55c0e462c8acac6afd299491ef78bba6 *DESCRIPTION
38f794510c47dbf6eaf1df6ebaee682f *NAMESPACE
dff6460ac1a6caff8f7b87b0757b93d6 *R/BICompare.R
4900f55b40fdd4409a6d4a730c6a936f *R/CreateBioGeoB_Object_subclade.R
122ac1ab6bb6b87c7865ef817ea9c89d *R/CreateClassObject.R
e8ef3d6648c49defd4b8634a96fd7de0 *R/CreateGeoObject.R
f19f97b5e988da2df68338fd9876100d *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
10c60a350ee4b21e3c246980d5294a7d *R/JSDt_cluster.R
cb561ccd53630f806ffc54813cb0575a *R/JSDtree.R
7d104826e713cfdf3d72ef7f978d87b5 *R/JSDtree_cluster.R
5cea1b03cb4d0d3d226ec79c5ac75f88 *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
ae5d5f82231c7dce84b4bbc78f4432ac *R/aPhenotypicModel.class.R
a44fdc9b33180d848f061699ed47ed5f *R/base_sgd.R
db73a57669567068541e5a76fb315e17 *R/createModel.R
0b88f48ebf50a970990e5033fd08673c *R/delineate_phylotypes.R
04fdff781e9b36399e74bead09ae1f00 *R/fitTipData.R
00945a941c87eef455646963ff6c1455 *R/fit_ClaDS.R
9c17b651835c15d3149e00e17aaf7226 *R/fit_ClaDS0.R
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7117cf2145f8d63a6e17b0d19c0e0aec *R/fit_coal_cst.R
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6119aea7f88a5139b049d3c520a1490b *R/fit_t_comp.R
55f315bea80562fa9b81d21c5160f593 *R/fit_t_comp_subgroup.R
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1aab8ebdf982ee7a3a37a4d263045d00 *R/full.R
153292303cb54a68297de46c7eb32ec3 *R/getDataLikelihood.R
5b70993fe34c8935bf84e56fb61eef63 *R/getMAPS_ClaDS.R
3a9ea6b63fc9bfadc862a3e6f1b1fb2c *R/getMAPS_ClaDS0.R
4eb5702427a8c6f3e38f6a50481f341e *R/getTipDistribution.R
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f9e529b5ec78defae66c8c9ea8714221 *R/likelihood_bd.R
1fdfd4057e6e4c0394bfc37d5e3b8318 *R/likelihood_coal_cst.R
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939b14961eac07c4e420f2f8ba5dc47f *R/likelihood_coal_var.R
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7b7268c7c2688c94d3038ab3c44ad529 *R/likelihood_t_MC.R
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53bef064da807783490893cd48797faf *R/likelihood_t_env.R
5ae93a44d79907db1ba2015b4f27893d *R/mantel_test.R
3ee70ef678aa432a75a89bcfc842ac70 *R/mantel_test_nbpartners.R
409b918113715915c556378e615ae95e *R/misc_functions.R
0f91f068389d6ac025b3f024a1db1e09 *R/modelSelection.R
0bd63dbbc38b252b04d186dd4cfa8e0b *R/pblm.R
5ff48a074fee35e535a4583c8093e8a4 *R/phyl.pca_pl.R
428d60df577eaa1e7fce177fe5f6f1fa *R/phylosignal_network.R
b625b8ea326f154d1b7f60dbea4e19d4 *R/phylosignal_sub_network.R
e37b0465e50805d9b8cd1a3a5317cb19 *R/pi_estimator.R
a3eb21cf3d730c69d1d02ee6b60f629a *R/pi_per_site.R
c4f64c58bbf7f195bd22c406bba37e2b *R/plot.fit_t.env.r
baec2f80828bcfa98fc138a0c4023cd7 *R/plot_BICompare.R
b6066f53e26d711ad52a7f6e457f697a *R/plot_BipartiteEvol.R
77eeda3c04784adcb28ca1f1b0568855 *R/plot_ClaDS0_chains.R
a9d0dbc0f59df7ffc535dc42a191ac5d *R/plot_ClaDS_chains.R
1c46d150da690433f623418043c5a2db *R/plot_ClaDS_phylo.R
eeec66c3618f53416ed78e29af6ba90a *R/plot_dtt.R
5170654f843cf0d5d5c6c8bc0c6529d0 *R/plot_fit_bd.R
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7626dace92bd1ed6307ca3da07234dbb *R/plot_phylosignal_sub_network.R
d95d4ac624746c288608cf31cc53810f *R/plot_prob_dtt.R
aae3c96d3d7e89a6a175a51e12f462d7 *R/plot_spectR.R
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e93c6a64ad98de36e50805a628ab988b *R/print.fit_pl.R
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6049df1e598bde96a00904dff117ee15 *R/proposal.R
d59452a25b11edb9b064032748228eef *R/resortGeoObject.R
