f1d92c7ebd85ffaf241592d458d6735e *DESCRIPTION
011638a0580276b97228af8eefa0ae27 *NAMESPACE
bd92e3848acc730b596740294ac4a479 *R/BICompare.R
2fea1688977ea86e6dbef548bc5a3bc3 *R/CreateBioGeoB_Object_subclade.R
ae77b566cd5080a2247efcab157ea190 *R/CreateClassObject.R
e8ef3d6648c49defd4b8634a96fd7de0 *R/CreateGeoObject.R
011ff3c96625e4b5bcf1121e56a0543a *R/CreateGeoObject_BioGeoBEARS.R
59c544589f2b58424a165e6f3204a887 *R/CreateGeobyClassObject.R
7350ac55775cea778207a64d9f3ef538 *R/CreateSMatrix.R
af08bf4feb7799b54ccc73f52bd888b8 *R/DDexp.rescale.R
05a17e2d443df9c89c6f10aa7ea47852 *R/DDexp.rescale.geog.R
691127b7591fe1770aa90d2689bb75b1 *R/DDexpMulti_geo_ADiag.R
8f2ff5dbec3a67519577d7d66e47de59 *R/DDexpMulti_geo_ADiag_ME.R
f3d1a73fa3b3c0df5bb7d14991195126 *R/DDexpMulti_nogeo_ADiag.R
d07b69c6f7901c2c896baf79c510d02c *R/DDexpMulti_nogeo_ADiag_ME.R
35b80ac62c4a096a0c59c5942faf74e5 *R/DDexp_geo_ADiag.R
b1959a4984d83bd6b3219cd71c28f456 *R/DDexp_geo_ADiag_ME.R
a4521c50fdcd4655c2ea0f1ec1567bc9 *R/DDexp_nogeo_ADiag.R
8c40cf7f98bf5b66baaaf864fdb74183 *R/DDexp_nogeo_ADiag_ME.R
9dd75fe2ae09753657bc8e845e33da43 *R/DDlin.rescale.R
e6af86c43b4a99054cef04fe4e444b0c *R/DDlin.rescale.geog.R
60a7085697c2db2c871d8a8e296fa46f *R/DDlinMulti_geo_ADiag.R
095183de4c9161be4378af540ccaa455 *R/DDlinMulti_geo_ADiag_ME.R
0f7d8bd438ec4cf7f871dbf5dfabe9e2 *R/DDlinMulti_nogeo_ADiag.R
0e1af0febcf7147b37151ddc65016619 *R/DDlinMulti_nogeo_ADiag_ME.R
63a951df8b834dcdefca882234041085 *R/DDlin_geo_ADiag.R
21a95d0e1a42f499594d8edc2340177a *R/DDlin_geo_ADiag_ME.R
0327ef7b8cf091bf2b4c12dc1d84bd4e *R/DDlin_nogeo_ADiag.R
f6684ecfeb7a8aaa5ace51ee4ff63b60 *R/DDlin_nogeo_ADiag_ME.R
13e50b5d88c5a5a0325726f20934387e *R/GIC.R
4f0726bee1e920d4bf0470ed523dc092 *R/JSDt_cluster.R
d14253c4ec06bd469d33e33e35cc808b *R/JSDtree.R
050e6374eceeffccc59bb2a013f7fd80 *R/JSDtree_cluster.R
a68cc3765a1a419aa6f0a9414c81adee *R/MC.rescale.R
2d4e17a42ce28b189f2cf13ade35b294 *R/MC.rescale_geog.R
268539d58227d9af2d25509aae9202db *R/MC_geo_PM.R
ddf2784b95fb53b58710b097ef320ca1 *R/MC_geo_PM_ME.R
b2c96b3d4e6bf0295d0f2a8586c620fa *R/MC_nogeo_ADiag.R
64a230b6a1bbdb0f3ed93723503a6af0 *R/MC_nogeo_ADiag_ME.R
8bae1412d5e27459e3e61e87f7fca6da *R/MC_twoS_PM.R
ce9bb85501446c6923ee3bf111bf03dd *R/MC_twoS_PM_ME.R
416ff17d58ee1a4c7eab62f64810bc0b *R/MC_twoS_PM_geo.R
22294bb9e41d3851018d83311e2cb60a *R/MC_twoS_PM_geo_ME.R
97016ec9db45d4fe935583fba2ae8720 *R/MPhiAbstract.class.R
06c02efcfdf5b493f9de8561bd85c097 *R/MPhiFFT.class.R
af8b3aab9e4246bbd9e1b35e1935c646 *R/Phi.R
3d1ea2baa9f284f4fec94581cc6ad6ac *R/Psi.R
