9976f0d7f4801fb7ebda2f898f7fba05 *DESCRIPTION
f0db1bb7fbda4e899eee2ffc0b0113ba *NAMESPACE
6c70311efee1585c741f85e54683d7ce *NEWS.md
4a6b5fa07711c043af788c0407f42598 *R/RcppExports.R
025e1ec251d86db6a929c790ac8cc375 *R/build_historical_assoc_mat.R
b42d5309d00ace8bcc1cfbe4752bf1da *R/calculate_cophylo_summary_stat.R
8c26b1d174476108815ef581c3a245b6 *R/calculate_genetree_summary_stat.R
59b3761e36b47fe73b76cc26573ae34b *R/convert_assoc_tab_to_mat.R
a3d9c0cea69a7c466cb426a5a3606496 *R/convert_to_cophylo.R
a3d6a7560c40e54d4f06b3cce63e023f *R/deprecated_sim_functions.R
48164c921298885f68a38742862e9ce4 *R/estimate_node_heights.R
f88fe1210a50e0808206eeabd14afdb3 *R/is.cophylo.R
77044388a598b0b21f3c587836fcb82f *R/plot_cophy.R
4edef15fdb7a4d5cab46358e83bae57e *R/sim_multilocus.R
6fcf9208dc6cdacbe9357573df869459 *R/summary_cophylo.R
5993c4fd8922ebd5f44e806c23d2aeee *R/utilities.R
a54fe41b0cc15d2550516c0209ffaa87 *README.md
232fcced3355e931f411dabf8d62212d *build/vignette.rds
9f483f0dcd63df61ead03747f8825d1c *inst/doc/cophylogenetic_sim.R
cc841a11f106f33169f5019f4dd0c8bd *inst/doc/cophylogenetic_sim.Rmd
875ba4cba4ff397f087c95dc74963a02 *inst/doc/cophylogenetic_sim.html
ca853b63fc85ce1f9e3eabe3e38c6732 *inst/extdata/gopher_lice_mapping.txt
b8da8e73843b4975b817cfed5d1b16ca *inst/extdata/gophers_bd.tre
59d0a177a330d9678edf90dbadf03c65 *inst/extdata/lice_bd.tre
c8290f249401ff6e46ceddd2052db8df *man/add_events.Rd
4a797c888f72f036bdba19df190079f7 *man/add_scalebar.Rd
c9eef161fb8b432e8d444ae7cac35f33 *man/build_historical_association_matrix.Rd
268fa3f28765e718854cf8221dbd43a6 *man/c.cophy.Rd
ad78fc975dabf1899b1217c42893c1a7 *man/calculate_expected_leaves_locustree.Rd
2df4283d85d063a39095d787b74b0665 *man/calculate_expected_leaves_sptree.Rd
f5b0f6988508018dcf2d158cd880a098 *man/collapse_locus_subtree.Rd
680a8945a0dd04c65061a5b21273ce66 *man/convert_assoc_table_to_matrix.Rd
f98ac156a59af2b882b6c2670284d62b *man/convert_to_cophy.Rd
f72f2181c698247417e7002dca70e0d7 *man/cophy_summary_stat.Rd
9b071dcd17a34d7d2f2bd64f6f074472 *man/count_cherries.Rd
53f619c23a6679a60598d523507f58d7 *man/draw_cophy.Rd
062c76e4ff9b04abfb860e657ae8c398 *man/draw_curve.Rd
338a378e4af39d522255766a7c98c96c *man/drop_extinct.Rd
c1fe883bb75f476a58ff9a00217f52a1 *man/estimate_node_heights.Rd
b334e29fea3c3a9f3824690644e6f824 *man/genetree_summary_stat.Rd
35ecdae34147552eb52cd1bb482d6272 *man/get_ana_events.Rd
259e2f7933a00db26df0bed534bc60f8 *man/get_loci.Rd
59a50b46ab83fba9ddbb783add124aca *man/get_tip_labels_tree_list.Rd
2cb836aebb034086c6b6cbde00553d09 *man/is.cophy.Rd
91ce7ae4e31075b8553488b01ff34a47 *man/is_extinct.Rd
341a3af7dc30c971a9f27ab85c713357 *man/make_textbox.Rd
dcfcb0c0d74d06d57758093eaed7af7c *man/parafit_stat.Rd
c381dc57e6e91c908f77142c62364b01 *man/plot.cophy.Rd
38a5e032f7d0a0067ae79c6a206f951f *man/print.cophy.Rd
6e0637d0bc87dcc29e1efe20bef602d2 *man/retrieve_parent_genetrees.Rd
683be7335a41a1bc84842e5ee90bea1a *man/sim_cophyBD.Rd
ca31943ea76a2c35e5cac67f3d351e3e *man/sim_cophyBD_ana.Rd
dc0bef63b8dd6902faaa7a7cef3c5d7d *man/sim_ltBD.Rd
61ef9ac249c3b92fdb50cf25ad17962a *man/sim_msc.Rd
49b9c51d7edfe805277f01dd5a59b695 *man/sim_multilocus_coal.Rd
935fe7eecad0c840f103a2483ac0f892 *man/sim_stBD.Rd
0eace5befbfb76aa9a102bae2945acae *man/sim_stBD_t.Rd
8bdc8997f86957bba82312e6e611d8f8 *man/str.multiCophy.Rd
ca5fe14b13b8f080f408e592b48a3f7a *man/summary.cophy.Rd
4c73fbf86f054981aee64c60a0d144df *man/treeducken-package.Rd
8ebbf638798dface57ab950190563af2 *src/Cophylo.cpp
1b48e1b1a737da17ee5f4899e50b6cf1 *src/GeneTree.cpp
43cb36009016b3dc04e1e6341953698a *src/GeneTree.h
2afbed9fd2c0c54be9e97264ae22e6a3 *src/LocusTree.cpp
3eb4676ccb8cea45e6a2d0f59611f65e *src/LocusTree.h
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
de0f6330ebc8bfb6bdd4ca47db1659e1 *src/RcppExports.cpp
d17908250f0edd21efad5d927b2dfb5f *src/Simulator.cpp
4ffaa835558ed1af6523deccbded8c6d *src/Simulator.h
10ce2080c546c97b5d94d2137850fffc *src/SpeciesTree.cpp
20e119bb315a535937b09b89c5ded965 *src/SpeciesTree.h
c595b7b9e73c54cd38f30a670596e9d3 *src/SymbiontTree.cpp
b5331e0af342562fd11241aed91aabbc *src/SymbiontTree.h
c0a51de4fd309db2a93e0b7fdbdba654 *src/Tree.cpp
bb90886d965bc0a92c89d45301092cfe *src/Tree.h
f638855f5102ba05291487660567992e *src/Treeducken.cpp
49fa0d70b0c2db6ec0207aac186eb554 *src/rcpp_treeducken.cpp
4dd3fad2735096bbb426f1fdfa432234 *tests/lldb-testr.sh
3b8eb7d4e3123a041ab4bafefe84da22 *tests/testthat.R
7315b746474cb58e6e41d2b77ef411ae *tests/testthat/test_cophylo.R
314f07d3c4c9753f7a32c84323088ab8 *tests/testthat/test_cophylo_obj.R
cfcdfd9643eca47ba68c1d7da556428f *tests/testthat/test_locus_gene.R
31b952f2196f1b2b1482002d78005308 *tests/testthat/test_sptree_gsa.R
cc841a11f106f33169f5019f4dd0c8bd *vignettes/cophylogenetic_sim.Rmd
