Files in mailund/admixture_graph
Admixture Graph Manipulation and Fitting

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md R/admixture_graph.R R/agraph.R R/data.R R/evaluate-f-statistics.R R/export.R R/f-statistics.R R/f4_plotting.R R/filter.R R/fitted_plotting.R R/fitting.R R/mcmc.R R/overlaps.R R/paths.R R/plot.R R/project_and_split.R R/propose.R R/signs.R R/summary-statistics.R R/symbolic-f-statistics.R
README-fitted_data-1.png
README-graph-1.png
README.Rmd README.md
README_cache/markdown_github/__packages
README_cache/markdown_github/unnamed-chunk-3_a41d20584bc77181b0ba71b185d8e4c9.RData
README_cache/markdown_github/unnamed-chunk-3_a41d20584bc77181b0ba71b185d8e4c9.rdb
README_cache/markdown_github/unnamed-chunk-3_a41d20584bc77181b0ba71b185d8e4c9.rdx
admixture_graph.Rproj
admixture_graph.Rproj.Rcheck/00check.log
cran-comments.md
data/bears.RData
data/graphs_2_0.RData
data/graphs_3_0.RData
data/graphs_3_1.RData
data/graphs_4_0.RData
data/graphs_4_1.RData
data/graphs_4_2.RData
data/graphs_5_0.RData
data/graphs_5_1.RData
data/graphs_5_2.RData
data/graphs_6_0.RData
data/graphs_6_1.RData
data/graphs_6_2.RData
data/graphs_7_0.RData
data/graphs_7_1.RData
data/graphs_8_0.RData
man/add_a_leaf.Rd man/add_an_admixture.Rd man/add_an_admixture2.Rd man/add_graph_f4.Rd man/add_graph_f4_sign.Rd man/admix_props.Rd man/admixture_edge.Rd man/admixture_proportions.Rd man/admixturegraph-package.Rd man/agraph.Rd man/agraph_children.Rd man/agraph_parents.Rd man/agraph_weights.Rd man/all_graphs.Rd man/all_path_overlaps.Rd man/all_paths.Rd man/bears.Rd man/build_edge_optimisation_matrix.Rd man/burn_in.Rd man/calculate_concentration.Rd man/canonise_expression.Rd man/canonise_graph.Rd man/coef.agraph_fit.Rd man/cost_function.Rd man/edge.Rd man/edge_optimisation_function.Rd man/eight_leaves_trees.Rd man/evaluate_f4.Rd man/examine_edge_optimisation_matrix.Rd man/export_to_qpGraph.Rd man/extract_admixture_proportion_parameters.Rd man/extract_graph_parameters.Rd man/extract_trees.Rd man/f2.Rd man/f3.Rd man/f4.Rd man/f4stats.Rd man/fast_fit.Rd man/fast_plot.Rd man/filter_on_leaves.Rd man/fit_graph.Rd man/fit_graph_list.Rd man/fit_permutations_and_graphs.Rd man/fitted.agraph_fit.Rd man/five_leaves_graphs.Rd man/format_path.Rd man/four_leaves_graphs.Rd man/get_graph_f4_sign.Rd man/graph_environment.Rd man/graph_to_vector.Rd man/graphs_2_0.Rd man/graphs_3_0.Rd man/graphs_3_1.Rd man/graphs_4_0.Rd man/graphs_4_1.Rd man/graphs_4_2.Rd man/graphs_5_0.Rd man/graphs_5_1.Rd man/graphs_5_2.Rd man/graphs_6_0.Rd man/graphs_6_1.Rd man/graphs_6_2.Rd man/graphs_7_0.Rd man/graphs_7_1.Rd man/graphs_8_0.Rd man/is_descendant_of.Rd man/is_negative.Rd man/is_positive.Rd man/is_unknown.Rd man/is_zero.Rd man/log_likelihood.Rd man/log_sum_of_logs.Rd man/make_an_outgroup.Rd man/make_mcmc_model.Rd man/make_permutations.Rd man/model_bayes_factor_n.Rd man/model_likelihood.Rd man/model_likelihood_n.Rd man/mynonneg.Rd man/no_admixture_events.Rd man/no_admixture_events.agraph.Rd man/no_admixture_events.agraph_fit.Rd man/no_admixture_events.agraph_fit_list.Rd man/no_poor_fits.Rd man/no_poor_fits.agraph_fit.Rd man/no_poor_fits.agraph_fit_list.Rd man/overlaps_sign.Rd man/parent_edges.Rd man/path_overlap.Rd man/plot.agraph.Rd man/plot.agraph_fit.Rd man/plot.f4stats.Rd man/plot_fit_1.Rd man/plot_fit_2.Rd man/poor_fits.Rd man/poor_fits.agraph_fit.Rd man/poor_fits.agraph_fit_list.Rd man/print.agraph_fit.Rd man/project_to_population.Rd man/remove_duplicates.Rd man/rename_nodes.Rd man/residuals.agraph_fit.Rd man/run_metropolis_hasting.Rd man/seven_leaves_graphs.Rd man/seven_leaves_trees.Rd man/sf2.Rd man/sf3.Rd man/sf4.Rd man/six_leaves_graphs.Rd man/split_population.Rd man/split_population.agraph_fit.Rd man/split_population.data.frame.Rd man/sum_of_squared_errors.Rd man/sum_of_squared_errors.agraph_fit.Rd man/sum_of_squared_errors.agraph_fit_list.Rd man/summary.agraph_fit.Rd man/thinning.Rd man/vector_to_graph.Rd test.R tests/testthat.R tests/testthat/test_f_statistics.R tests/testthat/test_graph_construction.R tests/testthat/test_path_overlaps.R tests/testthat/test_paths.R tests/testthat/test_plots.R tests/testthat/test_signs.R vignettes/admixturegraph.R vignettes/admixturegraph.Rmd vignettes/admixturegraph.md
vignettes/admixturegraph_files/figure-html/bears_graph-1.png
vignettes/admixturegraph_files/figure-html/new_admixtures-1.png
vignettes/admixturegraph_files/figure-html/new_leaves-1.png
vignettes/admixturegraph_files/figure-html/new_root-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-1-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-10-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-11-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-12-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-13-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-14-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-3.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-4.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-3-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-4-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-5-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-6-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-7-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-8-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-9-1.png
vignettes/admixturegraph_files/figure-latex/bears_graph-1.pdf vignettes/admixturegraph_files/figure-latex/new_admixtures-1.pdf vignettes/admixturegraph_files/figure-latex/new_leaves-1.pdf vignettes/admixturegraph_files/figure-latex/new_root-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-1-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-11-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-12-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-13-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-14-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-2.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-2.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-2.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-3.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-4.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-3-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-4-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-5-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-6-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-7-1.pdf vignettes/admixturegraph_files/figure-latex/unnamed-chunk-9-1.pdf
vignettes/bibliography.bib
mailund/admixture_graph documentation built on April 3, 2018, 9:28 p.m.