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revbayes · Jan 25, 2024 · 5447df9 · 5447df9
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diff --git a/tutorials/data/1.nex b/tutorials/data/1.nex
@@ -0,0 +1,24 @@
+#NEXUS
+[Data written by write.nexus.data.R, Fri Aug  4 10:29:15 2023]
+BEGIN DATA;
+  DIMENSIONS NTAX=15 NCHAR=65;
+  FORMAT DATATYPE=STANDARD MISSING=? GAP=- INTERLEAVE=NO symbols="0123456789";
+  MATRIX
+    Leonhardtina_ORIG_Leonhardtina               42102222200001121210010200211002001101000110011100001101010100101
+    missing_ORIG_Procerberus_and_Cimolestes      00121212210012021202002122021220101011101100011100101001010101101
+    Brychotherium_ORIG_Brychotherium             31200012100222021011222012111222010100011100000110101001000001111
+    Dissopsalis_ORIG_Dissopsalis                 33210012000111002002222022121122101110000000001100101100010100111
+    Anasinopa_ORIG_Anasinopa                     33110110200021021111210100121012211100101110100100001000110100111
+    Metasinopa_ORIG_Metasinopa                   33120012221002021011210010121202211101111110000100101001000111011
+    Masrasector_ORIG_Masrasector                 30120012210202020011011010121222100101011010010100011000110110011
+    Kyawdawia_ORIG_Kyawdawia                     32120002000222021010220110121222110100011000011110111001010000011
+    Paratritemnodon_ORIG_Paratritemnodon         32122012200211021100020110221222201110010101000100111001011101011
+    Prodissopsalis_ORIG_Prodissopsalis           31120002222212021001222010121212011111001010101000001010010111011
+    Eurotherium_ORIG_Eurotherium                 31120022222200021011212010120212211101001010101000100100010110101
+    Cynohyaenodon_ORIG_Cynohyaenodon             11120022122200021210200000001022211101000110101000101000000100110
+    no_age_data_ORIG_Paracynohyaenodon           01110022111202021112010010121222211111000110100000101100010110111
+    missing_ORIG_Proviverra_and_Lesmesodon       10120022110022021212211200111102211110001011101000001101100111001
+    Allopterodon_ORIG_Allopterodon               00020022110222021011000200121022001101010111111101100100110101101
+  ;
+END;
+
diff --git a/tutorials/data/Agnolin_2007a_paleobiodb.nex b/tutorials/data/Agnolin_2007a_paleobiodb.nex
@@ -0,0 +1,22 @@
+#NEXUS
+[File downloaded from graemetlloyd.com]
+BEGIN DATA;
+DIMENSIONS  NTAX=12 NCHAR=51;
+	FORMAT DATATYPE = STANDARD SYMBOLS= " 0 1 2 3" MISSING=? GAP=- ;
+MATRIX
+Tinamidae_ORIG_Tinamidae       000000000000000000000000000000000000000000000000000
+Rallidae_ORIG_Rallidae        000000000000000000000000000000000000000000000000000
+no_age_data_ORIG_Paraphysornis   0????0??????0??0?00000010?0100000??010???0001000010
+Patagornis_ORIG_Tolmodus        000000000000?00000000001000100000??0000000001000010
+Phorusrhacos_ORIG_Phorusrhacos    0????0????????0??00???????0100000???0????0001000010
+Galliformes_ORIG_Galliformes     000000000000000011000012000010000000000000000000010
+Diatryma_ORIG_Diatryma        0100010010011010111011130001101010?0001111111101001
+Brontornis_ORIG_Brontornis      ?????????????????110?1?11?1??????0???????111110?001
+Dromornithidae_ORIG_Dromornithidae  0100010?101111?0111111111?11??1??00??01111111101001
+no_age_data_ORIG_Anhimidae       011111111111111111111111111111111111111111111101010
+Anseranatidae_ORIG_Anseranatidae   111111111110111111111111111111111111111111111101010
+Anatoidea_ORIG_Anatoidea       111011011010111111111111111110001000001111111111110
+;
+END;
+
+
diff --git a/tutorials/data/Egi_etal_2005.nex b/tutorials/data/Egi_etal_2005.nex
@@ -0,0 +1,23 @@
+#NEXUS
+[File downloaded from graemetlloyd.com]
+BEGIN DATA;
+DIMENSIONS  NTAX=15 NCHAR=65;
+	FORMAT DATATYPE = STANDARD SYMBOLS= " 0 1 2 3 4" MISSING=? GAP=- ;
+MATRIX
+missing_ORIG_Procerberus_and_Cimolestes  0000000100000000001000?0010000000000001100000001000000?0000000000
+missing_ORIG_Proviverra_and_Lesmesodon   100????0?00110001001010??0001013111021??20?1100001021010000110000
+Allopterodon_ORIG_Allopterodon                10121110110110111111110?11001121000111101011000002121000020100000
+Leonhardtina_ORIG_Leonhardtina                11121210210011110001000?11000120000110212022120001120000120200001
+Eurotherium_ORIG_Eurotherium                 201100101011001011111102110011000011100120111122010211001022000?0
+Prodissopsalis_ORIG_Prodissopsalis              3010001011110001111?1112??0?0010001110010111110201001100110200000
+Cynohyaenodon_ORIG_Cynohyaenodon               11111001011110211111111100011000000120102011010200110101110200000
+no_age_data_ORIG_Paracynohyaenodon           111110010111112111111101110?111000012010201111020112110110?200000
+Brychotherium_ORIG_Brychotherium               10110????11112?1111111021001200100012020201210221201120102?300111
+Metasinopa_ORIG_Metasinopa                  21???????00112101110110??1111002000120202011111212111111100200010
+Dissopsalis_ORIG_Dissopsalis                 420100121122011111202222101?1?02000022100111111212011101010300110
+Anasinopa_ORIG_Anasinopa                   311??011112210101120110??0000001000020200121111212110111110201010
+Paratritemnodon_ORIG_Paratritemnodon             100101121101121011101122010?0?11??0021101102011212110101001000010
+Masrasector_ORIG_Masrasector                 10100002?00112?01111001??1011010000020200111011112110001101101010
+Kyawdawia_ORIG_Kyawdawia                   420102121110121011111110010???00?0?1201001120111121?0001101100010
+;
+END;
diff --git a/tutorials/divrate/div_rate_intro.html b/tutorials/divrate/div_rate_intro.html
@@ -357,14 +357,14 @@ <h3 class="subsection" id="the-birth-death-branching-process">The birth-death br
 <li><span id="Condamine2018">Condamine F.L., Rolland J., Höhna S., Sperling F.A.H., Sanmartín I. 2018. Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies. Systematic Biology. 67:940–964.</span>
 
