├── .Rbuildignore ├── .github └── workflows │ ├── R-CMD-check.yaml │ └── r.yml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── RcppExports.R ├── bayou-custommodel-input.R ├── bayou-deprecated.R ├── bayou-likelihood.R ├── bayou-mcmc-utilities.R ├── bayou-mcmc.R ├── bayou-models.R ├── bayou-moves.R ├── bayou-package.R ├── bayou-plotting.R ├── bayou-prior.R ├── bayou-simulation.r ├── bayou-steppingstone.R ├── bayou-utilities.R ├── bayou-weight_matrix.R ├── conversion-utilities.R ├── probability.R └── teaching-functions.R ├── README.md ├── figure ├── unnamed-chunk-10.png ├── unnamed-chunk-121.png ├── unnamed-chunk-122.png ├── unnamed-chunk-123.png ├── unnamed-chunk-13.png ├── unnamed-chunk-15.png ├── unnamed-chunk-16.png ├── unnamed-chunk-20.png ├── unnamed-chunk-22.png ├── unnamed-chunk-23.png ├── unnamed-chunk-24.png ├── unnamed-chunk-271.png ├── unnamed-chunk-272.png ├── unnamed-chunk-273.png ├── unnamed-chunk-274.png ├── unnamed-chunk-291.png ├── unnamed-chunk-292.png ├── unnamed-chunk-3.png ├── unnamed-chunk-33.png ├── unnamed-chunk-351.png ├── unnamed-chunk-352.png ├── unnamed-chunk-36.png ├── unnamed-chunk-37.png ├── unnamed-chunk-38.png ├── unnamed-chunk-391.png ├── unnamed-chunk-3910.png ├── unnamed-chunk-3911.png ├── unnamed-chunk-3912.png ├── unnamed-chunk-3913.png ├── unnamed-chunk-3914.png ├── unnamed-chunk-3915.png ├── unnamed-chunk-3916.png ├── unnamed-chunk-392.png ├── unnamed-chunk-393.png ├── unnamed-chunk-394.png ├── unnamed-chunk-395.png ├── unnamed-chunk-396.png ├── unnamed-chunk-397.png ├── unnamed-chunk-398.png ├── unnamed-chunk-399.png ├── unnamed-chunk-4.png ├── unnamed-chunk-81.png ├── unnamed-chunk-82.png └── unnamed-chunk-9.png ├── inst └── tests │ ├── test-data_load.r │ ├── test-likelihood.r │ ├── test-prior.r │ └── test-weight_matrix.r ├── man ├── Lposterior.Rd ├── OU.lik.Rd ├── OU.repar.Rd ├── OUphenogram.Rd ├── OUwie2bayou.Rd ├── QG.alpha.Rd ├── QG.sig2.Rd ├── bayou-deprecated.Rd ├── bayou-package.Rd ├── bayou.checkModel.Rd ├── bayou.lik.Rd ├── bayou.makeMCMC.Rd ├── bayou2OUwie.Rd ├── cdpois.Rd ├── combine.chains.Rd ├── dataSim.Rd ├── dhalfcauchy.Rd ├── dloc.Rd ├── dsb.Rd ├── gelman.R.Rd ├── identifyBranches.Rd ├── load.bayou.Rd ├── make.powerposteriorFn.Rd ├── make.prior.Rd ├── make.refFn.Rd ├── makeBayouModel.Rd ├── makeTransparent.Rd ├── model.OU.Rd ├── parmap.W.Rd ├── pars2simmap.Rd ├── phenogram.density.Rd ├── plot.bayouMCMC.Rd ├── plot.ssMCMC.Rd ├── plotBayoupars.Rd ├── plotBranchHeatMap.Rd ├── plotOUtreesim.Rd ├── plotRegimes.Rd ├── plotShiftSummaries.Rd ├── plotSimmap.mcmc.Rd ├── print.bayouFit.Rd ├── print.bayouMCMC.Rd ├── print.priorFn.Rd ├── print.refFn.Rd ├── print.ssMCMC.Rd ├── priorSim.Rd ├── pull.pars.Rd ├── regime.plot.Rd ├── set.burnin.Rd ├── shiftSummaries.Rd ├── simmapW.Rd └── summary.bayouMCMC.Rd ├── src ├── Makevars ├── RcppExports.cpp ├── branches.cpp ├── threepoint.cpp └── weightmatrix.cpp ├── tutorial.Rmd ├── tutorial.md └── tutorial.nb.html /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/.github/workflows/R-CMD-check.yaml -------------------------------------------------------------------------------- /.github/workflows/r.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/.github/workflows/r.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/.travis.yml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/RcppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/RcppExports.R -------------------------------------------------------------------------------- /R/bayou-custommodel-input.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-custommodel-input.R -------------------------------------------------------------------------------- /R/bayou-deprecated.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-deprecated.R -------------------------------------------------------------------------------- /R/bayou-likelihood.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-likelihood.R -------------------------------------------------------------------------------- /R/bayou-mcmc-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-mcmc-utilities.R -------------------------------------------------------------------------------- /R/bayou-mcmc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-mcmc.R -------------------------------------------------------------------------------- /R/bayou-models.R: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /R/bayou-moves.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-moves.R -------------------------------------------------------------------------------- /R/bayou-package.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-package.R -------------------------------------------------------------------------------- /R/bayou-plotting.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-plotting.R -------------------------------------------------------------------------------- /R/bayou-prior.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-prior.R -------------------------------------------------------------------------------- /R/bayou-simulation.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-simulation.r -------------------------------------------------------------------------------- /R/bayou-steppingstone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-steppingstone.R -------------------------------------------------------------------------------- /R/bayou-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-utilities.R -------------------------------------------------------------------------------- /R/bayou-weight_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/bayou-weight_matrix.R -------------------------------------------------------------------------------- /R/conversion-utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/conversion-utilities.R -------------------------------------------------------------------------------- /R/probability.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/probability.R -------------------------------------------------------------------------------- /R/teaching-functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/R/teaching-functions.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/README.md -------------------------------------------------------------------------------- /figure/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-10.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-121.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-121.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-122.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-122.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-123.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-123.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-13.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-15.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-15.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-16.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-20.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-22.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-22.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-23.