d712c4fadc1785f1e1b25f00cb750383 *DESCRIPTION
a91f2e4e8911bea9f5ef140c54d982be *NAMESPACE
295ff33049e49c76246345cfa1a9aa69 *R/admixture_graph.R
99c9ed6a852e8d0b9481da22755864b0 *R/agraph.R
d2e9b7818f2a9779549bcfbf21f68308 *R/data.R
67b5edd0e2fc569bf0b861bc13961037 *R/evaluate-f-statistics.R
d27892badf6a977ebf4fcd2b50a86e63 *R/f-statistics.R
4420d0e4d777279ab8bdd2171247004b *R/f4_plotting.R
1b5634ef27ff49877e8bb721a8f01bc3 *R/filter.R
282bb967cbf25077e887a57fe91ecb85 *R/fitted_plotting.R
2677b3bf70242f48edf0216ef5114877 *R/fitting.R
9cfbe70f67f18d91cf6d86eb7dd9b936 *R/mcmc.R
84851d4e83d28d215e29250ccd91be09 *R/overlaps.R
c10e2436120c5d84adf43599a0bc61f9 *R/paths.R
c74bfb6d6a742d203fe40377ebdbb84d *R/plot.R
6e551ff80af797e470997103d3f2e608 *R/project_and_split.R
abfd82625915cf959e81f700b62b5404 *R/propose.R
6e7007b88c2626e6a5526459295b487b *R/signs.R
b6204fe5d6cbdf669e630a9ca9c147a9 *R/summary-statistics.R
b90c766bf875b0b59ad5260e86cd3eed *R/symbolic-f-statistics.R
0b4a0edbc05b1d8e78c293001a2b0995 *README.md
d6d441c169f067b1c4b66ffb7083c0a5 *build/vignette.rds
d8c8bb298c25f6fbefb1452bef287360 *data/bears.RData
da25c3d8325becc126ceee229e4039d9 *data/datalist
6e0e84dbc70ba1de5369a46a3440dc06 *data/graphs_2_0.RData
cf72f71ee0d9196641f391b12f9cd124 *data/graphs_3_0.RData
2904ec67ecaa68df865475f9403ac206 *data/graphs_3_1.RData
ad33d7f04c10165fbe9aa1eb08bb33ba *data/graphs_4_0.RData
684459f32bc763c70f183f3d2bfb33fa *data/graphs_4_1.RData
ba32f180ae8bc7997a4a875f17e434ad *data/graphs_4_2.RData
e0ec5311d9433cb6e6d8583e59486f6c *data/graphs_5_0.RData
92bf26ed0083835854f85163536fc226 *data/graphs_5_1.RData
0d3bba6921b6dda0ed02c7f5d3fc93c9 *data/graphs_5_2.RData
d0423033996978829e83b80079055f31 *data/graphs_6_0.RData
bf9b12051a737fba62f76e0780a0ce5a *data/graphs_6_1.RData
c2f3d681f8ea36f0504edfd6e59d877c *data/graphs_6_2.RData
4d0d063956aa814b7e5718e0ffee02f7 *data/graphs_7_0.RData
190f0bf6463fdebabf6fc87d923fe87f *data/graphs_7_1.RData
bf34744ac1a674534bf8f4792fedbc7a *data/graphs_8_0.RData
5334ca44ecdc2197d99ac521fa1b5620 *inst/doc/admixturegraph.R
552967a4c779275403b5e42d70dc0eb6 *inst/doc/admixturegraph.Rmd
a734e9bd78d328fe06c85f0b382237c4 *inst/doc/admixturegraph.html
096b22bfca396ab4e70aa3469656275e *man/add_a_leaf.Rd
52b4af03c39de39bb993e4f0c64aea25 *man/add_an_admixture.Rd
3a8de7276b00d870d83145f8685d78cc *man/add_an_admixture2.Rd
da399ec6ffcb91516df439ee10db7645 *man/add_graph_f4.Rd
97aab6482b2b2295c307fedec93e4991 *man/add_graph_f4_sign.Rd
c20984c597daa7ea7532a5d28bdc4135 *man/admix_props.Rd
35cbd157294a0289f2db31de78f43378 *man/admixture_edge.Rd
5f5c4a3ebf9f9769f3d036f40413c9b3 *man/admixture_proportions.Rd
1f6860aa29fe41182b7ab083bc51b9e8 *man/admixturegraph-package.Rd
727e6f809e77bb3e7c2cd3106d1e96a6 *man/agraph.Rd
27110c996c0b4b8c9080547c0a579539 *man/agraph_children.Rd