 </li>
-<li><span id="Hoehna2014a">Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.</span>
+<li><span id="Hoehna2013">Höhna S. 2013. Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. Bioinformatics. 29:1367–1374.</span>
 
-<a href="https://doi.org/10.1371/journal.pone.0084184">10.1371/journal.pone.0084184</a>
+<a href="https://doi.org/10.1093/bioinformatics/btt153">10.1093/bioinformatics/btt153</a>
 
 </li>
-<li><span id="Hoehna2013">Höhna S. 2013. Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes. Bioinformatics. 29:1367–1374.</span>
+<li><span id="Hoehna2014a">Höhna S. 2014. Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling. PLoS One. 9:e84184.</span>
 
-<a href="https://doi.org/10.1093/bioinformatics/btt153">10.1093/bioinformatics/btt153</a>
+<a href="https://doi.org/10.1371/journal.pone.0084184">10.1371/journal.pone.0084184</a>
 
 </li>
 <li><span id="Hoehna2015a">Höhna S. 2015. The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events. Journal of Theoretical Biology. 380:321–331.</span>

diff --git a/tutorials/fbd_simple/index.html b/tutorials/fbd_simple/index.html
@@ -888,10 +888,10 @@ <h3 class="subsection" id="summary">Summary</h3>
 <a href="https://doi.org/10.1093/molbev/mss075">10.1093/molbev/mss075</a>
 
 </li>
-<li><span id="Freyman2019">Freyman W.A., Höhna S. 2019. Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages. Systematic Biology. 68:505–519.</span>
+<li><span id="Freyman2018">Freyman W.A., Höhna S. 2018. Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach. Systematic Biology. 67:1995–215.</span>
 
 </li>
-<li><span id="Freyman2018">Freyman W.A., Höhna S. 2018. Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach. Systematic Biology. 67:1995–215.</span>
+<li><span id="Freyman2019">Freyman W.A., Höhna S. 2019. Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages. Systematic Biology. 68:505–519.</span>
 
