Files in admixturegraph
Admixture Graph Manipulation and Fitting
MD5
DESCRIPTION
README.md
NAMESPACE
inst/doc/admixturegraph.html
inst/doc/admixturegraph.R
inst/doc/admixturegraph.Rmd
vignettes/bibliography.bib
vignettes/admixturegraph.md
vignettes/admixturegraph.Rmd
vignettes/admixturegraph_files/figure-html/new_root-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-2.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-1-1.png
vignettes/admixturegraph_files/figure-html/new_admixtures-1.png
vignettes/admixturegraph_files/figure-html/new_leaves-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-9-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-2.png
vignettes/admixturegraph_files/figure-html/bears_graph-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-1.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-4-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-3.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-3-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-4.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-5-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-11-1.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-10-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-12-1.png
vignettes/admixturegraph_files/figure-html/unnamed-chunk-8-1.png
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-3.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-5-1.pdf
vignettes/admixturegraph_files/figure-latex/new_leaves-1.pdf
vignettes/admixturegraph_files/figure-latex/bears_graph-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-4.pdf
vignettes/admixturegraph_files/figure-latex/new_admixtures-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-13-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-6-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-11-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-4-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-2.pdf
vignettes/admixturegraph_files/figure-latex/new_root-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-14-1.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-15-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-12-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-9-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-2.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-1-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-3-1.pdf
vignettes/admixturegraph_files/figure-latex/unnamed-chunk-7-1.pdf
R/data.R
R/paths.R
R/fitted_plotting.R
R/overlaps.R
R/plot.R
R/propose.R
R/admixture_graph.R
R/filter.R
R/evaluate-f-statistics.R
R/f-statistics.R
R/mcmc.R
R/project_and_split.R
R/signs.R
R/summary-statistics.R
R/fitting.R
R/f4_plotting.R
R/symbolic-f-statistics.R
R/agraph.R
man/graphs_4_1.Rd
man/f3.Rd
man/mynonneg.Rd
man/make_an_outgroup.Rd
man/sf3.Rd
man/six_leaves_graphs.Rd
man/graphs_6_1.Rd
man/make_mcmc_model.Rd
man/is_unknown.Rd
man/graph_to_vector.Rd
man/calculate_concentration.Rd
man/sf2.Rd
man/graphs_7_0.Rd
man/split_population.data.frame.Rd
man/graphs_5_0.Rd
man/sum_of_squared_errors.Rd
man/graphs_6_2.Rd
man/seven_leaves_trees.Rd
man/add_graph_f4.Rd
man/fit_permutations_and_graphs.Rd
man/parent_edges.Rd
man/sum_of_squared_errors.agraph_fit.Rd
man/add_a_leaf.Rd
man/get_graph_f4_sign.Rd
man/eight_leaves_trees.Rd
man/sf4.Rd
man/no_poor_fits.agraph_fit_list.Rd
man/seven_leaves_graphs.Rd
man/admixture_proportions.Rd
man/graphs_3_0.Rd
man/poor_fits.agraph_fit.Rd
man/graphs_2_0.Rd
man/model_likelihood.Rd
man/summary.agraph_fit.Rd
man/all_paths.Rd
man/residuals.agraph_fit.Rd
man/burn_in.Rd
man/split_population.agraph_fit.Rd
man/vector_to_graph.Rd
man/plot_fit_2.Rd
man/split_population.Rd
man/path_overlap.Rd
man/rename_nodes.Rd
man/model_likelihood_n.Rd
man/extract_trees.Rd
man/agraph_weights.Rd
man/extract_graph_parameters.Rd
man/no_admixture_events.agraph_fit_list.Rd
man/fitted.agraph_fit.Rd
man/graphs_5_2.Rd
man/plot.f4stats.Rd
man/agraph.Rd
man/overlaps_sign.Rd
man/plot.agraph.Rd
man/graphs_8_0.Rd
man/canonise_graph.Rd
man/admixturegraph-package.Rd
man/no_admixture_events.agraph.Rd
man/examine_edge_optimisation_matrix.Rd
man/graphs_7_1.Rd
man/edge.Rd
man/model_bayes_factor_n.Rd
man/print.agraph_fit.Rd
man/thinning.Rd
man/f4stats.Rd
man/poor_fits.agraph_fit_list.Rd
man/no_poor_fits.Rd
man/add_an_admixture.Rd
man/fast_fit.Rd
man/plot.agraph_fit.Rd
man/bears.Rd
man/graphs_6_0.Rd
man/five_leaves_graphs.Rd
man/all_path_overlaps.Rd
man/is_descendant_of.Rd
man/extract_admixture_proportion_parameters.Rd
man/fit_graph.Rd
man/is_positive.Rd
man/fit_graph_list.Rd
man/run_metropolis_hasting.Rd
man/is_negative.Rd
man/project_to_population.Rd
man/poor_fits.Rd
man/graph_environment.Rd
man/plot_fit_1.Rd
man/no_admixture_events.Rd
man/four_leaves_graphs.Rd
man/make_permutations.Rd
man/edge_optimisation_function.Rd
man/agraph_parents.Rd
man/add_graph_f4_sign.Rd
man/fast_plot.Rd
man/coef.agraph_fit.Rd
man/f2.Rd
man/graphs_5_1.Rd
man/admix_props.Rd
man/cost_function.Rd
man/filter_on_leaves.Rd
man/evaluate_f4.Rd
man/agraph_children.Rd
man/canonise_expression.Rd
man/remove_duplicates.Rd
man/admixture_edge.Rd
man/format_path.Rd
man/all_graphs.Rd
man/log_likelihood.Rd
man/graphs_4_2.Rd
man/no_poor_fits.agraph_fit.Rd
man/sum_of_squared_errors.agraph_fit_list.Rd
man/no_admixture_events.agraph_fit.Rd
man/is_zero.Rd
man/log_sum_of_logs.Rd
man/add_an_admixture2.Rd
man/graphs_3_1.Rd
man/graphs_4_0.Rd
man/build_edge_optimisation_matrix.Rd
man/f4.Rd
build/vignette.rds
tests/testthat.R
tests/testthat/test_path_overlaps.R
tests/testthat/test_paths.R
tests/testthat/test_graph_construction.R
tests/testthat/test_signs.R
tests/testthat/test_f_statistics.R
tests/testthat/test_plots.R
data/graphs_5_2.RData
data/graphs_6_0.RData
data/graphs_4_2.RData
data/graphs_7_0.RData
data/graphs_5_1.RData
data/graphs_4_1.RData
data/bears.RData
data/graphs_8_0.RData
data/graphs_7_1.RData
data/graphs_6_1.RData
data/graphs_3_1.RData
data/graphs_6_2.RData
data/graphs_2_0.RData
data/graphs_5_0.RData
data/graphs_4_0.RData
data/graphs_3_0.RData
data/datalist