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-23.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-24.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-24.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-271.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-271.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-272.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-272.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-273.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-273.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-274.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-274.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-291.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-291.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-292.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-292.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-33.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-351.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-351.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-352.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-352.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-36.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-37.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-37.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-38.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-38.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-391.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-391.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3910.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3910.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3911.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3911.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3912.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3912.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3913.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3913.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3914.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3914.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3915.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3915.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-3916.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-3916.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-392.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-392.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-393.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-393.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-394.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-394.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-395.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-395.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-396.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-396.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-397.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-397.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-398.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-398.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-399.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-399.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-4.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-81.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-81.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-82.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-82.png -------------------------------------------------------------------------------- /figure/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/figure/unnamed-chunk-9.png -------------------------------------------------------------------------------- /inst/tests/test-data_load.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/inst/tests/test-data_load.r -------------------------------------------------------------------------------- /inst/tests/test-likelihood.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/inst/tests/test-likelihood.r -------------------------------------------------------------------------------- /inst/tests/test-prior.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/inst/tests/test-prior.r -------------------------------------------------------------------------------- /inst/tests/test-weight_matrix.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/inst/tests/test-weight_matrix.r -------------------------------------------------------------------------------- /man/Lposterior.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/Lposterior.Rd -------------------------------------------------------------------------------- /man/OU.lik.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/OU.lik.Rd -------------------------------------------------------------------------------- /man/OU.repar.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/OU.repar.Rd -------------------------------------------------------------------------------- /man/OUphenogram.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/OUphenogram.Rd -------------------------------------------------------------------------------- /man/OUwie2bayou.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/OUwie2bayou.Rd -------------------------------------------------------------------------------- /man/QG.alpha.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/QG.alpha.Rd -------------------------------------------------------------------------------- /man/QG.sig2.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/QG.sig2.Rd -------------------------------------------------------------------------------- /man/bayou-deprecated.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/bayou-deprecated.Rd -------------------------------------------------------------------------------- /man/bayou-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/bayou-package.Rd -------------------------------------------------------------------------------- /man/bayou.checkModel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/bayou.checkModel.Rd -------------------------------------------------------------------------------- /man/bayou.lik.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/bayou.lik.Rd -------------------------------------------------------------------------------- /man/bayou.makeMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/bayou.makeMCMC.Rd -------------------------------------------------------------------------------- /man/bayou2OUwie.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/bayou2OUwie.Rd -------------------------------------------------------------------------------- /man/cdpois.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/cdpois.Rd -------------------------------------------------------------------------------- /man/combine.chains.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/combine.chains.Rd -------------------------------------------------------------------------------- /man/dataSim.