2fc34c1115098a330c8fff65c9b2acbc *man/agraph_parents.Rd
c3c8e1273f720c8cc6e04cbddffa13f3 *man/agraph_weights.Rd
2b50bcd2819879be12891c8c0a9baf1a *man/all_graphs.Rd
957c8805de071aac8960c6919cc27157 *man/all_path_overlaps.Rd
05e7a6794e9702c3a3fa9d1f7ed21d63 *man/all_paths.Rd
7122b23e1dfb9a31262b1cdf5739980e *man/bears.Rd
05032809fea33f2e9da8ca3a43cbd023 *man/build_edge_optimisation_matrix.Rd
2c4c5d460f579f5006d4a08994497830 *man/burn_in.Rd
5419bfdeaaa7cdfe350b24b13e789c05 *man/calculate_concentration.Rd
890a8e7195300c756221a5cdcd907e7c *man/canonise_expression.Rd
9d8a0781c39be14e609d79cd2a1e23e7 *man/canonise_graph.Rd
4a73df42cc65aea2702a6eb94fb97b0a *man/coef.agraph_fit.Rd
b2936fd21a53dce221c7a0b6427e101d *man/cost_function.Rd
b9750dfbff94e3330cd0d7262c1dcd13 *man/edge.Rd
37f3d92327316c9eef1e6788c168c5b0 *man/edge_optimisation_function.Rd
85318c1f3a2672710d40f273c602e23b *man/eight_leaves_trees.Rd
b26fb02abc3165de4048b268b6005e1d *man/evaluate_f4.Rd
f9608ce67ad57db57cefd450ad68baf3 *man/examine_edge_optimisation_matrix.Rd
3be79ad8e9bb86e76c652848a619b64b *man/extract_admixture_proportion_parameters.Rd
753663a53c50cc8bb8c748c13ab08c6c *man/extract_graph_parameters.Rd
e99777b6e2483f5c2c02c4b9e0b63cbb *man/extract_trees.Rd
2fcc4e9085a5ded336f3a47b4b903b37 *man/f2.Rd
a463ea3b8d8a5c51951666104624a7fa *man/f3.Rd
810d9ddab9c40c484084debc04eb971d *man/f4.Rd
6bc771d89d63ad722a705f28d93e8e62 *man/f4stats.Rd
add7ee66fb8e05b4f2a1959803b71963 *man/fast_fit.Rd
4ef2e2c0eee34c72704e02d95b47138f *man/fast_plot.Rd
b9b2dced00d5f75fc75ef9cba18823f7 *man/filter_on_leaves.Rd
15b119a7b9e3b85f5a966fff56e68cbb *man/fit_graph.Rd
b5140d2c1ce65f2969109a9401d776dc *man/fit_graph_list.Rd
dff8af00cf4359086e40892f76c15e1c *man/fit_permutations_and_graphs.Rd
ea7d30c8bace971ed5ddf168cce4a89f *man/fitted.agraph_fit.Rd
1d9af24f5e4dbed8484b54df3b4b7834 *man/five_leaves_graphs.Rd
781c3a7412ab3061a7b1eeba64a9c43e *man/format_path.Rd
b863920c274e0dbd5a9231145f541ae4 *man/four_leaves_graphs.Rd
5ca969b9fc448993a4054adf11d1dd98 *man/get_graph_f4_sign.Rd
62e2ce9df721e018c33d4f8a2da56e06 *man/graph_environment.Rd
419e1aa8a4eda003bdc00853f327c40e *man/graph_to_vector.Rd
62c8419faffa9594864de4e405809db8 *man/graphs_2_0.Rd
fad5a26b88b363dc8ecdef99b7c1dd37 *man/graphs_3_0.Rd
3d4c6bd5989d85c2c0a562999a2bddc0 *man/graphs_3_1.Rd
3b9d20845e8029e8d6accfb43af43fdf *man/graphs_4_0.Rd
6ded16ea9d8072d4800b0fa7fe464126 *man/graphs_4_1.Rd
6bbd5f5b242281799717d123046f813b *man/graphs_4_2.Rd
3fd32fa561798d130a31da3f271ed1bb *man/graphs_5_0.Rd
7157fe6cdf618043fa08d37245493346 *man/graphs_5_1.Rd
26e92faf4ed750290dc15e11443751e7 *man/graphs_5_2.Rd
7bdb514ee579af2e8e69f91b07a41cb9 *man/graphs_6_0.Rd
74c13974f46717e7f72ff762caae8932 *man/graphs_6_1.Rd
95dd272b6a6e4961b08c11873c299b3f *man/graphs_6_2.Rd
d42ee0304d1820c8ce12f06df8c58c4e *man/graphs_7_0.Rd
