Merge branch 'master' of https://github.com/beast-dev/beast-mcmc into…

… nonparametrics
beast-dev · Sep 26, 2024 · cf1f7f9 · cf1f7f9
2 parents cdcfb32 + 3519890
commit cf1f7f9
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diff --git a/.gitignore b/.gitignore
@@ -18,5 +18,13 @@ out/
 zig_zag
 src/revision.txt
 *.dmg
+*.zip
+*.tgz
 release/Mac
+release/Linux
+release/Windows
 src/revision.txt
+
+*.citations.txt
+*.ops
+*.MLE
diff --git a/build.xml b/build.xml
@@ -296,15 +296,22 @@
                 <include name="dr/app/beauti/util/**/*.class"/>
                 <include name="dr/app/beauti/options/**/*.class"/>
                 <include name="dr/app/gui/**/*.class"/>
+                <include name="dr/app/gui/**/*.png"/>
                 <include name="dr/app/tools/*.class"/>
                 <include name="dr/app/util/*.class"/>
                 <include name="dr/evolution/tree/**/*.class"/>
+                <include name="dr/evolution/datatype/*.class"/>
+                <include name="dr/evolution/sequence/*.class"/>
+                <include name="dr/evolution/alignment/*.class"/>
                 <include name="dr/evolution/io/*.class"/>
                 <include name="dr/evolution/util/*.class"/>
                 <include name="dr/math/**/*.class"/>
                 <include name="dr/stats/**/*.class"/>
                 <include name="dr/util/**/*.class"/>
             </fileset>
+            <fileset dir="${src}">
+                <include name="dr/app/gui/**/*.png"/>
+            </fileset>
         </jar>
     </target>
 
@@ -372,6 +379,8 @@
                     <!-- <exclude name="test/dr/evomodel/treedatalikelihood/hmc/PrecisionGradientTest.java"/> -->
                     <exclude name="test/dr/multidimensionalscaling/MDSRotationTest.java"/>
                     <exclude name="test/dr/evomodel/branchratemodel/StrictClockTest.java"/>
+                    <exclude name="test/dr/evomodel/speciation/YuleModelTest.java"/>
+                    <exclude name="test/dr/evomodel/substmodel/GeneralSubstitutionModelTest.java"/>
 <!--                    <exclude name="test/dr/evomodel/substmodel/TimeIrreversibleTest.java"/>--> <!--sometimes fails-->
 
