├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── admix.R ├── averagePairWiseSimilarityH.R ├── averageQ.R ├── bestK.R ├── clumpak.R ├── clumpp.R ├── fineStruct.R ├── get-methods.R ├── loadAdmixture.R ├── loadFineStructure.R ├── loadStructure.R ├── plotBar.R ├── plotFineStructDendro.R ├── plotMCMC.R ├── plotMDS.R ├── plotMultiK.R ├── plotPWCoancestry.R ├── plotPWCoincidence.R ├── plotTreeBar.R ├── run-structure.R ├── simulateQmatrix.R └── struct.R ├── README.Rmd ├── README.md ├── cran-comments.md ├── inst ├── extdata │ ├── fine_structure_files │ │ ├── EastAsiaSimple.EMlinked.chunkcounts.out │ │ ├── EastAsiaSimple.EMlinked.mapstate.csv │ │ ├── EastAsiaSimple.EMlinked.mcmc.xml │ │ ├── EastAsiaSimple.EMlinked.meancoincidence.csv │ │ └── EastAsiaSimple.EMlinked.tree.xml │ ├── hapmap3_files │ │ ├── hapmap3.1.P │ │ ├── hapmap3.1.Q │ │ ├── hapmap3.2.P │ │ ├── hapmap3.2.Q │ │ ├── hapmap3.3.P │ │ ├── hapmap3.3.Q │ │ ├── hapmap3.3.Q_bias │ │ ├── hapmap3.3.Q_se │ │ ├── hapmap3.4.P │ │ ├── hapmap3.4.Q │ │ ├── hapmap3.5.P │ │ ├── hapmap3.5.Q │ │ ├── hapmap3.fam │ │ ├── hapmap3.map │ │ ├── log1.out │ │ ├── log2.out │ │ ├── log3.out │ │ ├── log4.out │ │ └── log5.out │ └── microsat_testfiles │ │ ├── chain_K10.log │ │ ├── chain_K6.log │ │ ├── extraparams │ │ ├── locprior.str │ │ ├── locprior_K1.out_f │ │ ├── locprior_K10.out_f │ │ ├── locprior_K2.out_f │ │ ├── locprior_K3.out_f │ │ ├── locprior_K4.out_f │ │ ├── locprior_K5.out_f │ │ ├── locprior_K6.out_f │ │ ├── locprior_K7.out_f │ │ ├── locprior_K8.out_f │ │ ├── locprior_K9.out_f │ │ ├── mainparams │ │ ├── run10_chain_K10.log │ │ ├── run10_locprior_K10.out_f │ │ ├── run2_chain_K10.log │ │ ├── run2_chain_K6.log │ │ ├── run2_locprior_K1.out_f │ │ ├── run2_locprior_K10.out_f │ │ ├── run2_locprior_K2.out_f │ │ ├── run2_locprior_K3.out_f │ │ ├── run2_locprior_K4.out_f │ │ ├── run2_locprior_K5.out_f │ │ ├── run2_locprior_K6.out_f │ │ ├── run2_locprior_K7.out_f │ │ ├── run2_locprior_K8.out_f │ │ ├── run2_locprior_K9.out_f │ │ ├── run3_chain_K10.log │ │ ├── run3_locprior_K10.out_f │ │ ├── run4_chain_K10.log │ │ ├── run4_locprior_K10.out_f │ │ ├── run5_chain_K10.log │ │ ├── run5_locprior_K10.out_f │ │ ├── run6_chain_K10.log │ │ ├── run6_locprior_K10.out_f │ │ ├── run7_chain_K10.log │ │ ├── run7_locprior_K10.out_f │ │ ├── run8_chain_K10.log │ │ ├── run8_locprior_K10.out_f │ │ ├── run9_chain_K10.log │ │ └── run9_locprior_K10.out_f └── vignette-supp │ ├── clump-example-1.png │ ├── evanno-lyf-1.png │ ├── evanno-lyf-2.png │ ├── mcmc1-1.png │ ├── plot-bar-1.png │ ├── plot-bar2-1.png │ ├── plot-multiK-1.png │ ├── plotMDS-1.png │ ├── unnamed-chunk-2-1.png │ └── unnamed-chunk-5-1.png ├── man ├── admix.Rd ├── admixList.Rd ├── averagePairWiseSimilarityH.Rd ├── averageQ.Rd ├── bestK.Rd ├── clumpak.Rd ├── clumpp.Rd ├── exampleAdmixture.Rd ├── exampleStructure.Rd ├── fineStruct.Rd ├── getClusterAlleleFreqMat.Rd ├── getCompleteAlleleFreqMat.Rd ├── getD.Rd ├── getK.Rd ├── getQ.Rd ├── getStephens.Rd ├── loadAdmixture.Rd ├── loadFineStructure.Rd ├── loadStructure.Rd ├── plotBar.Rd ├── plotFineStructDendro.Rd ├── plotMCMC.Rd ├── plotMDS.Rd ├── plotMultiK.Rd ├── plotPWCoancestry.Rd ├── plotPWCoincidence.Rd ├── plotTreeBar.Rd ├── runStructure.Rd ├── simulateQ.Rd ├── struct.Rd └── structList.Rd ├── starmie.Rproj ├── tests ├── testthat.R └── testthat │ ├── test-bestK.R │ ├── test-clumpp.R │ ├── test-loadAdmixture.R │ ├── test-loadStructure.R │ └── test-plotMCMC.R └── vignettes ├── using-starmie-admixture.Rmd └── using-starmie.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sa-lee/starmie/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sa-lee/starmie/HEAD/.gitignore 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