faaf4566fd41211f952bd919266033cf *R/ReconcileGeoObjectSMatrix.R
c64a0c49d260ed38159a48270298c395 *R/aPhenotypicModel.class.R
9766b2b4edf0215ea68277f89f47afdf *R/add.gts.R
3390a83d255a23742bd7c05a4e43526c *R/all_comb_models.R
eb240e340b0e6a9e8a91490b67b92e57 *R/apply_prob_dtt.R
a44fdc9b33180d848f061699ed47ed5f *R/base_sgd.R
db73a57669567068541e5a76fb315e17 *R/createModel.R
9360dd7012fd720c606bcc6617102944 *R/delineate_phylotypes.R
9cce929962c51435d27c39fd405a3b47 *R/div.models.R
bc88a2288e4bcba4de026f22b75daa49 *R/div.rates.R
c6bc1e56dfc2cf6190b5e6358729d08e *R/extract.clade.ln.R
76e1d1f3d0b8f2ce90c5f5144f15105a *R/fitTipData.R
283d2d6edadc14e5b2352428dd3c4883 *R/fit_ClaDS.R
03a57c1256e4c3ee8f74144258f12c78 *R/fit_ClaDS0.R
f529ae7f922cc2e51319ac087883d405 *R/fit_bd.R
3d157a3b775f957209b5ed6cf34df27e *R/fit_bd_backbone.R
2511e72c1123c8d1f3068aa4ffb94d36 *R/fit_bd_backbone_c.R
38dcfd4b8b90d01e9aa80076986d0fc8 *R/fit_bd_in_past.R
7117cf2145f8d63a6e17b0d19c0e0aec *R/fit_coal_cst.R
b8bb60aec95ea5640f23ee747a801d2b *R/fit_coal_var.R
9023e17b7e69385efda42a77320f3be1 *R/fit_env.R
7a24ad07a71594cc1ac2a4fee46528ad *R/fit_t_comp.R
ee12f28e3ca1d164c307033bc18ce082 *R/fit_t_comp_subgroup.R
5437b42c1fa6e5cf0a5f0e854ea8b6c5 *R/fit_t_env.R
1997a1b4fab3c7da14f6651a4161c82f *R/fit_t_env_ou.R
f2df3e23a144706e127336dd4bc75df2 *R/fit_t_pl.R
7d830c924218afe630b3263374f99c32 *R/fit_t_standard.R
1aab8ebdf982ee7a3a37a4d263045d00 *R/full.R
3c75e322dd7c05c863e67a8d805b6ffc *R/get.branching.nodes.R
a270447c917ede7abb38d8aa1f3c2b94 *R/get.comb.shift.R
94bb95fa5390b0b0c072f9b3f37ba49e *R/get.node.ages.R
4bb1fcf1119ace63542c91e3ccaaa378 *R/get.sampling.fractions.R
bfef90a3fcbc0117bb19fec7e70acb64 *R/getDataLikelihood.R
5b70993fe34c8935bf84e56fb61eef63 *R/getMAPS_ClaDS.R
3a9ea6b63fc9bfadc862a3e6f1b1fb2c *R/getMAPS_ClaDS0.R
599951919fbe9761ed0b928031b223ff *R/getTipDistribution.R
145164b064d4563595a8681ac7eacf2f *R/globals.R
0cb82953636d402b83bc712c5761fbf6 *R/integrate.R
f9e529b5ec78defae66c8c9ea8714221 *R/likelihood_bd.R
b23187781e62d18d0f59953d425a1e11 *R/likelihood_bd_backbone.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
212e6a0a1519705e566a3d4f803a0f47 *R/likelihood_subgroup_model.R
a7803fe3d6f70e293f57f7505a4688d3 *R/likelihood_t_DD.R
d4b9f84f4228a19b4eef8560391c1b2a *R/likelihood_t_DD_geog.R
a0f5807b58fa0b1d2945d4dd379fb7c3 *R/likelihood_t_MC.R
f3e4cb07b19d7e5a87cc7b8dbe35a9b9 *R/likelihood_t_MC_geog.R
97a7552fb663a8adb26bedc504771e81 *R/likelihood_t_env.R
ef184d424d34c5602e161f72cd1d5fa0 *R/make.simmap.BGB.R
5ae93a44d79907db1ba2015b4f27893d *R/mantel_test.R
eb22d94a7fbc1242870b9c4e2fd58d0a *R/mantel_test_nbpartners.R
