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shortened class name.
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@fkmendes
fkmendes committed Oct 1, 2020
1 parent 41ead1a commit c14cfa3
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Showing 18 changed files with 44 additions and 44 deletions.
2 changes: 1 addition & 1 deletion examples/testing/BMMVNLikelihoodOneTrait_YuleTree.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">4.1 4.5 5.9 0.0</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>

<sigmasq id="rateValue" dimension="1" spec="parameter.RealParameter">1.4822794118</sigmasq>

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2 changes: 1 addition & 1 deletion examples/testing/BMMVNLikelihoodOneTrait_fixedtree.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">4.1 4.5 5.9 0.0</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>

<sigmaSq id="rateValue" dimension="1" spec="parameter.RealParameter">1.4822794118</sigmaSq>

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2 changes: 1 addition & 1 deletion examples/testing/BMMVNShiftLikelihoodOneTrait_FBDTree_RateCatClock.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">0.3975946 0.2423501 -0.6398611 0.3134564</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 f1 f2" value="0.3975946 0.2423501 -0.6398611 0.3134564"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 f1 f2" value="0.3975946 0.2423501 -0.6398611 0.3134564"/>

<rateManager id="rateManager" spec="contraband.clock.TreeToVCVMat" coalCorrection="false">
<branchRateModel id="rateCatClock" spec="contraband.clock.RateCategoryClockModel" nCat="2">
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2 changes: 1 addition & 1 deletion examples/testing/BMMVNShiftLikelihoodOneTrait_YuleTree_RateCatClock.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">4.1 4.5 5.2</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 sp3" value="4.1 4.5 5.2"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3" value="4.1 4.5 5.2"/>

<rateManager id="rateManager" spec="contraband.clock.TreeToVCVMat" coalCorrection="false">
<branchRateModel id="rateCatClock" spec="contraband.clock.RateCategoryClockModel" nCat="2">
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2 changes: 1 addition & 1 deletion examples/testing/BMMVNShiftLikelihoodOneTrait_fixedtree_RateCatClock.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">4.1 4.5</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2" value="4.1 4.5"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2" value="4.1 4.5"/>

