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Merge pull request #86 from revbayes/sse_tutorials
Fossilized SSE tutorials
2 parents 8bc7c9f + ffc855d commit 1573607

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‎_bibliography/references.bib

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@@ -456,6 +456,22 @@ @article{Beaulieu2016
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year = {2016}
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}
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@article{Beaulieu2023,
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title = {Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity},
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volume = {72},
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issn = {1063-5157},
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url = {https://doi.org/10.1093/sysbio/syac049},
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doi = {10.1093/sysbio/syac049},
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number = {1},
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urldate = {2024-03-17},
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journal = {Systematic Biology},
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author = {Beaulieu, Jeremy M and O’Meara, Brian C},
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month = jan,
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year = {2023},
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pages = {50--61},
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}
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@article{bjork1970,
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author = {Bjork, Philip Reese},
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journal = {Transactions of the American Philosophical Society},
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year = {2003}
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}
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@article{Slater2015,
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title = {Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution},
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volume = {112},
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issn = {0027-8424, 1091-6490},
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url = {https://www.pnas.org/content/112/16/4897},
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doi = {10.1073/pnas.1403666111},
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number = {16},
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urldate = {2021-03-29},
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journal = {Proceedings of the National Academy of Sciences},
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author = {Slater, Graham J.},
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month = apr,
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year = {2015},
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pmid = {25901311},
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note = {Publisher: National Academy of Sciences
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Section: Biological Sciences},
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keywords = {Canidae, adaptive radiation, macroevolution, phylogenetics, rates},
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pages = {4897--4902},
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}
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@article{Springer2012,
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author = {Springer, Mark S and Meredith, Robert W and Gatesy, John and Emerling, Christopher A and Park, Jong and Rabosky, Daniel L and Stadler, Tanja and Steiner, Cynthia and Ryder, Oliver A and Jane{\v{c}}ka, Jan E and others},
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doi = {10.1371/journal.pone.0049521},

‎tutorials/run_tutorial_tests.sh

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@@ -83,11 +83,12 @@ for t in */tests.txt; do
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(
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cd scripts
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cat "$script" |
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sed 's/generations=[0-9]*/generations=1/g' |
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sed 's/generations[[:space:]]*=[[:space:]]*[0-9]*/generations=1/g' |
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sed 's/rules[[:space:]]*=[[:space:]]*[^,]*/generations=1/g' |
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sed 's/^n_gen *= *[0-9]*/n_gen = 1/' |
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sed 's/\.burnin([0-9][0-9]*/.burnin(1/' |
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sed 's/\.run([0-9][0-9]*/.run(1/' |
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sed 's/checkpointInterval=[0-9]*/checkpointInterval=1/g' > "cp_$script"
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sed 's/checkpointInterval[[:space:]]*=[[:space:]]*[0-9]*/checkpointInterval=1/g' > "cp_$script"
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)
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${rb_exec} -b scripts/cp_$script &> "output/${script%.[Rr]ev}.errout"
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script_result="$?"

‎tutorials/sse/bisse

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‎tutorials/sse/data/canidae_diet.nex

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#NEXUS
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[Data written by write.nexus.data.R, Wed Apr 30 14:49:11 2025]
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BEGIN DATA;
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DIMENSIONS NTAX=94 NCHAR=1;
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FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="01";
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MATRIX
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Aelurodon_asthenostylus 0
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Aelurodon_ferox 0
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Aelurodon_mcgrewi 0
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Aelurodon_stirtoni 0
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Aelurodon_taxoides 0
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Archaeocyon_leptodus 1
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Archaeocyon_pavidus 1
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Borophagus_diversidens 0
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Borophagus_hilli 0
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Borophagus_orc 0
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Borophagus_parvus 0
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Borophagus_pugnator 0
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Borophagus_secundus 0
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Canis_armbrusteri 0
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Canis_dirus 0
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Canis_edwardii 1
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Canis_ferox 1
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Canis_lepophagus 1
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Canis_thooides 1
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Carpocyon_compressus 1
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Carpocyon_robustus 0
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Carpocyon_webbi 0
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Cerdocyon_texanus 1
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Cormocyon_copei 1
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Cormocyon_haydeni 1
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Cynarctoides_accridens 1
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Cynarctoides_gawanae 1
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Cynarctoides_lemur 1
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Cynarctoides_luskensis 1
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Cynarctus_crucidens 1
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Cynarctus_galushai 1
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Cynarctus_saxatilis 1
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Cynarctus_voorhiesi 1
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Cynodesmus_thooides 0
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Desmocyon_matthewi 1
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Desmocyon_thomsoni 1
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Ectopocynus_antiquus 1
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Ectopocynus_intermedius 0
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Ectopocynus_simplicidens 0
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Enhydrocyon_basilatus 0
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Enhydrocyon_crassidens 0
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Enhydrocyon_pahinsintewakpa 0
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Enhydrocyon_stenocephalus 0
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Epicyon_haydeni 0
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Epicyon_saevus 0
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Eucyon_davisi 1
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Euoplocyon_brachygnathus 0
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Hesperocyon_coloradensis 1
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Hesperocyon_gregarius 1
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Leptocyon_gregorii 1
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Leptocyon_leidyi 1
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Leptocyon_vafer 1
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Leptocyon_vulpinus 1
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Mesocyon_coryphaeus 0
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Mesocyon_temnodon 1
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Metalopex_macconnelli 1
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Metalopex_merriami 1
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Metatomarctus_canavus 1
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Microtomarctus_conferta 1
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Osbornodon_brachypus 1
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Osbornodon_fricki 0
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Osbornodon_iamonensis 1
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Osbornodon_renjiei 1
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Osbornodon_sesnoni 1
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Otarocyon_cooki 1
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Otarocyon_macdonaldi 1
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Paracynarctus_kelloggi 1
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Paracynarctus_sinclari 1
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Paraenhydrocyon_josephi 0
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Paraenhydrocyon_wallovianus 0
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Paratomarctus_euthos 1
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Paratomarctus_temerarius 1
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Philotrox_condoni 0
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Phlaocyon_annectens 1
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Phlaocyon_latidens 1
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Phlaocyon_leucosteus 1
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Phlaocyon_marshlandensis 1
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Phlaocyon_minor 1
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Prohesperocyon_wilsoni 1
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Protepicyon_raki 0
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Protomarctus_opatus 1
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Psalidocyon_marianae 1
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Rhizocyon_oreganensis 1
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Sunkahetanka_geringensis 0
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Tomarctus_brevirostris 0
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Tomarctus_hippophaga 1
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Urocyon_citronus 1
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Urocyon_galushi 1
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Vulpes_stenognathus 1
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Xenocyon_texanus 0
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Canis_latrans 1
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Canis_lupus 0
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Cuon_alpinus 0
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Urocyon_cinereoargenteus 1
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;
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END;
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‎tutorials/sse/data/canidae_diet_mult.nex