 <!--                    <include name="test/dr/distibutions/**/*Test.java"/>-->

diff --git a/build_tempest.xml b/build_tempest.xml
diff --git a/examples/ContinuousTraits/mammals.nwk b/examples/ContinuousTraits/mammals.nwk
@@ -0,0 +1 @@
+((((((Marmota_marmota:89.00000000000001,Ochotona_pusilla:89.0):2.9,(Gorilla_gorilla:91.8,Tupaia_glis:91.8):0.1):4.3,(((((Madoqua_guentheri:59.5,Eschrichtius_robustus:59.5):25.8,Equus_caballus:85.3):0.1,(Mustela_nigripes:81.0,Manis_crassicaudata:81.0):4.4):0.2,Rousettus_aegyptiacus:85.6):2.9,(Atelerix_frontalis:75.4,Blarina_brevicauda:75.4):13.1):7.7):2.5,(Dasypus_novemcinctus:71.3,Myrmecophaga_tridactyla:71.3):27.4):0.2,(((Tenrec_ecaudatus:87.5,Elephantulus_rufescens:87.5):1.8,Orycteropus_afer:89.3):0.2,(Heterohyrax_brucei:75.8,Loxodonta_africana:75.8):13.7):9.4):48.2,(((Petauroides_volans:63.7,Dasyurus_geoffroii:63.699999999999996):2.1,Isoodon_macrourus:65.8):16.7,Philander_opossum:82.5):64.6);
diff --git a/examples/ContinuousTraits/mammals.txt b/examples/ContinuousTraits/mammals.txt
@@ -0,0 +1,24 @@
+MSW05_Binomial	5-1_AdultBodyMass_g	2-1_AgeatEyeOpening_d	3-1_AgeatFirstBirth_d	7-1_DispersalAge_d	9-1_GestationLen_d	15-1_LitterSize	16-1_LittersPerYear	17-1_MaxLongevity_m	5-3_NeonateBodyMass_g	23-1_SexualMaturityAge_d	25-1_WeaningAge_d
+Madoqua_guentheri	8.442956595606232	NA	NA	5.881007734025406	5.233832177321627	0.6830968447064438	NA	5.303304908059076	6.529418838262226	5.138559328162834	4.55650501400681
+Mustela_nigripes	6.83050699659619	3.58351893845611	NA	5.016219672390156	4.01656318470207	1.4724720573609429	NA	5.176149732573829	2.127040520479115	5.99918467012312	4.390242789445222
+Philander_opossum	6.0966575487361165	NA	5.727922088842681	4.628300603376946	NA	1.749199854809259	1.3862943611198906	4.31748811353631	0.1823215567939546	5.5299051646449096	4.612840692292311
+Atelerix_frontalis	5.851282516508119	2.3978952727983707	NA	NA	3.9047969603364066	1.7900914121273581	0.9162907318741551	NA	2.446685436967803	6.094246741751008	4.021773869387265
+Gorilla_gorilla	11.631664043949645	NA	8.219864741912652	8.571647285210108	5.596605495412042	0.7178397931503168	NA	6.523562306149512	7.648210573636696	8.127106231132263	6.847315015170721
+Marmota_marmota	8.313290835314902	NA	NA	7.1560674271492095	3.865560131017805	1.6094379124341003	0.6931471805599453	5.517452896464707	3.4255647381104497	6.75642063041436	4.2510633701550695
+Eschrichtius_robustus	17.123277559391283	NA	NA	NA	5.972307211566287	0.6931471805599453	0.4054651081081644	6.863803391452954	13.122365377402328	8.07748440414794	5.44979304317089
+Equus_caballus	12.908221910469969	0.0	6.8839747503167334	6.650473078921439	5.862152810627642	0.6931471805599453	0.6931471805599453	6.655440350367647	10.542732512101392	6.764565969890049	5.893741458579367
+Petauroides_volans	7.1512738427684805	4.804021044733257	6.677083461247136	5.981010089204123	NA	0.6931471805599453	0.6931471805599453	5.3612921657094255	0.23901690047049992	6.640084962284453	5.519098128673058
+Rousettus_aegyptiacus	5.027557961292164	NA	NA	NA	4.911919321157098	0.7275486072772779	1.0986122886681098	5.729450221404779	3.0022112396517002	5.850908539546495	4.836281906951478
+Blarina_brevicauda	3.6141559079179997	2.970414465569701	4.852030263919617	NA	3.4992311219335206	1.8547342683894434	1.3862943611198906	4.189654742026425	0.6365768290715511	4.635311342900078	3.7591048990034333
+Dasypus_novemcinctus	8.285909095597159	0.0	NA	NA	4.987093685513222	1.601405740736836	NA	5.3612921657094255	4.579647228757006	6.297164567026571	5.061771909543635
+Elephantulus_rufescens	4.267457179930745	0.0	5.337538079701318	NA	4.2414706271123945	0.8796267475025636	NA	4.653960350157523	2.4239173781615704	4.54052499249456	3.825375198702474
+Loxodonta_africana	15.156953591129533	0.0	8.169477988848977	NA	6.511016981253914	0.6097655716208942	NA	6.900730664045173	11.561725152903833	8.519093384904531	7.011935097891801
+Heterohyrax_brucei	7.812871811381358	NA	NA	6.50666558477462	5.4832604840469426	1.0612565021243408	0.6931471805599453	5.303304908059076	5.420534999272286	6.295837793654872	5.010901925213687
+Myrmecophaga_tridactyla	10.293852220716696	1.9459101490553132	NA	NA	5.274280788719795	0.6931471805599453	0.6931471805599453	5.84354441703136	7.313886831633462	7.138065091201048	4.6147243987929025
+Dasyurus_geoffroii	7.025698301839886	NA	NA	NA	3.40684805317097	1.8671761085128091	0.6931471805599453	4.532599493153256	0.009950330853168092	6.107535006030503	5.165471453214607
+Tenrec_ecaudatus	6.80920485525286	NA	NA	4.1219597292550745	4.287028906051602	2.884241897520628	0.6931471805599453	4.687671407499835	3.228430037673012	5.475584504594719	3.7581722806098856
+Isoodon_macrourus	7.329310248239249	3.855452653939752	5.356586274672012	NA	3.219675505038765	1.4182774069729414	1.297463147413275	4.23410650459726	0.1570037488096647	5.378929143040425	4.430697744137536
+Ochotona_pusilla	5.081776966367399	NA	NA	NA	3.5409593240373143	2.2607208888953467	1.5040773967762742	4.394449154672439	2.046401687601636	4.15481230898919	3.7376696182833684
+Manis_crassicaudata	8.991701658625722	0.0	NA	NA	4.382151626862033	0.6931471805599453	0.6931471805599453	5.272999558563747	5.7433877292485604	6.668253661055109	NA
+Orycteropus_afer	10.936560997688801	0.0	7.055312843339752	NA	5.4577114186982865	0.7419373447293773	0.6931471805599453	5.771441123130016	7.549966995862329	6.668253661055109	4.125843229281472
+Tupaia_glis	5.017213609456379	NA	5.590053709327858	NA	4.069026754237811	1.169381359556317	1.252762968495368	5.204006687076795	2.6100697927420065	5.041099834900075	4.012230265845171