486e160eba4480e665e488966346d961 *man/graphs_7_1.Rd
a374b9562bc42c645c89f119d815ec9d *man/graphs_8_0.Rd
75b5ece23a7fa345316da8c246c9b076 *man/is_descendant_of.Rd
d0745380efd59072f13eefad433aa84c *man/is_negative.Rd
8ccb8cf9e9fdf13a7ce576427bfdc747 *man/is_positive.Rd
7772d0dd9724bd5712fc988aa6fd3581 *man/is_unknown.Rd
8150298fdf425eeb0a215287bb3ff845 *man/is_zero.Rd
995ddcff8a0dcb5b4a18ea79e27120af *man/log_likelihood.Rd
052054c1a5d57a6bb7cd11aa667773ce *man/log_sum_of_logs.Rd
d04e309b83bde798d0da8f842a86a6ff *man/make_an_outgroup.Rd
a11df9c18b2dda74a433854283545d7a *man/make_mcmc_model.Rd
72ea833219182cf82fc512754f59d8f8 *man/make_permutations.Rd
7b0e01c7d33d4473a53ed169dbdc5138 *man/model_bayes_factor_n.Rd
1eb66de7421ed5211ed66c91556d0679 *man/model_likelihood.Rd
2487a716fde13fa763ada1a29a9ad079 *man/model_likelihood_n.Rd
84f46221bec7e191e369ed0eb4649ad4 *man/mynonneg.Rd
4c1f84ca556e41effac3a54a446726bc *man/no_admixture_events.Rd
d056ca65f17f040217e36b0a99d52938 *man/no_admixture_events.agraph.Rd
8401c757b37340820b70f2247897730f *man/no_admixture_events.agraph_fit.Rd
4b8c36e647af94ed9572f39d75f94a9d *man/no_admixture_events.agraph_fit_list.Rd
d3a1b9573d83a07b8c70953d79b302ce *man/no_poor_fits.Rd
5e20304b4dd8cc9d7dfa8cde11e10c42 *man/no_poor_fits.agraph_fit.Rd
5764b65a118d4b665e6eba35831b5cc7 *man/no_poor_fits.agraph_fit_list.Rd
0dab7ce787e06d283c0f85cf3b50423b *man/overlaps_sign.Rd
4348281ffb31d8d00a706f12884caff0 *man/parent_edges.Rd
78ae52e643f9bc90e4804b22c0329844 *man/path_overlap.Rd
2c8b130bad23d60854e7b027b1c50869 *man/plot.agraph.Rd
888476d739f41df1a1e8e0deec3d3b61 *man/plot.agraph_fit.Rd
d71338ba7b60ca699c9f23050072f96d *man/plot.f4stats.Rd
a55b69b2b5da99722a42b7c2cb3f960b *man/plot_fit_1.Rd
626ff42a5b3043ecdd46529363949b28 *man/plot_fit_2.Rd
ef5a552156d5827ab0f9e527a8f8220a *man/poor_fits.Rd
e31fa37775a63fb1a3018d219a6d5427 *man/poor_fits.agraph_fit.Rd
12751edc4f497ee2f527a58be909ee36 *man/poor_fits.agraph_fit_list.Rd
bed49ecc704bf8437d1773f01c8ed745 *man/print.agraph_fit.Rd
9becf4b54b5863ac3d31ed36a2df28d6 *man/project_to_population.Rd
19f0657540121cf9eda3f68a01cf2480 *man/remove_duplicates.Rd
d9e9f1410b04a46219cfa4a13b8a30ad *man/rename_nodes.Rd
b863c8841da81174fecff54477d364fe *man/residuals.agraph_fit.Rd
816b260afbd539c9bf009137cc7af7a9 *man/run_metropolis_hasting.Rd
2ca8341739e6d2fed873bad2218355d4 *man/seven_leaves_graphs.Rd
a9c0c3ad94ea47f4c29b6d4f63973835 *man/seven_leaves_trees.Rd
727294c224269bc65dc55841d7a6974d *man/sf2.Rd
85278dfe6c6706a6bde12a7a368f7d64 *man/sf3.Rd
29fde7b9b0f997be4a50732c9de931a0 *man/sf4.Rd
34bcedebd5182a1e0ceac1247bef29d1 *man/six_leaves_graphs.Rd
01b78401816e4917bbf3eda062ed65f0 *man/split_population.Rd
03471d98c6c21871b9c9a229dc3049d9 *man/split_population.agraph_fit.Rd
c3787f44f4e8b090f59ff387226a3c5c *man/split_population.data.frame.Rd
