26e448a9e919b48fb3d6407b6f0b827b *DESCRIPTION
d5d0fd06cc3035dfa9be28ec30976a73 *NAMESPACE
6b5018e17d9439e6a898389e68e08b63 *R/BGB_functions.R
6acbfae966a7bfa53bf9e1b9893d0a2b *R/BICompare.R
4900f55b40fdd4409a6d4a730c6a936f *R/CreateBioGeoB_Object_subclade.R
ec278e6b4c609c9fdd9ad3202f878f8a *R/CreateClassObject.R
e8ef3d6648c49defd4b8634a96fd7de0 *R/CreateGeoObject.R
f19f97b5e988da2df68338fd9876100d *R/CreateGeoObject_BioGeoBEARS.R
59c544589f2b58424a165e6f3204a887 *R/CreateGeobyClassObject.R
af08bf4feb7799b54ccc73f52bd888b8 *R/DDexp.rescale.R
05a17e2d443df9c89c6f10aa7ea47852 *R/DDexp.rescale.geog.R
35b80ac62c4a096a0c59c5942faf74e5 *R/DDexp_geo_ADiag.R
a4521c50fdcd4655c2ea0f1ec1567bc9 *R/DDexp_nogeo_ADiag.R
9dd75fe2ae09753657bc8e845e33da43 *R/DDlin.rescale.R
e6af86c43b4a99054cef04fe4e444b0c *R/DDlin.rescale.geog.R
63a951df8b834dcdefca882234041085 *R/DDlin_geo_ADiag.R
0327ef7b8cf091bf2b4c12dc1d84bd4e *R/DDlin_nogeo_ADiag.R
13e50b5d88c5a5a0325726f20934387e *R/GIC.R
3581d522228c1c8b21b6bfd062fcdc31 *R/JSDtree.R
5bf565a704551cc52293af2386ab306b *R/JSDtree_cluster.R
d1a85b17809f93c4bc835874db8ba31c *R/MC.rescale.R
d2fe378689e28557a2d9cf9075d8d9b2 *R/MC.rescale_geog.R
268539d58227d9af2d25509aae9202db *R/MC_geo_PM.R
b2c96b3d4e6bf0295d0f2a8586c620fa *R/MC_nogeo_ADiag.R
ae5d5f82231c7dce84b4bbc78f4432ac *R/PhenotypicModel.class.R
c4a2f67b579002675cc4a5a44e2e9e46 *R/Phi.R
3d1ea2baa9f284f4fec94581cc6ad6ac *R/Psi.R
a44fdc9b33180d848f061699ed47ed5f *R/base_sgd.R
db73a57669567068541e5a76fb315e17 *R/createModel.R
1c9d013962287e796f6936718a4d06d6 *R/fitTipData.R
f529ae7f922cc2e51319ac087883d405 *R/fit_bd.R
7117cf2145f8d63a6e17b0d19c0e0aec *R/fit_coal_cst.R
b8bb60aec95ea5640f23ee747a801d2b *R/fit_coal_var.R
6f64a066447111c0f4ee2a65fd2c5e5a *R/fit_env.R
c0e04be86e53f1ad4447e1082ab82bb4 *R/fit_sgd.R
851327fa3d5bffd8bf206b761071423a *R/fit_t_comp.R
9af405330f64950bf51b7007d023c533 *R/fit_t_comp_subgroup.R
48da37ff22a0a19547ee57a69a2707d5 *R/fit_t_env.R
5ea2421b8d0007ba21ddd98cd0ab40ac *R/fit_t_pl.R
19eeafd9d39dafa7616c04d40bf3d75d *R/getDataLikelihood.R
4eb5702427a8c6f3e38f6a50481f341e *R/getTipDistribution.R
56867e40d6f023820f709d445cd861e4 *R/integrate.R
f9e529b5ec78defae66c8c9ea8714221 *R/likelihood_bd.R
1fdfd4057e6e4c0394bfc37d5e3b8318 *R/likelihood_coal_cst.R
97702cf15506ba337c79aee355fd4d91 *R/likelihood_coal_cst_mod.R
c093daac9626b39be3ca89d17422018c *R/likelihood_coal_exp_mod.R
939b14961eac07c4e420f2f8ba5dc47f *R/likelihood_coal_var.R
efc70cf7e97c0e858e4b0f28b92d1306 *R/likelihood_sgd.R
61c0f4ec99aeb2e50f66731c0817bbe2 *R/likelihood_subgroup_model.R
2edaac105fec59d62f1146e6b6dd01d9 *R/likelihood_t_DD.R
