Fossilized SSE tutorials

_bibliography/references.bib

@@ -456,6 +456,22 @@ @article{Beaulieu2016
     year = {2016}
 }
 
+@article{Beaulieu2023,
+	title = {Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity},
+	volume = {72},
+	issn = {1063-5157},
+	url = {https://doi.org/10.1093/sysbio/syac049},
+	doi = {10.1093/sysbio/syac049},
+	number = {1},
+	urldate = {2024-03-17},
+	journal = {Systematic Biology},
+	author = {Beaulieu, Jeremy M and O’Meara, Brian C},
+	month = jan,
+	year = {2023},
+	pages = {50--61},
+}
+
+
 @article{bjork1970,
     author = {Bjork, Philip Reese},
     journal = {Transactions of the American Philosophical Society},
@@ -2692,6 +2708,25 @@ @article{Seiffert2003
     year = {2003}
 }
 
+@article{Slater2015,
+	title = {Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution},
+	volume = {112},
+	issn = {0027-8424, 1091-6490},
+	url = {https://www.pnas.org/content/112/16/4897},
+	doi = {10.1073/pnas.1403666111},
+	number = {16},
+	urldate = {2021-03-29},
+	journal = {Proceedings of the National Academy of Sciences},
+	author = {Slater, Graham J.},
+	month = apr,
+	year = {2015},
+	pmid = {25901311},
+	note = {Publisher: National Academy of Sciences
+Section: Biological Sciences},
+	keywords = {Canidae, adaptive radiation, macroevolution, phylogenetics, rates},
+	pages = {4897--4902},
+}
+
 @article{Springer2012,
     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},
     doi = {10.1371/journal.pone.0049521},

tutorials/run_tutorial_tests.sh

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

tutorials/sse/data/canidae_diet.nex

@@ -0,0 +1,103 @@
+#NEXUS
+[Data written by write.nexus.data.R, Wed Apr 30 14:49:11 2025]
+BEGIN DATA;
+  DIMENSIONS NTAX=94 NCHAR=1;
+  FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="01";
+  MATRIX
+    Aelurodon_asthenostylus          0
+    Aelurodon_ferox                  0
+    Aelurodon_mcgrewi                0
+    Aelurodon_stirtoni               0
+    Aelurodon_taxoides               0
+    Archaeocyon_leptodus             1
+    Archaeocyon_pavidus              1
+    Borophagus_diversidens           0
+    Borophagus_hilli                 0
+    Borophagus_orc                   0
+    Borophagus_parvus                0
+    Borophagus_pugnator              0
+    Borophagus_secundus              0
+    Canis_armbrusteri                0
+    Canis_dirus                      0
+    Canis_edwardii                   1
+    Canis_ferox                      1
+    Canis_lepophagus                 1
+    Canis_thooides                   1
+    Carpocyon_compressus             1
+    Carpocyon_robustus               0
+    Carpocyon_webbi                  0
+    Cerdocyon_texanus                1
+    Cormocyon_copei                  1
+    Cormocyon_haydeni                1
+    Cynarctoides_accridens           1
+    Cynarctoides_gawanae             1
+    Cynarctoides_lemur               1
+    Cynarctoides_luskensis           1
+    Cynarctus_crucidens              1
+    Cynarctus_galushai               1
+    Cynarctus_saxatilis              1
+    Cynarctus_voorhiesi              1
+    Cynodesmus_thooides              0
+    Desmocyon_matthewi               1
+    Desmocyon_thomsoni               1
+    Ectopocynus_antiquus             1
+    Ectopocynus_intermedius          0
+    Ectopocynus_simplicidens         0
+    Enhydrocyon_basilatus            0
+    Enhydrocyon_crassidens           0
+    Enhydrocyon_pahinsintewakpa      0
+    Enhydrocyon_stenocephalus        0
+    Epicyon_haydeni                  0
+    Epicyon_saevus                   0
+    Eucyon_davisi                    1
+    Euoplocyon_brachygnathus         0
+    Hesperocyon_coloradensis         1
+    Hesperocyon_gregarius            1
+    Leptocyon_gregorii               1
+    Leptocyon_leidyi                 1
+    Leptocyon_vafer                  1
+    Leptocyon_vulpinus               1
+    Mesocyon_coryphaeus              0
+    Mesocyon_temnodon                1
+    Metalopex_macconnelli            1
+    Metalopex_merriami               1
+    Metatomarctus_canavus            1
+    Microtomarctus_conferta          1
+    Osbornodon_brachypus             1
+    Osbornodon_fricki                0
+    Osbornodon_iamonensis            1
+    Osbornodon_renjiei               1
+    Osbornodon_sesnoni               1
+    Otarocyon_cooki                  1
+    Otarocyon_macdonaldi             1
+    Paracynarctus_kelloggi           1
+    Paracynarctus_sinclari           1
+    Paraenhydrocyon_josephi          0
+    Paraenhydrocyon_wallovianus      0
+    Paratomarctus_euthos             1
+    Paratomarctus_temerarius         1
+    Philotrox_condoni                0
+    Phlaocyon_annectens              1
+    Phlaocyon_latidens               1
+    Phlaocyon_leucosteus             1
+    Phlaocyon_marshlandensis         1
+    Phlaocyon_minor                  1
+    Prohesperocyon_wilsoni           1
+    Protepicyon_raki                 0
+    Protomarctus_opatus              1
+    Psalidocyon_marianae             1
+    Rhizocyon_oreganensis            1
+    Sunkahetanka_geringensis         0
+    Tomarctus_brevirostris           0
+    Tomarctus_hippophaga             1
+    Urocyon_citronus                 1
+    Urocyon_galushi                  1
+    Vulpes_stenognathus              1
+    Xenocyon_texanus                 0
+    Canis_latrans                    1
+    Canis_lupus                      0
+    Cuon_alpinus                     0
+    Urocyon_cinereoargenteus         1
+  ;
+END;
+