3f5978783a1070fb48ca9920f48ed6a5 *man/sum_of_squared_errors.Rd
59ae2f3cfef24552fd305f668e3fbb8e *man/sum_of_squared_errors.agraph_fit.Rd
200a2117554974f18522522888ef504c *man/sum_of_squared_errors.agraph_fit_list.Rd
1cef5038a6631fb00b66c4e505014386 *man/summary.agraph_fit.Rd
326084960be2640cd15f485c609445d4 *man/thinning.Rd
92b8046cbb82a12b6e930baec1f08b8d *man/vector_to_graph.Rd
205fca2a9fe53f35b2c701623e524c97 *tests/testthat.R
b5b4095e5dae4554dbe7a2e6f0578805 *tests/testthat/test_f_statistics.R
5393976eac48eece79ef2092244c4a43 *tests/testthat/test_graph_construction.R
50d7a6e6b67a57f997d3b773269aad07 *tests/testthat/test_path_overlaps.R
2e105ba101d14c6efb8692729d196e50 *tests/testthat/test_paths.R
ad14fd75f0035bcee488bcc6bea8a274 *tests/testthat/test_plots.R
5c96e1845a9c73a8314b717cf1dd37bd *tests/testthat/test_signs.R
552967a4c779275403b5e42d70dc0eb6 *vignettes/admixturegraph.Rmd
3e8d3f66dcff68a8515a41d17abc06ac *vignettes/admixturegraph.md
b57a08edca6d125663c324aa9efbbc84 *vignettes/admixturegraph_files/figure-html/bears_graph-1.png
46abaebc3d8d62c0095e3d3c27066471 *vignettes/admixturegraph_files/figure-html/new_admixtures-1.png
d09ec5834ca60a7ac280f06e78c1d7bb *vignettes/admixturegraph_files/figure-html/new_leaves-1.png
79f15a857cb1bdaee287a8058c9934db *vignettes/admixturegraph_files/figure-html/new_root-1.png
7d5450332ef66d258d58a9f81a434081 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-1-1.png
c89ff907d7887036acb58bc7b0c04c30 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-10-1.png
a333255b784cd70325af81c776c5d952 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-11-1.png
077819d6f8d2aec34c7fd6b106400ee6 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-12-1.png
20056fad5d0a6ae077424d468c0194a4 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-13-1.png
ae880dcacbdb75b3af82b30e1aab2327 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-14-1.png
aaf24b06c9d6cfe6c788537c8fdf73de *vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-1.png
aaf24b06c9d6cfe6c788537c8fdf73de *vignettes/admixturegraph_files/figure-html/unnamed-chunk-15-2.png
425549cf4fc6c65dd0c3e5e3fa3d816e *vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-1.png
b52e1a7473c86162e34bc9ecef0d1beb *vignettes/admixturegraph_files/figure-html/unnamed-chunk-18-2.png
8bf5cdcb0be842b3467de227df9aab3b *vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-1.png
0763ffb7debd765a4ed5474549c5ef80 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-2.png
567c55cac3bbd0ac4dc0346e2081296f *vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-3.png
d5d9014fd7b818e4273051cd16245279 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-19-4.png
15a8ef9b65df79798b0bf745a9094ad9 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-3-1.png