f446ca3dbbe2ca433538f33f6e289f89 *R/likelihood_t_DD_geog.R
d083bd9d0ac8ba4a92a73c4d2334330f *R/likelihood_t_MC.R
e08efbb0303b483022d3eb10f18ed221 *R/likelihood_t_MC_geog.R
53bef064da807783490893cd48797faf *R/likelihood_t_env.R
0f91f068389d6ac025b3f024a1db1e09 *R/modelSelection.R
2ace1735f576fd5810587af51d14513f *R/phyl.pca_pl.R
c4f64c58bbf7f195bd22c406bba37e2b *R/plot.fit_t.env.R
baec2f80828bcfa98fc138a0c4023cd7 *R/plot_BICompare.R
eeec66c3618f53416ed78e29af6ba90a *R/plot_dtt.R
e1b1e7f3be6c6a4940367e7e1661a9d6 *R/plot_fit_bd.R
1d9179600508bb6212b3750690bae4ed *R/plot_fit_env.R
d95d4ac624746c288608cf31cc53810f *R/plot_prob_dtt.R
aae3c96d3d7e89a6a175a51e12f462d7 *R/plot_spectR.R
e6992a5435075fa0f04ef73d965154b7 *R/print.fit.bd.R
e3c208749c52727e539c52c7f25e8f92 *R/print.fit.env.R
e93c6a64ad98de36e50805a628ab988b *R/print.fit_pl.R
bbfe811102fe81578e3ba31e097470ad *R/print.fit_t.env.R
ca2d3e1f8b87d53ae3b0028b528d2af3 *R/prob_dtt.R
d59452a25b11edb9b064032748228eef *R/resortGeoObject.R
5546fac46c467f90e968030a3629acee *R/sim.convergence.geo.R
2864890a49612475ed5d793f5a123405 *R/sim.divergence.geo.R
3fda6e826acdfc30480af1f8e9506cee *R/sim_env_bd.R
0add8eacf65f899d0652ace486f37a0f *R/sim_sgd.R
1055b91978a36002740071a720d2c6e3 *R/sim_t_comp.R
2294c7efd93093e9735ef1f8d33fd6b9 *R/sim_t_env.R
b07c7aa23531002efd1462e783effae3 *R/simulateTipData.R
a363f6564404974c2091eba571f689a8 *R/spectR.R
290c89ef86637c7b1baba5b2a8642d8b *R/stratified_BGB_to_tables.R
6d34125af3f95b90f319f81344644d70 *R/trimSimmap.R
638d9dcb597153bd59c340506bccfa26 *R/utils.R
d6f4928ffded96f86c6edf798ab1ae35 *README.md
62ee0303bff7bebb70ca713d4ca70f4c *data/Anolis.data.rda
9d53cee50578274b2a08eb9d9463a421 *data/BGB.examples.rda
1fe9cbc326c7f5b869c8fdf253fdfd45 *data/Balaenopteridae.rda
5c338b4f3304a098487530669ec052f3 *data/Calomys.rda
511e11d15dff02377a061fb106884b19 *data/Cetacea.rda
9c2e301ba5dc6d025d3324b4b725b12c *data/InfTemp.rda
c11074a547b6a1a94c4cf8481562b237 *data/Phocoenidae.rda
35b5faacf13850161d6eda60324e92f5 *data/Phyllostomidae.rda
e22c72d36f75fc3cf26be9327fcaa015 *data/Phyllostomidae_genera.rda
24523b604b26a96dbf808b591db02d9e *data/co2.rda
4a573e0f542b41399c8ec399ed95ed2d *data/co2_res.rda
ff79a8c9ac6cd48972dd545b55f2138e *data/coccolithophore.rda
be1a127c80449076c3ff3855ca32afa2 *data/d13c.rda
dc06c56806579d6c99a4f7f56b11aa16 *data/foraminifera.rda
508fa6ba1f3077913fed92c9cfbb73a7 *data/greenalgae.rda
facbc22dfdba883d888d7d46316538ec *data/landplant.rda
9fc52f937b946d54b23be9b062ae372c *data/ostracoda.rda
296ff5dce986ae75d28619a33662b5be *data/radiolaria.rda
3a7a4300515c14d51381a44629c9531d *data/redalgae.rda
a97bcdbbd769bccfaa64e67cad9fdac5 *data/sealevel.rda
