssc.rmsSEQ.rda

Archive/sample.data/ssc.rmsSSR.rda

Archive/test.code/100loci.issue/all4outputs.rda

Archive/test.code/100loci.issue/fscSEQ.1.10-1.par

Archive/test.code/100loci.issue/fscSEQ.2.10-2.par

Archive/test.code/Analysis_working_codeBits_MEDL.R

Archive/test.code/Connect or not out puts from SkeleSim/Connect or not Sn1.rdata

Archive/test.code/Connect or not out puts from SkeleSim/Connect or not Sn2.rdata

Archive/test.code/Connect or not out puts from SkeleSim/Connect_or_not.20170215.1437.2230.params.rdata

Archive/test.code/Connect or not out puts from SkeleSim/Connect_or_not.20170215.1437.2230.script.R

Archive/test.code/Connect or not out puts from SkeleSim/Connect_or_not.20170215.1437.2230.script.Rout

Archive/test.code/Connect.or.not.out.puts.from.SkeleSim.zip

Archive/test.code/Connect_or_not.20170215.1437.2230.params.zip

Archive/test.code/analysis_funcs.R Archive/test.code/calcMratio.R Archive/test.code/connect_or_not-1-landscape-fun.R Archive/test.code/connect_or_not-2-landscape-fun.R

Archive/test.code/connect_or_not.20160418.1234.4075.params.rdata

Archive/test.code/connect_or_not.20160418.1234.4075.script.R

Archive/test.code/connect_or_not.20160418.1235.1353.params.rdata

Archive/test.code/connect_or_not.20160418.1235.1353.script.R Archive/test.code/create multidna test data.R

Archive/test.code/fsc.testing/fastsimcoal.output.par

Archive/test.code/fsc.testing/fsc code.R Archive/test.code/fsc.testing/fsc test script.R Archive/test.code/fsc.testing/fsc.classes.R Archive/test.code/fsc.testing/fsc.histEvMat.R Archive/test.code/fsc.testing/fsc.loadScenario.R Archive/test.code/fsc.testing/fsc.run.R

Archive/test.code/fsc.testing/fsc.run.par

Archive/test.code/fsc.testing/fsc.run/fsc.run_1.arb

Archive/test.code/fsc.testing/fsc.run/fsc.run_1.simparam

Archive/test.code/fsc.testing/fsc.run/fsc.run_1_1.arp

Archive/test.code/fsc.testing/fsc.scenarioCheck.R

Archive/test.code/fsc.testing/seed.txt

Archive/test.code/fscSSR.20160517.1149.6906.params.rdata

Archive/test.code/fscwrite.R

Archive/test.code/multidna test data.rdata

Archive/test.code/multigene sapply example.R

Archive/test.code/paiklinsawat/t1.rdata

Archive/test.code/paiklinsawat/wdTest/g.rda

Archive/test.code/paiklinsawat/wdTest/tmpskeleland.rda

Archive/test.code/phist test g.rdata

Archive/test.code/skelesimulations/Readme.txt

Archive/test.code/skelesimulations/fsc simulator errors.txt

Archive/test.code/skelesimulations/prova.20170518.1123.4808.params.rdata

Archive/test.code/skelesimulations/rmetasim errors.txt

Archive/test.code/skelesimulations/sessionInfo.txt

Archive/test.code/skelesimulations/sessionInfo2.txt

Archive/test.code/skelesimulations/tryfor.20170518.1113.5335.params.rdata

Archive/test.code/test g.rdata

Archive/test.code/test.20160308.1226.2546.params.rdata

Archive/test.code/test.20160320.1328.6482.params.rdata

Archive/test.code/test.genind2hierfstat.R

Archive/test.code/testRun result.rdata

Archive/test.code/testRun.wd/seed.txt

Archive/test.code/testRun.wd/testRun.1.1.results.gtype.rdata

Archive/test.code/testRun.wd/testRun.1.1/testRun.1.1.params.rdata

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Archive/test.code/testRun.wd/testRun.1.2/testRun.1.2.params.rdata

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Archive/test.code/testRun.wd/testRun.1.3/testRun.1.3.params.rdata

Archive/test.code/testRun.wd/testRun.1.4.results.gtype.rdata

Archive/test.code/testRun.wd/testRun.1.4/testRun.1.4.params.rdata

Archive/test.code/testRunFastsimcoal.R Archive/test.code/testRunMetaSim.R

Archive/test.code/wdTest3/fscSSR.1.1.results.gtype.rdata

Archive/test.code/wdTest3/fscSSR.1.1/fscSSR.1.1.params.rdata

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Archive/test.code/wdTest3/fscSSR.3.6/fscSSR.3.6.params.rdata