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#NEXUS
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[Data written by write.nexus.data.R, Wed Apr 30 17:05:27 2025]
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BEGIN DATA;
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DIMENSIONS NTAX=94 NCHAR=1;
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FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="0123456789";
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MATRIX
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Aelurodon_asthenostylus 0
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Aelurodon_ferox 0
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Aelurodon_mcgrewi 0
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Aelurodon_stirtoni 0
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Aelurodon_taxoides 0
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Archaeocyon_leptodus 2
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Archaeocyon_pavidus 2
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Borophagus_diversidens 0
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Borophagus_hilli 0
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Borophagus_orc 0
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Borophagus_parvus 0
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Borophagus_pugnator 0
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Borophagus_secundus 0
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Canis_armbrusteri 0
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Canis_dirus 0
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Canis_edwardii 1
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Canis_ferox 1
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Canis_lepophagus 1
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Canis_thooides 1
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Carpocyon_compressus 1
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Carpocyon_robustus 0
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Carpocyon_webbi 0
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Cerdocyon_texanus 2
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Cormocyon_copei 2
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Cormocyon_haydeni 2
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Cynarctoides_accridens 2
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Cynarctoides_gawanae 1
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Cynarctoides_lemur 2
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Cynarctoides_luskensis 2
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Cynarctus_crucidens 2
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Cynarctus_galushai 1
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Cynarctus_saxatilis 2
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Cynarctus_voorhiesi 2
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Cynodesmus_thooides 0
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Desmocyon_matthewi 1
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Desmocyon_thomsoni 1
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Ectopocynus_antiquus 1
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Ectopocynus_intermedius 0
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Ectopocynus_simplicidens 0
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Enhydrocyon_basilatus 0
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Enhydrocyon_crassidens 0
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Enhydrocyon_pahinsintewakpa 0
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Enhydrocyon_stenocephalus 0
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Epicyon_haydeni 0
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Epicyon_saevus 0
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Eucyon_davisi 2
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Euoplocyon_brachygnathus 0
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Hesperocyon_coloradensis 1
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Hesperocyon_gregarius 2
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Leptocyon_gregorii 1
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Leptocyon_leidyi 2
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Leptocyon_vafer 1
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Leptocyon_vulpinus 1
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Mesocyon_coryphaeus 0
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Mesocyon_temnodon 1
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Metalopex_macconnelli 2
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Metalopex_merriami 2
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Metatomarctus_canavus 2
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Microtomarctus_conferta 1
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Osbornodon_brachypus 1
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Osbornodon_fricki 0
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Osbornodon_iamonensis 1
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Osbornodon_renjiei 2
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Osbornodon_sesnoni 2
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Otarocyon_cooki 2
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Otarocyon_macdonaldi 1
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Paracynarctus_kelloggi 2
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Paracynarctus_sinclari 1
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Paraenhydrocyon_josephi 0
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Paraenhydrocyon_wallovianus 0
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Paratomarctus_euthos 1
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Paratomarctus_temerarius 1
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Philotrox_condoni 0
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Phlaocyon_annectens 2
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Phlaocyon_latidens 2
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Phlaocyon_leucosteus 2
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Phlaocyon_marshlandensis 2
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Phlaocyon_minor 2
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Prohesperocyon_wilsoni 2
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Protepicyon_raki 0
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Protomarctus_opatus 1
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Psalidocyon_marianae 1
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Rhizocyon_oreganensis 2
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Sunkahetanka_geringensis 0
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Tomarctus_brevirostris 0
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Tomarctus_hippophaga 1
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Urocyon_citronus 2
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Urocyon_galushi 2
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Vulpes_stenognathus 2
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Xenocyon_texanus 0
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Canis_latrans 1
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Canis_lupus 0
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Cuon_alpinus 0
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Urocyon_cinereoargenteus 2
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;
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END;
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