eec86a171873ea4db1ee272741e0234b *data/silica.rda
f1fa6bd46ac2a46c80181d7de63c5ed2 *inst/CITATION
dbdf6982b47acbe6076727543ad76fb4 *man/Anolis.data.Rd
e33b5c9826e7f6faba249c3c3de9c75b *man/BGB.examples.Rd
ca245416dd1834a7d5acd09c0057af6f *man/BICompare.Rd
faf28dde1e16a097473d87fed05f9fd8 *man/Balaenopteridae.Rd
5a4694406c9233108d4337e11733c13e *man/Calomys.Rd
cfe18d17bc205d610c70b8540b462916 *man/Cetacea.Rd
0a3826bec35341e1bdaaa2fd40b335c9 *man/CreateClassObject.Rd
c4b993a9cbd5e2d67db94af3a65fdf67 *man/CreateGeoObject.Rd
eacb898fd8c21ffcc28ef13c5230ae44 *man/CreateGeoObject_BioGeoBEARS.Rd
3776e24e9e7d9b797ffba1a5bc63bb00 *man/CreateGeobyClassObject.Rd
7ab55965cbcd66cfebe0c2bbddd20cdd *man/GIC.Rd
67078d0e5dfe4989bb429ccc46808719 *man/InfTemp.Rd
e5a2569635314fcea24caf76f968f885 *man/JSDtree.Rd
b8d39096343e1555d5d4bbc15825192e *man/JSDtree_cluster.Rd
ca14d3c0428cb99b4d3aa364e132530d *man/PhenotypicACDC-class.Rd
c067eec4e0580517fe7ed6f6ec1b40eb *man/PhenotypicADiag-class.Rd
aa251ebd7bbcf4ba1f2ad714ef7206f1 *man/PhenotypicBM-class.Rd
b07ed0aa0aca8965513cbfe9dc693df1 *man/PhenotypicDD-class.Rd
0d94462c9674ca5c505b710f7581f049 *man/PhenotypicGMM-class.Rd
c4d73b88cdb749d869e4972e144b90b8 *man/PhenotypicModel-class.Rd
7378a8beeecf731a6f6dac626a78b2fb *man/PhenotypicOU-class.Rd
1574d334f198f87452d46e377686f21d *man/PhenotypicPM-class.Rd
05487bef9337a0add225f8df17d64592 *man/Phocoenidae.Rd
202e18392532a4da4cc56814f0cf913a *man/Phyllostomidae.Rd
da5d184254d121be4ede02104112ed1a *man/Phyllostomidae_genera.Rd
9d18f677132a9e213de7dcce0c4d986f *man/Posdef.Rd
bb5086cdaa66b55b75532249080a8504 *man/RPANDA-package.Rd
dcae8400f4c81ebb520e916a6d800759 *man/ancestral.Rd
5326212d91c0e6322350cb905a10dfbd *man/co2.Rd
ec102e0ea9348d5b4498e4532b393cac *man/co2_res.Rd
2ad02b97a2b4c9c4d40a2a33710d39a3 *man/coccolithophore.Rd
339f33e10ffdcb2b89945cbffce95695 *man/createModel.Rd
4ef88425d9fcece9f2eb4479c230fb1a *man/createModelCoevolution.Rd
a76990c85354a723f39d9fe9c3e1e7e3 *man/d13c.Rd
a6bf13d764fdfc5375316738b6b06ec2 *man/fitTipData-methods.Rd
aab54d9c9f453c8155ea07d7a7207f20 *man/fitTipData.Rd
27ed52bd82036113f4c5eca013abd323 *man/fit_bd.Rd
f20804bd1864fce0aa451062e02eba2d *man/fit_coal_cst.Rd
d4f4c6ec4d4c6bad7fb896d229d784bf *man/fit_coal_var.Rd
026d843c05eb1bb87d4a3e3f2f2ad336 *man/fit_env.Rd
4cef65cea72cb7a61780c3c8bc4b1365 *man/fit_sgd.Rd
0bb7bc603c67f3e5990e2c4443728730 *man/fit_t_comp.Rd
420e05aa74722a829c323ccf59566b55 *man/fit_t_comp_subgroup.Rd
55c91b2ea44ff384e0833bdc185fa546 *man/fit_t_env.Rd
ffb6c3d645c76a8bd9236db34b7c66f5 *man/fit_t_pl.Rd
9e66f2ad4738e132adc9d38559da20d2 *man/foraminifera.Rd