tutorials/sse/data/canidae_diet_mult.nex

@@ -0,0 +1,103 @@
+#NEXUS
+[Data written by write.nexus.data.R, Wed Apr 30 17:05:27 2025]
+BEGIN DATA;
+  DIMENSIONS NTAX=94 NCHAR=1;
+  FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="0123456789";
+  MATRIX
+    Aelurodon_asthenostylus          0
+    Aelurodon_ferox                  0
+    Aelurodon_mcgrewi                0
+    Aelurodon_stirtoni               0
+    Aelurodon_taxoides               0
+    Archaeocyon_leptodus             2
+    Archaeocyon_pavidus              2
+    Borophagus_diversidens           0
+    Borophagus_hilli                 0
+    Borophagus_orc                   0
+    Borophagus_parvus                0
+    Borophagus_pugnator              0
+    Borophagus_secundus              0
+    Canis_armbrusteri                0
+    Canis_dirus                      0
+    Canis_edwardii                   1
+    Canis_ferox                      1
+    Canis_lepophagus                 1
+    Canis_thooides                   1
+    Carpocyon_compressus             1
+    Carpocyon_robustus               0
+    Carpocyon_webbi                  0
+    Cerdocyon_texanus                2
+    Cormocyon_copei                  2
+    Cormocyon_haydeni                2
+    Cynarctoides_accridens           2
+    Cynarctoides_gawanae             1
+    Cynarctoides_lemur               2
+    Cynarctoides_luskensis           2
+    Cynarctus_crucidens              2
+    Cynarctus_galushai               1
+    Cynarctus_saxatilis              2
+    Cynarctus_voorhiesi              2
+    Cynodesmus_thooides              0
+    Desmocyon_matthewi               1
+    Desmocyon_thomsoni               1
+    Ectopocynus_antiquus             1
+    Ectopocynus_intermedius          0
+    Ectopocynus_simplicidens         0
+    Enhydrocyon_basilatus            0
+    Enhydrocyon_crassidens           0
+    Enhydrocyon_pahinsintewakpa      0
+    Enhydrocyon_stenocephalus        0
+    Epicyon_haydeni                  0
+    Epicyon_saevus                   0
+    Eucyon_davisi                    2
+    Euoplocyon_brachygnathus         0
+    Hesperocyon_coloradensis         1
+    Hesperocyon_gregarius            2
+    Leptocyon_gregorii               1
+    Leptocyon_leidyi                 2
+    Leptocyon_vafer                  1
+    Leptocyon_vulpinus               1
+    Mesocyon_coryphaeus              0
+    Mesocyon_temnodon                1
+    Metalopex_macconnelli            2
+    Metalopex_merriami               2
+    Metatomarctus_canavus            2
+    Microtomarctus_conferta          1
+    Osbornodon_brachypus             1
+    Osbornodon_fricki                0
+    Osbornodon_iamonensis            1
+    Osbornodon_renjiei               2
+    Osbornodon_sesnoni               2
+    Otarocyon_cooki                  2
+    Otarocyon_macdonaldi             1
+    Paracynarctus_kelloggi           2
+    Paracynarctus_sinclari           1
+    Paraenhydrocyon_josephi          0
+    Paraenhydrocyon_wallovianus      0
+    Paratomarctus_euthos             1
+    Paratomarctus_temerarius         1
+    Philotrox_condoni                0
+    Phlaocyon_annectens              2
+    Phlaocyon_latidens               2
+    Phlaocyon_leucosteus             2
+    Phlaocyon_marshlandensis         2
+    Phlaocyon_minor                  2
+    Prohesperocyon_wilsoni           2
+    Protepicyon_raki                 0
+    Protomarctus_opatus              1
+    Psalidocyon_marianae             1
+    Rhizocyon_oreganensis            2
+    Sunkahetanka_geringensis         0
+    Tomarctus_brevirostris           0
+    Tomarctus_hippophaga             1
+    Urocyon_citronus                 2
+    Urocyon_galushi                  2
+    Vulpes_stenognathus              2
+    Xenocyon_texanus                 0
+    Canis_latrans                    1
+    Canis_lupus                      0
+    Cuon_alpinus                     0
+    Urocyon_cinereoargenteus         2
+  ;
+END;
+