ddf6ffef17049f8ae5464ddfd6685388 *R/misc_functions.R
d4a4ee6027b1a97c566392ad6a4d3c7c *R/modelSelection.R
08cedb0cdff2fa06bc300f68bf1ba854 *R/paleodiv.R
0bd63dbbc38b252b04d186dd4cfa8e0b *R/pblm.R
5ff48a074fee35e535a4583c8093e8a4 *R/phyl.pca_pl.R
2f3979d473c5c8e2fc1bdf500993c7a6 *R/phylosignal_network.R
fb22c2d279edcb982a601aed1a9959ac *R/phylosignal_sub_network.R
e37b0465e50805d9b8cd1a3a5317cb19 *R/pi_estimator.R
a3eb21cf3d730c69d1d02ee6b60f629a *R/pi_per_site.R
c4f64c58bbf7f195bd22c406bba37e2b *R/plot.fit_t.env.r
9b5fc00f95007c9275ec0fcbf6723830 *R/plot.fit_t_env.ou.R
baec2f80828bcfa98fc138a0c4023cd7 *R/plot_BICompare.R
f27acf57bc1df00dcebf04fefa0a7b58 *R/plot_BipartiteEvol.R
77eeda3c04784adcb28ca1f1b0568855 *R/plot_ClaDS0_chains.R
a9d0dbc0f59df7ffc535dc42a191ac5d *R/plot_ClaDS_chains.R
d5bcd50eefa372f8ffafa7f9bb0727fb *R/plot_ClaDS_phylo.R
eeec66c3618f53416ed78e29af6ba90a *R/plot_dtt.R
5170654f843cf0d5d5c6c8bc0c6529d0 *R/plot_fit_bd.R
a9e4a6b3893df59df6f435ba07d27bb4 *R/plot_fit_env.R
8b038a8caba6ce88b56501e85eb811f9 *R/plot_phylo_comb.R
997b9049232e8900f164520b75a7efe2 *R/plot_phylosignal_sub_network.R
0dc0aba13a86ca8d8df4d230376d5cff *R/plot_prob_dtt.R
ab84c71b9e30f7b31912bebf90464bec *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
5267b84a7ed7e3339d91adb562e8e2a5 *R/prob_dtt.R
6049df1e598bde96a00904dff117ee15 *R/proposal.R
906d3684ce3d09862f8ca44e4441c290 *R/remove.model.R
d59452a25b11edb9b064032748228eef *R/resortGeoObject.R
cde2a7645e8b40706efc5da95242abd2 *R/resortSMatrix.R
ebda28d4561ccf8ce13c3a10debf1171 *R/seg_sites_fasta.R
9546e35fe81279b68e757b944c0df423 *R/shift.estimates.R
f0d5844682dc090016c0c72032ebc0b1 *R/sim.BipartiteEvol.R
a149ae98a013e66913741f8d0c47cb0e *R/sim.convergence.geo.R
2864890a49612475ed5d793f5a123405 *R/sim.divergence.geo.R
07274efcda4a6139db91bb537f9704ed *R/sim_ClaDS.R
09000a9b42f312e8cfe22ea609bbf9fd *R/sim_MCBD.R
3fda6e826acdfc30480af1f8e9506cee *R/sim_env_bd.r
0add8eacf65f899d0652ace486f37a0f *R/sim_sgd.R
c8012dde2403f5355a3a04f525bb0867 *R/sim_t_comp.R
66b21f1ba829a78463cd4394db90794c *R/sim_t_env.R
71bae10d9bbd1c1d9619b4b7a06ec537 *R/sim_t_env_ou.R
236dc5800aa6c282f4c285844c3c05fc *R/sim_t_tworegime.R
10645d688d1230713ad9a407f30ea2d4 *R/simul.comb.shift.R
27b52fc80cda33a4ca340c1eee96054a *R/simulateTipData.R
b28252de8744209e10041f89d3f33dee *R/spectR.R
ae98899c46a7bf5fb56570c7ed2a5960 *R/spectR_t.R
582bcdf022fecd4d5d52e22c66a3cfe8 *R/stratified_BGB_to_tables.R
dc2e8df002dea1b9b1f3d01105211d45 *R/subtree.R
2fd7a782f9a2a2a6f7d6cce0fcc9503c *R/theta_estimator.R