9623257898df367d96035f1b37a7a039 *man/getDataLikelihood-methods.Rd
aefcb615da7f5702623915de01da7b18 *man/getDataLikelihood.Rd
bc1cc9f484759eb75932b97ba4679004 *man/getTipDistribution-methods.Rd
7431e7f448bc5bbd7d82039e28c6cbe2 *man/getTipDistribution.Rd
3436a0df2f66b753f94530d2f5ec4d04 *man/gic_criterion.Rd
5a41d73befbaebdf1d55d2898d0e0e06 *man/greenalgae.Rd
3ea04a679e1fb5f9b3f386108eed0c86 *man/landplant.Rd
818535f33616daa80ab5f933a9b4112a *man/likelihood_bd.Rd
4e7332d922646c5d352f3a02e45477d9 *man/likelihood_coal_cst.Rd
9128d250b18f8b4b765bebbc9950ec28 *man/likelihood_coal_var.Rd
1f0161ddf5593bf6ff6e3e0568e33d48 *man/likelihood_sgd.Rd
4246a02d83e24f3acb326e5f80871341 *man/likelihood_subgroup_model.Rd
8bdd3693e4377d71f7415736a3eb48c5 *man/likelihood_t_DD.Rd
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88df548926f32682db3d2c40df5a1517 *man/likelihood_t_MC.Rd
7bcce30e94d2a20130a2a65ff9fcc623 *man/likelihood_t_MC_geog.Rd
da687ad870e3038a35ff4e9dae2944ba *man/likelihood_t_env.Rd
d799cf5700eec9197797fb35fd206364 *man/lines.fit_t.env.Rd
7584e508414e19d1d5cd344001302f33 *man/modelSelection-methods.Rd
f94b5f31e72a24b2bff48e520ffff6de *man/modelSelection.Rd
37946c945a3a0c76cc6a602bd3c04463 *man/ostracoda.Rd
c3cf67258b794c281cbfb2c41209b77c *man/phyl.pca_pl.Rd
994eb6bde8b5e8001138a5e07b6515f9 *man/plot.fit_t.env.Rd
eb24e38f8c37d9885a67cf17d3f0589d *man/plot_BICompare.Rd
1425385ac0807b36bdbf0d824632d516 *man/plot_dtt.Rd
080223618337d716a89d1dadf4436f7f *man/plot_fit_bd.Rd
592b55f33745711f2b55816940d2d56e *man/plot_fit_env.Rd
b16bcc1ff45ae97652875042c5f1533a *man/plot_prob_dtt.Rd
81f77d0b7df8b279c88d29e17af7a4ba *man/plot_spectR.Rd
db8a51b8b80d6521aa9d87cb0a6c7ba8 *man/prob_dtt.Rd
f23903e57272fd66f43a7b269e838f1f *man/radiolaria.Rd
19dd1a573a33dd8d99064aeead2589e2 *man/redalgae.Rd
68dc9e69c2f43b1b013ae8ef91ffbd9e *man/sealevel.Rd
8549a9b7cce38c1126dee9445e385618 *man/silica.Rd
c3e25d8576a44a26c087932e3225bda7 *man/sim.convergence.geo.Rd
a5394ec49140eff86d4206e0c4b1559a *man/sim.divergence.geo.Rd
918ecf907728b549fe94dc9febf7fc0f *man/sim_env_bd.Rd
dbfecd8d80bd0f9b23b687a5f7d19f30 *man/sim_sgd.Rd
98c8a28cfc4d14cacc47f519a529b74a *man/sim_t_comp.Rd
f58815f2cf87d31f27afe1d393aaa81b *man/sim_t_env.Rd
e4c4dc565fc6fde567620e441f1c7882 *man/simulateTipData-methods.Rd
b90d596dc794df55223ed1a456432c28 *man/simulateTipData.Rd
461b81aec49e2de7666dd255bf7eb4d6 *man/spectR.Rd
13ac1121f103157b1ed76045747d3a1a *tests/test-all.R
f521acc16768d96677b570061d06ddce *tests/testthat/test-fit-bd.r
7547a294f56d8f0b2015f5a34e66d991 *tests/testthat/test-fit-coal.r
393d53ecefefb035bd040544051dc8e2 *tests/testthat/test-fit-env-bd.r