 </li>
 <li><span id="Gavryushkina2016">Gavryushkina A., Heath T.A., Ksepka D.T., Stadler T., Welch D., Drummond A.J. 2017. Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins. Systematic Biology. 66:57–73.</span>

diff --git a/tutorials/figures/workflow.png b/tutorials/figures/workflow.png
diff --git a/tutorials/pps_morpho/data/Agnolin_2007a_paleobiodb.nex b/tutorials/pps_morpho/data/Agnolin_2007a_paleobiodb.nex
@@ -0,0 +1,20 @@
+#NEXUS
+[File downloaded from graemetlloyd.com]
+BEGIN DATA;
+DIMENSIONS  NTAX=12 NCHAR=51;
+	FORMAT DATATYPE = STANDARD SYMBOLS= " 0 1 2 3" MISSING=? GAP=- ;
+MATRIX
+Tinamidae_ORIG_Tinamidae       000000000000000000000000000000000000000000000000000
+Rallidae_ORIG_Rallidae        000000000000000000000000000000000000000000000000000
+no_age_data_ORIG_Paraphysornis   0????0??????0??0?00000010?0100000??010???0001000010
+Patagornis_ORIG_Tolmodus        000000000000?00000000001000100000??0000000001000010
+Phorusrhacos_ORIG_Phorusrhacos    0????0????????0??00???????0100000???0????0001000010
+Galliformes_ORIG_Galliformes     000000000000000011000012000010000000000000000000010
+Diatryma_ORIG_Diatryma        0100010010011010111011130001101010?0001111111101001
+Brontornis_ORIG_Brontornis      ?????????????????110?1?11?1??????0???????111110?001
+Dromornithidae_ORIG_Dromornithidae  0100010?101111?0111111111?11??1??00??01111111101001
+no_age_data_ORIG_Anhimidae       011111111111111111111111111111111111111111111101010
+Anseranatidae_ORIG_Anseranatidae   111111111110111111111111111111111111111111111101010
+Anatoidea_ORIG_Anatoidea       111011011010111111111111111110001000001111111111110
+;
+END;
diff --git a/tutorials/pps_morpho/data/Egi_etal_2005a_paleobiodb.nex b/tutorials/pps_morpho/data/Egi_etal_2005a_paleobiodb.nex
@@ -0,0 +1,23 @@
+#NEXUS
+[File downloaded from graemetlloyd.com]
+BEGIN DATA;
+DIMENSIONS  NTAX=15 NCHAR=65;
+	FORMAT DATATYPE = STANDARD SYMBOLS= " 0 1 2 3 4" MISSING=? GAP=- ;
+MATRIX
+missing_ORIG_Procerberus_and_Cimolestes  0000000100000000001000?0010000000000001100000001000000?0000000000
+missing_ORIG_Proviverra_and_Lesmesodon   100????0?00110001001010??0001013111021??20?1100001021010000110000
+Allopterodon_ORIG_Allopterodon                10121110110110111111110?11001121000111101011000002121000020100000
+Leonhardtina_ORIG_Leonhardtina                11121210210011110001000?11000120000110212022120001120000120200001
+Eurotherium_ORIG_Eurotherium                 201100101011001011111102110011000011100120111122010211001022000?0
+Prodissopsalis_ORIG_Prodissopsalis              3010001011110001111?1112??0?0010001110010111110201001100110200000
+Cynohyaenodon_ORIG_Cynohyaenodon               11111001011110211111111100011000000120102011010200110101110200000
+no_age_data_ORIG_Paracynohyaenodon           111110010111112111111101110?111000012010201111020112110110?200000
+Brychotherium_ORIG_Brychotherium               10110????11112?1111111021001200100012020201210221201120102?300111
+Metasinopa_ORIG_Metasinopa                  21???????00112101110110??1111002000120202011111212111111100200010
+Dissopsalis_ORIG_Dissopsalis                 420100121122011111202222101?1?02000022100111111212011101010300110
+Anasinopa_ORIG_Anasinopa                   311??011112210101120110??0000001000020200121111212110111110201010
+Paratritemnodon_ORIG_Paratritemnodon             100101121101121011101122010?0?11??0021101102011212110101001000010
+Masrasector_ORIG_Masrasector                 10100002?00112?01111001??1011010000020200111011112110001101101010
+Kyawdawia_ORIG_Kyawdawia                   420102121110121011111110010???00?0?1201001120111121?0001101100010
+;
+END;
diff --git a/tutorials/pps_morpho/figures/Ma_results.png b/tutorials/pps_morpho/figures/Ma_results.png