c39596724399b19b87f534a39d7b5e32 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-4-1.png
184da3003f0ba5ee0f637a7ae87a2856 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-5-1.png
8a1bc3667fbd737f04f5a0296a39765d *vignettes/admixturegraph_files/figure-html/unnamed-chunk-6-1.png
3c32c537d3be98afca3af9cfc2fc72e9 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-7-1.png
d3f4e77d9cd4b27ada0aeb7290483c46 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-8-1.png
184ea93f2b254a71125035e8173bdaa4 *vignettes/admixturegraph_files/figure-html/unnamed-chunk-9-1.png
c8364f4fb38adb86ddd8ea26650fb47e *vignettes/admixturegraph_files/figure-latex/bears_graph-1.pdf
936c54452407523729d4eeb096721ceb *vignettes/admixturegraph_files/figure-latex/new_admixtures-1.pdf
5e4f6af0da42a100f8d61bceb230de78 *vignettes/admixturegraph_files/figure-latex/new_leaves-1.pdf
80a41797015029b114623d0d38133592 *vignettes/admixturegraph_files/figure-latex/new_root-1.pdf
90a875819d0d6f74b41f709db0564c8b *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-1-1.pdf
4e04ee82798bca9252e659f9f3d6fae7 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-11-1.pdf
aac55ca63f9ce8b63e3374844f2589b0 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-12-1.pdf
0f2d6cd1f3c95a75c01b0a9d237a7680 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-13-1.pdf
93ee1a0bff90dbade0c157987b5cdd6e *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-14-1.pdf
0a1aa3156405920480cfb42ad4dfc56f *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-1.pdf
6cf5593d38085ca3611a497cbe445205 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-15-2.pdf
3dc5c5d28e782a0b3c36129d92d1950b *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-1.pdf
ea200c1c641a37a3d5b785756aee4bc7 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-18-2.pdf
efd6e817747bc82e90f72970f3468c38 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-1.pdf
c8383d6be7cece5b5d00233a675cebcd *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-2.pdf
fd6ac2553390c7637f372272b1a3668d *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-3.pdf
7691ecab18e3c02933cb703b292c8e6b *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-19-4.pdf
fac82a9a95d2a2c1bf0d814e329645b7 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-3-1.pdf
5f8d080ad09a1a0e60f2399a6f441af6 *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-4-1.pdf
46ff434f760c068450be6ecc46a8495a *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-5-1.pdf
fe1e2628237f2f6e0a6c7e91f29c228e *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-6-1.pdf
7d364fceea83ccbb70c18051d5e80abc *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-7-1.pdf
6c1689fb725c3c7553bfb7383d40ecee *vignettes/admixturegraph_files/figure-latex/unnamed-chunk-9-1.pdf
5e9e5ea452b18c05c7ce8d585b6902c4 *vignettes/bibliography.bib
