d73a3e127dd14b97bc03c5b81c228124 *DESCRIPTION
2b78d89a40dd60d9d95267e2a24958b1 *NAMESPACE
9d50369447feebfffcedd30c3fe54457 *NEWS.md
4ec6a157473381371bc8cd0eeb2c59f0 *R/RcppExports.R
0a1440f1e58ac1bb1127608075486c61 *R/build_historical_assoc_mat.R
b4c930841f60609e5aede2f829a9ba11 *R/calculate_cophylo_summary_stat.R
83c0d08830da4652716e75610cf12d14 *R/calculate_genetree_summary_stat.R
878314ad088f9a70b7db6b6a206bea28 *R/convert_assoc_tab_to_mat.R
9ae6edabe0df5ee9c010b4d51c6a4880 *R/convert_to_cophylo.R
f4745db8a0efe02099160c46a6817491 *R/estimate_node_heights.R
1f3347bfe92943fa149a80a539e6e3e2 *R/is.cophylo.R
5559a7b5809c36b23f9be99ee86bbe95 *R/plot_cophy.R
26a4171c86aa738c73bcb9bde02ac9a6 *R/sim_multilocus.R
b2b1b584971518cbec2b36bfa786ba20 *R/summary_cophylo.R
bec4b7696692869cd3d2470b4f765604 *R/utilities.R
fc32e27adb47dd9d3d841f23a76fc7b9 *README.md
fbe4d6121398112349334afea9884974 *build/vignette.rds
1095b45283e33110c6d9b150701aebde *inst/doc/cophylogenetic_sim.R
18a86882a78dddc9e586c035f277f1b1 *inst/doc/cophylogenetic_sim.Rmd
7532a7fb0fc293a257995ddb72ac0f3c *inst/doc/cophylogenetic_sim.html
b9ec10a73378e54b374d55058d883311 *inst/extdata/gopher_lice_mapping.txt
052926981e2ee3db7f5a556ee28440f1 *inst/extdata/gophers_bd.tre
72992220a8cbb96bb6a1a4a00cb0c4fa *inst/extdata/lice_bd.tre
3a2564e387d08b63fb53e938a6441931 *man/add_scalebar.Rd
b91e07f89d6204cd3fd4acc65d287460 *man/build_historical_association_matrix.Rd
68e7d63f05a886a8267b4a16f8e0bb49 *man/c.cophy.Rd
838ad6856835cd98f49c1f311fc6d4d6 *man/calculate_expected_leaves_locustree.Rd
019e6f2040cddb01924333d39189705b *man/calculate_expected_leaves_sptree.Rd
94f221b35aab337a665e9fde5cadf0f5 *man/collapse_locus_subtree.Rd
e304ac68e623aac0a2737c3818358ecc *man/convert_assoc_table_to_matrix.Rd
33e42de0892c9c9c012546c4d9f114f0 *man/convert_to_cophy.Rd
6761e53202d3b831fa8f7401631957ed *man/cophy_summary_stat.Rd
d7997fc7d6da97465fbc50c6c74799b0 *man/count_cherries.Rd
a1132b44737b37aa74e2a0f4886808b5 *man/draw_cophy.Rd
51f2b84382ffd9cca4c065dc36f90205 *man/draw_curve.Rd
1e53d267c8243055bcc32ce07f24ae06 *man/drop_extinct.Rd
111c63553e255f9a21bb8ba47149d438 *man/estimate_node_heights.Rd
bbd0c13a2c6af732d3f9978953fdc57c *man/genetree_summary_stat.Rd
ecd98c80350d8e4fb3fbdb507f5e8afa *man/get_tip_labels_tree_list.Rd
f2c3c46e5a8daab9917a0ef0d824e7cc *man/is.cophy.Rd
873533818aae4a0c272c07bf4078ea27 *man/is_extinct.Rd
dc15a062cf03646b9ee5e48e06a92576 *man/make_textbox.Rd
908c33c8a525330814e9539d6273a613 *man/parafit_stat.Rd
e8741beef4be8c22cbd979ba6dcae2b3 *man/plot.cophy.Rd
1cb11c07396f29e3c15d788c42b7c836 *man/print.cophy.Rd
1ba0c04499f267ecea6b347fda1cf9b3 *man/retrieve_parent_genetrees.Rd
e2541600e1d03e30b768f78d2f4be363 *man/seperate_into_loci.Rd
51e2663badc2df612c6cf569e9f86331 *man/sim_cophylo_bdp.Rd
fe637a47704fa7f9108bfc994a616d4b *man/sim_locustree_bdp.Rd
633c3d3be4ba4caf17dd2243747a0ec3 *man/sim_multilocus_coal.Rd
cb46efc9a8581339ee01f957450f4396 *man/sim_multispecies_coal.Rd
4e9efa66044308bb3d3458bf828e356d *man/sim_sptree_bdp.Rd
0d661dac762656f31a0e69c3e4e0ee44 *man/sim_sptree_bdp_time.Rd
6bab68dbb343ffbb98aecf73df29dfa6 *man/str.multiCophy.Rd
66ae22e6711a5818fa0096390fb4881e *man/summary.cophy.Rd
7043017ac383c9b5bde35b67d691565a *man/treeducken-package.Rd
2bbb947204e7e11e35b7031f2709f6d1 *src/Cophylo.cpp
1b48e1b1a737da17ee5f4899e50b6cf1 *src/GeneTree.cpp
43cb36009016b3dc04e1e6341953698a *src/GeneTree.h
2afbed9fd2c0c54be9e97264ae22e6a3 *src/LocusTree.cpp
3eb4676ccb8cea45e6a2d0f59611f65e *src/LocusTree.h
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
6cac6fb378c485ba5eb1784d765da330 *src/RcppExports.cpp
55d6e8fb3708da4993637cc258ca28b2 *src/Simulator.cpp
b0be498060cbd14f45ed6c47527dc1b7 *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
c5ad86ea306becf8e09b603b3f0e2570 *src/Treeducken.cpp
353ad3a2a82baf8e94a5a0d3141de491 *src/rcpp_treeducken.cpp
c41f69dce359d87b767e9470d42c93ea *tests/testthat.R
eb979b1c6398f47b60e84c243a83d5e7 *tests/testthat/test_cophylo.R
314f07d3c4c9753f7a32c84323088ab8 *tests/testthat/test_cophylo_obj.R
efe437bdc6a7058f0c2738b63904dfe8 *tests/testthat/test_locus_gene.R
958dd49efc5326499f356a2e56b93fc1 *tests/testthat/test_sptree_gsa.R
18a86882a78dddc9e586c035f277f1b1 *vignettes/cophylogenetic_sim.Rmd