6d34125af3f95b90f319f81344644d70 *R/trimSimmap.R
37f8a614e4e116cb57ce917be67b5025 *R/utils.R
bdb9116f037845e24627f592215d5c76 *R/utils_BipartiteEvol.R
c13b6db4e0e8e22ad921907e7d8dacc4 *README.md
9cb68376288bd6e482a03a2fec5880f9 *data/Anolis.data.rda
bea072a0086ddb231bde6bd83a5bb398 *data/BGB.examples.rda
44b3ef9f95e10176b4c9b8964fcc4907 *data/Balaenopteridae.rda
2f188f3ddc8f2b94da963b8094a9baeb *data/Calomys.rda
1c63a51d6199123d0e5cb31604f6101c *data/Caprimulgidae.rda
fa2e8f8c2535a0fc9b8fcbdd10c07883 *data/Caprimulgidae_ClaDS2.rda
1a01898e5f7814a368964a2cb8ed858e *data/Cetacea.rda
b9209b18f447af991f2ffec0bc01b885 *data/Cetacea_clades.rda
5f2b4f8ee2e31049173cf4def2f12145 *data/ClaDS0_example.rda
7129d2cab2428a26b0704f4a24d0d7ed *data/InfTemp.rda
291d2744e58ad57d66c80c01565aa256 *data/Phocoenidae.rda
55e106a18928f19ceaca3da8e7392830 *data/Phyllostomidae.rda
22a7928e0d562ae4e3b026628d871aec *data/Phyllostomidae_genera.rda
36577e963f4660811da0999ef9124172 *data/co2.rda
5b6e6ff417accb38196d78b12dfec43c *data/co2_res.rda
1bbab9d79cdf8fc1d8fcc2b126e01183 *data/coccolithophore.rda
7296a3bd223e4e31751b987361025968 *data/d13c.rda
964bd1152fae17ee4b12641e8ce163b6 *data/datalist
d27e6edd3fd4bf840a5b34607d77ebeb *data/foraminifera.rda
a4e103b888e0ceefe1b5ad214154e3c9 *data/greenalgae.rda
d63525e3fc508c321bd13183a6e3649e *data/landplant.rda
85d3ef74aabb0b33cb85163b3dcfeb01 *data/mycorrhizal_network.rda
88dbffcf18f9fcc2e6f17b7d8f639a0f *data/ostracoda.rda
986cef9f117b155820cf373e70cf6880 *data/radiolaria.rda
faf20597cbc5f3346db1cc805c6280ce *data/redalgae.rda
a97bcdbbd769bccfaa64e67cad9fdac5 *data/sealevel.rda
488bfe38e09c971a978279a364d21928 *data/shifts_cetacea.rda
a33ee6d190d084d5afdbca902fdb5bcf *data/silica.rda
cf6d3683eea938113f5b517b99bdc05c *data/taxo_cetacea.rda
ad40838cb0aa9abe4d9858616c9851f1 *inst/CITATION
dbdf6982b47acbe6076727543ad76fb4 *man/Anolis.data.Rd
4d7e365e248923049a19007b8ea72e53 *man/BGB.examples.Rd
d07844727d4fe2a9c1924591cdb09af6 *man/BICompare.Rd
faf28dde1e16a097473d87fed05f9fd8 *man/Balaenopteridae.Rd
5c663f6223006dc9668cb17d2fc88a43 *man/Calomys.Rd
f9a5f9b14f4288456fb73e9cd729e166 *man/Caprimulgidae.Rd
557608558515ec9a777368866ad75968 *man/Caprimulgidae_ClaDS2.Rd
cfe18d17bc205d610c70b8540b462916 *man/Cetacea.Rd
cff65560722a81e3c2b9c69e761aee7f *man/Cetacea_clades.Rd
5a1aa598d7a704948114097bf7a959cc *man/ClaDS0_example.Rd
d747ceaf5020a12a3bb2ba6f2c75f142 *man/CreateClassObject.Rd
07c3f861b6793854887e8b428b0f0e49 *man/CreateGeoObject.Rd
4e0059263d24eec6cbd6991953d349a3 *man/CreateGeoObject_BioGeoBEARS.Rd
65e1816a88575b9e556bd16768a7efff *man/CreateGeobyClassObject.Rd