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/dataSim.Rd -------------------------------------------------------------------------------- /man/dhalfcauchy.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/dhalfcauchy.Rd -------------------------------------------------------------------------------- /man/dloc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/dloc.Rd -------------------------------------------------------------------------------- /man/dsb.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/dsb.Rd -------------------------------------------------------------------------------- /man/gelman.R.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/gelman.R.Rd -------------------------------------------------------------------------------- /man/identifyBranches.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/identifyBranches.Rd -------------------------------------------------------------------------------- /man/load.bayou.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/load.bayou.Rd -------------------------------------------------------------------------------- /man/make.powerposteriorFn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/make.powerposteriorFn.Rd -------------------------------------------------------------------------------- /man/make.prior.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/make.prior.Rd -------------------------------------------------------------------------------- /man/make.refFn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/make.refFn.Rd -------------------------------------------------------------------------------- /man/makeBayouModel.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/makeBayouModel.Rd -------------------------------------------------------------------------------- /man/makeTransparent.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/makeTransparent.Rd -------------------------------------------------------------------------------- /man/model.OU.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/model.OU.Rd -------------------------------------------------------------------------------- /man/parmap.W.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/parmap.W.Rd -------------------------------------------------------------------------------- /man/pars2simmap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/pars2simmap.Rd -------------------------------------------------------------------------------- /man/phenogram.density.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/phenogram.density.Rd -------------------------------------------------------------------------------- /man/plot.bayouMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plot.bayouMCMC.Rd -------------------------------------------------------------------------------- /man/plot.ssMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plot.ssMCMC.Rd -------------------------------------------------------------------------------- /man/plotBayoupars.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plotBayoupars.Rd -------------------------------------------------------------------------------- /man/plotBranchHeatMap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plotBranchHeatMap.Rd -------------------------------------------------------------------------------- /man/plotOUtreesim.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plotOUtreesim.Rd -------------------------------------------------------------------------------- /man/plotRegimes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plotRegimes.Rd -------------------------------------------------------------------------------- /man/plotShiftSummaries.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plotShiftSummaries.Rd -------------------------------------------------------------------------------- /man/plotSimmap.mcmc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/plotSimmap.mcmc.Rd -------------------------------------------------------------------------------- /man/print.bayouFit.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/print.bayouFit.Rd -------------------------------------------------------------------------------- /man/print.bayouMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/print.bayouMCMC.Rd -------------------------------------------------------------------------------- /man/print.priorFn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/print.priorFn.Rd -------------------------------------------------------------------------------- /man/print.refFn.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/print.refFn.Rd -------------------------------------------------------------------------------- /man/print.ssMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/print.ssMCMC.Rd -------------------------------------------------------------------------------- /man/priorSim.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/priorSim.Rd -------------------------------------------------------------------------------- /man/pull.pars.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/pull.pars.Rd -------------------------------------------------------------------------------- /man/regime.plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/regime.plot.Rd -------------------------------------------------------------------------------- /man/set.burnin.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/set.burnin.Rd -------------------------------------------------------------------------------- /man/shiftSummaries.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/shiftSummaries.Rd -------------------------------------------------------------------------------- /man/simmapW.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/simmapW.Rd -------------------------------------------------------------------------------- /man/summary.bayouMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/man/summary.bayouMCMC.Rd -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/RcppExports.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/src/RcppExports.cpp -------------------------------------------------------------------------------- /src/branches.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/src/branches.cpp -------------------------------------------------------------------------------- /src/threepoint.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/src/threepoint.cpp -------------------------------------------------------------------------------- /src/weightmatrix.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/src/weightmatrix.cpp -------------------------------------------------------------------------------- /tutorial.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/tutorial.Rmd -------------------------------------------------------------------------------- /tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/tutorial.md -------------------------------------------------------------------------------- /tutorial.nb.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uyedaj/bayou/HEAD/tutorial.nb.html --------------------------------------------------------------------------------