cde2a7645e8b40706efc5da95242abd2 *R/resortSMatrix.R
ebda28d4561ccf8ce13c3a10debf1171 *R/seg_sites_fasta.R
070d0afeeddc4dab91a2194f27fd0817 *R/sim.BipartiteEvol.R
5546fac46c467f90e968030a3629acee *R/sim.convergence.geo.R
2864890a49612475ed5d793f5a123405 *R/sim.divergence.geo.R
81413eecd8a27549e4da0285448a2413 *R/sim_ClaDS.R
5858ef82bc6c4d0ca74521059d579a7b *R/sim_MCBD.R
3fda6e826acdfc30480af1f8e9506cee *R/sim_env_bd.r
0add8eacf65f899d0652ace486f37a0f *R/sim_sgd.R
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2294c7efd93093e9735ef1f8d33fd6b9 *R/sim_t_env.R
6cf893792a3d48a8cd195766e34b8d3f *R/sim_t_tworegime.R
af775e034518dd380bd1a00b13ac0322 *R/simulateTipData.R
0bad0e50905fb99e3125ab3046cb514f *R/spectR.R
ca54daa31b968cb94137cde38d0132a4 *R/spectR_t.R
290c89ef86637c7b1baba5b2a8642d8b *R/stratified_BGB_to_tables.R
2fd7a782f9a2a2a6f7d6cce0fcc9503c *R/theta_estimator.R
6d34125af3f95b90f319f81344644d70 *R/trimSimmap.R
13da068378ab8f15fab9269876bed712 *R/utils.R
8cb5633401de0cce4b790ed07b22da04 *R/utils_BipartiteEvol.R
9089d053e653a9ef4a387cb9c3a7b218 *README.md
d95ed2ed975ef9a85a4e061085b56aeb *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
c6bf2224f884a43b84a877440b61e3f9 *data/Cetacea.rda
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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
ff3dd9f062784d486ea3c41cf98951e6 *data/datalist
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a4e103b888e0ceefe1b5ad214154e3c9 *data/greenalgae.rda
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88dbffcf18f9fcc2e6f17b7d8f639a0f *data/ostracoda.rda
986cef9f117b155820cf373e70cf6880 *data/radiolaria.rda
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a97bcdbbd769bccfaa64e67cad9fdac5 *data/sealevel.rda
a33ee6d190d084d5afdbca902fdb5bcf *data/silica.rda
f1fa6bd46ac2a46c80181d7de63c5ed2 *inst/CITATION
dbdf6982b47acbe6076727543ad76fb4 *man/Anolis.data.Rd
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ca245416dd1834a7d5acd09c0057af6f *man/BICompare.Rd
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f9a5f9b14f4288456fb73e9cd729e166 *man/Caprimulgidae.Rd
557608558515ec9a777368866ad75968 *man/Caprimulgidae_ClaDS2.Rd
cfe18d17bc205d610c70b8540b462916 *man/Cetacea.Rd
cff65560722a81e3c2b9c69e761aee7f *man/Cetacea_clades.Rd
5a1aa598d7a704948114097bf7a959cc *man/ClaDS0_example.Rd
0a3826bec35341e1bdaaa2fd40b335c9 *man/CreateClassObject.Rd
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2553ea64a5c1756c8e39959eecac23dd *man/CreateGeobyClassObject.Rd
6eca26ef6400f679c09d924212a3679e *man/GIC.Rd
67078d0e5dfe4989bb429ccc46808719 *man/InfTemp.Rd
63a34f2471acbd3b214acef9f027326d *man/JSDt_cluster.Rd
e5a2569635314fcea24caf76f968f885 *man/JSDtree.Rd
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8ce4b50bdd2a799ace64f8bcf1f4c5df *man/MPhiFFT.Rd
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0d94462c9674ca5c505b710f7581f049 *man/PhenotypicGMM-class.Rd
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7378a8beeecf731a6f6dac626a78b2fb *man/PhenotypicOU-class.Rd
1574d334f198f87452d46e377686f21d *man/PhenotypicPM-class.Rd
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202e18392532a4da4cc56814f0cf913a *man/Phyllostomidae.Rd
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e58452f84251856c183746e218a5a0a7 *man/Posdef.Rd
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2ad02b97a2b4c9c4d40a2a33710d39a3 *man/coccolithophore.Rd
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