c2979163e29430f7d12ca821a5767897 *man/GIC.Rd
67078d0e5dfe4989bb429ccc46808719 *man/InfTemp.Rd
7a96c9f76434939ba745e4be3ad73f45 *man/JSDt_cluster.Rd
e5a2569635314fcea24caf76f968f885 *man/JSDtree.Rd
d40767957b44e9a8f7251def5b4c42e9 *man/JSDtree_cluster.Rd
8ce4b50bdd2a799ace64f8bcf1f4c5df *man/MPhiFFT.Rd
ca14d3c0428cb99b4d3aa364e132530d *man/PhenotypicACDC-class.Rd
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0d94462c9674ca5c505b710f7581f049 *man/PhenotypicGMM-class.Rd
c4d73b88cdb749d869e4972e144b90b8 *man/PhenotypicModel-class.Rd
7378a8beeecf731a6f6dac626a78b2fb *man/PhenotypicOU-class.Rd
1574d334f198f87452d46e377686f21d *man/PhenotypicPM-class.Rd
01481094e08ae9f2f8451625f51d4b00 *man/Phocoenidae.Rd
aef1043d4319e032539ea654f1c52312 *man/Phyllostomidae.Rd
da5d184254d121be4ede02104112ed1a *man/Phyllostomidae_genera.Rd
e58452f84251856c183746e218a5a0a7 *man/Posdef.Rd
27cf188970d7523444c9b311d843777c *man/RPANDA-package.Rd
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71effdd4d9c24b34239477e7032602d0 *man/ancestral.Rd
74cde7fdabe96843758bac56c8a6c98e *man/apply_prob_dtt.Rd
60b674f92d636ed5c3186d75bfbaf443 *man/build_network.BipartiteEvol.Rd
5326212d91c0e6322350cb905a10dfbd *man/co2.Rd
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2ad02b97a2b4c9c4d40a2a33710d39a3 *man/coccolithophore.Rd
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4ef88425d9fcece9f2eb4479c230fb1a *man/createModelCoevolution.Rd
a76990c85354a723f39d9fe9c3e1e7e3 *man/d13c.Rd
2d227462d8f92d5af9ee009e97485201 *man/define_species.BipartiteEvol.Rd
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583d928bce8054caf691bfb39c8170ad *man/div.models.Rd
a8fafa6e9ca8d23d055b44209ffd5a2e *man/div.rates.Rd
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0217ef85bcf0d6910b7cefe43110887b *man/fit_ClaDS0.Rd
42b44cd984b375671d618fbc0429a2c9 *man/fit_bd.Rd
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7c2227f8ad87bca6c795efc959405d9b *man/fit_bd_backbone_c.Rd
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24de8e0e303423a3ca5e75abe5d4d2a0 *man/fit_coal_cst.Rd
6f58d1144e0cf6b8d874fe68982d1c03 *man/fit_coal_var.Rd
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b8bbc172d800e73b32631c4f48d37e2e *man/fit_t_comp.Rd
43f7b1d3849a6961d8959c65a1800e74 *man/fit_t_comp_subgroup.Rd
a4ccae7c78b06591445e14678f4a51c1 *man/fit_t_env.Rd
c281ae2cd14d29ec27911e4290aa60a7 *man/fit_t_env_ou.Rd
837cd2f5d8e0f7eaa5b2b1ae9cf612e1 *man/fit_t_pl.Rd
4c87a57e1ebe52b4ac5395329f0082f3 *man/fit_t_standard.Rd
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