Archive/test.code/wdTest3/seed.txt

DESCRIPTION

NAMESPACE

R/analysis.funcs.R R/fsc.classes.R R/fsc.loadScenario.R R/fsc.run.R R/fsc.scenarioCheck.R R/getGammaMutRates.R R/rms.classes.R R/rms.convert.R R/rms.init.land.function.R R/rms.init.landscape.R R/rms.internals.R R/rms.run.R R/rms.scenarioCheck.R R/runSim.R R/skeleSim-package.R R/skeleSim.checks.R R/skeleSim.classes.R R/skeleSim.internals.R R/skeleSimGUI.R README.md

appveyor.yml

inst/shiny/skeleSimShinyGUI/README.md inst/shiny/skeleSimShinyGUI/debug.R inst/shiny/skeleSimShinyGUI/global.R inst/shiny/skeleSimShinyGUI/helpfiles/file-ops.md inst/shiny/skeleSimShinyGUI/helpfiles/help-history.md inst/shiny/skeleSimShinyGUI/helpfiles/help-migration.md inst/shiny/skeleSimShinyGUI/helpfiles/help-questions.md inst/shiny/skeleSimShinyGUI/helpfiles/lefkovitch.md inst/shiny/skeleSimShinyGUI/helpfiles/load-params.md inst/shiny/skeleSimShinyGUI/helpfiles/rmetasim-alleles.md inst/shiny/skeleSimShinyGUI/helpfiles/rmetasim-loci.md inst/shiny/skeleSimShinyGUI/helpfiles/save-params.md inst/shiny/skeleSimShinyGUI/helpfiles/simulations.md inst/shiny/skeleSimShinyGUI/helpfiles/skelesim-general-help.md inst/shiny/skeleSimShinyGUI/intro-questions-server.R inst/shiny/skeleSimShinyGUI/loadParams.R inst/shiny/skeleSimShinyGUI/make-skelesim-class.R inst/shiny/skeleSimShinyGUI/mig.matrix.R inst/shiny/skeleSimShinyGUI/modules/matrixInputs.R inst/shiny/skeleSimShinyGUI/modules/tableinput.R inst/shiny/skeleSimShinyGUI/rmetasim-server.R inst/shiny/skeleSimShinyGUI/runSim.R inst/shiny/skeleSimShinyGUI/sanity-checks.R inst/shiny/skeleSimShinyGUI/saveParams.R inst/shiny/skeleSimShinyGUI/scenarios-server.R inst/shiny/skeleSimShinyGUI/server.R inst/shiny/skeleSimShinyGUI/serverInit.R inst/shiny/skeleSimShinyGUI/serverplots.R inst/shiny/skeleSimShinyGUI/simcoal-history.R inst/shiny/skeleSimShinyGUI/simcoal-server.R

inst/shiny/skeleSimShinyGUI/test.ssClass.rdata

inst/shiny/skeleSimShinyGUI/ui.R inst/shiny/skeleSimShinyGUI/update-ui.R inst/shiny/skeleSimShinyGUI/utils.R inst/shiny/skeleSimShinyGUI/visualize.R inst/shiny/skeleSimShinyGUI/vizAbstract.R inst/shiny/skeleSimShinyGUI/vizServer.R inst/shiny/skeleSimShinyGUI/vizfuncs.R

inst/tableinput/tableinput.css

inst/tableinput/tableinput.js

man/analysis.funcs.Rd man/fastsimcoal.params-class.Rd man/fsc.loadScenario.Rd man/fsc.run.Rd man/fsc.scenarioCheck.Rd man/fsc.write.Rd man/getGammaMutRates.Rd man/rmetasim.classes.Rd man/rms.convert.Rd man/rms.init.landscape.Rd man/rms.init.landscape.func.Rd man/rms.run.Rd man/rms.scenarioCheck.Rd man/rms.write.Rd man/runSim.Rd man/skeleSim-package.Rd man/skeleSim.checks.Rd man/skeleSim.classes.Rd man/skeleSim.internals.Rd man/skeleSimGUI.Rd

skeleSim.Rproj

vignettes/Choosemetasim.png

vignettes/Choosermetasim2.png

vignettes/ForecastImages/RmetasimLocus.png

vignettes/ForecastImages/screen1_Actions.png

vignettes/ForecastImages/screen2_Gen_Conf.png

vignettes/ForecastImages/screen3_Pop_Samp_Sizes.png

vignettes/ForecastImages/screen4_Migr_rate.png

vignettes/ForecastImages/screen5_Loc_Mut_rate.png

vignettes/ForecastImages/screen6_Metasim_pop_matrices.png

vignettes/ForecastImages/screen7_Metasim_allele_freq.png

vignettes/ForecastImages/screen8_ssClass.png

vignettes/ForecastImages/screen9_Scen2_diff_migr.png

vignettes/Forecasting.R vignettes/Forecasting.Rmd

vignettes/Forecasting.html

vignettes/Installing.R vignettes/Installing.Rmd

vignettes/Installing.html

vignettes/SampleSize.R vignettes/SampleSize.Rmd

vignettes/SampleSize.html

vignettes/SampleSizeImages/screen2_GenConf.JPG

vignettes/SampleSizeImages/screen3_ScenConf.JPG

vignettes/SampleSizeImages/screen5_migr_rates.JPG

vignettes/SampleSizeImages/screen6_loci.JPG

vignettes/SampleSizeImages/screen7_simcoal_history.JPG

vignettes/ScenarioConf_LocChar.png

vignettes/ScenarioConf_PopChar.png

vignettes/Simulating.R vignettes/Simulating.Rmd

vignettes/Simulating.html

vignettes/obsvdheterozygosity.png

christianparobek/skeleSim documentation built on Feb. 29, 2020, 6:58 p.m.