<rateManager id="rateManager" spec="contraband.clock.TreeToVCVMat" coalCorrection="false">
<branchRateModel id="rateCatClock" spec="contraband.clock.RateCategoryClockModel" nCat="2">
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2 changes: 1 addition & 1 deletion examples/testing/OUMVNLikelihoodOneTrait_FBDTree_RandomLocalClock.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">5.38150901808057 5.39100391431842 5.44242801319197 5.39964756302886 5.40133725992169 5.44692271094288 5.41087039794454 5.36125469057044 5.37787612329788 5.38480950257093 5.43280869202231 5.40796406444915 5.40914145032705 5.40080243184839 5.38164224379707 5.44898808949184 5.41193212679478 5.34108745517387 5.41778218328783 5.38402962781306 5.36692456740256 5.39135469490656 5.36812672219487 5.37666766959369 5.37965304379843 5.34913426928506 5.42170409298673 5.40202962893574 5.3649033123079 5.43366341190228 5.40988002603016 5.38913844301124 5.4233523741016 5.42286390960096 5.42123822924372 -0.410688418525297 5.41354385849994 5.39584095647839 5.38882536033459 5.38668351086884 5.37765034510456 5.39164381615728 5.36124505715072 5.45997046083642 5.4323453051796 5.36533532398276 5.38604170923066 5.41231681663681 5.42004191844111 5.39522513623678 5.40490270329497 5.39680008017039 5.3963883247283 5.43696314155497 5.39113058561732 5.4412138293931 5.35309956781398 5.41442626199243 5.4011810663882 5.40382824917148 5.40853398147627 5.38318068663495 5.38804217162093 5.36834028137378</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="t26_1 t24_1 t33_1 t5_1 t44_1 t15_1 t49_1 t57_1 t6_1 t27_1 t37_1 t60_1 t40_1 t22_1 t47_1 t36_1 t17_1 t23_1 t45_1 t42_1 t11_1 t14_1 t59_1 t2_1 t39_1 t32_1 t64_1 t16_1 t10_1 t62_1 t13_1 t19_1 t48_1 t29_1 t54_1 t35_1 t7_1 t58_1 t63_1 t20_1 t25_1 t8_1 t3_1 t21_1 t55_1 t53_1 t4_1 t1_1 t18_1 t61_1 t9_1 t52_1 t51_1 t34_1 t12_1 t46_1 t38_1 t56_1 t28_1 t41_1 t30_1 t31_1 t43_1 t50_1" value="5.38150901808057 5.39100391431842 5.44242801319197 5.39964756302886 5.40133725992169 5.44692271094288 5.41087039794454 5.36125469057044 5.37787612329788 5.38480950257093 5.43280869202231 5.40796406444915 5.40914145032705 5.40080243184839 5.38164224379707 5.44898808949184 5.41193212679478 5.34108745517387 5.41778218328783 5.38402962781306 5.36692456740256 5.39135469490656 5.36812672219487 5.37666766959369 5.37965304379843 5.34913426928506 5.42170409298673 5.40202962893574 5.3649033123079 5.43366341190228 5.40988002603016 5.38913844301124 5.4233523741016 5.42286390960096 5.42123822924372 -0.410688418525297 5.41354385849994 5.39584095647839 5.38882536033459 5.38668351086884 5.37765034510456 5.39164381615728 5.36124505715072 5.45997046083642 5.4323453051796 5.36533532398276 5.38604170923066 5.41231681663681 5.42004191844111 5.39522513623678 5.40490270329497 5.39680008017039 5.3963883247283 5.43696314155497 5.39113058561732 5.4412138293931 5.35309956781398 5.41442626199243 5.4011810663882 5.40382824917148 5.40853398147627 5.38318068663495 5.38804217162093 5.36834028137378"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="t26_1 t24_1 t33_1 t5_1 t44_1 t15_1 t49_1 t57_1 t6_1 t27_1 t37_1 t60_1 t40_1 t22_1 t47_1 t36_1 t17_1 t23_1 t45_1 t42_1 t11_1 t14_1 t59_1 t2_1 t39_1 t32_1 t64_1 t16_1 t10_1 t62_1 t13_1 t19_1 t48_1 t29_1 t54_1 t35_1 t7_1 t58_1 t63_1 t20_1 t25_1 t8_1 t3_1 t21_1 t55_1 t53_1 t4_1 t1_1 t18_1 t61_1 t9_1 t52_1 t51_1 t34_1 t12_1 t46_1 t38_1 t56_1 t28_1 t41_1 t30_1 t31_1 t43_1 t50_1" value="5.38150901808057 5.39100391431842 5.44242801319197 5.39964756302886 5.40133725992169 5.44692271094288 5.41087039794454 5.36125469057044 5.37787612329788 5.38480950257093 5.43280869202231 5.40796406444915 5.40914145032705 5.40080243184839 5.38164224379707 5.44898808949184 5.41193212679478 5.34108745517387 5.41778218328783 5.38402962781306 5.36692456740256 5.39135469490656 5.36812672219487 5.37666766959369 5.37965304379843 5.34913426928506 5.42170409298673 5.40202962893574 5.3649033123079 5.43366341190228 5.40988002603016 5.38913844301124 5.4233523741016 5.42286390960096 5.42123822924372 -0.410688418525297 5.41354385849994 5.39584095647839 5.38882536033459 5.38668351086884 5.37765034510456 5.39164381615728 5.36124505715072 5.45997046083642 5.4323453051796 5.36533532398276 5.38604170923066 5.41231681663681 5.42004191844111 5.39522513623678 5.40490270329497 5.39680008017039 5.3963883247283 5.43696314155497 5.39113058561732 5.4412138293931 5.35309956781398 5.41442626199243 5.4011810663882 5.40382824917148 5.40853398147627 5.38318068663495 5.38804217162093 5.36834028137378"/>

<optimumManager id="optimumManager" spec="contraband.clock.TreeToVCVMat" coalCorrection="false">
<branchRateModel id="OUThetaRandomLocalColor" spec="contraband.clock.RandomLocalColorModel" scaling="false" includeRoot="true">
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2 changes: 1 addition & 1 deletion examples/testing/OUMVNLikelihoodOneTrait_FBDTree_RateCatClock.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">0.3975946 0.2423501 -0.6398611 0.3134564</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 f1 f2" value="0.3975 0.2423 -0.6398 0.3134"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 f1 f2" value="0.3975 0.2423 -0.6398 0.3134"/>

<optimumManager id="optimumManager" spec="contraband.clock.TreeToVCVMat" coalCorrection="false">
<branchRateModel id="rateCatClock" spec="contraband.clock.RateCategoryClockModel" nCat="2">
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2 changes: 1 addition & 1 deletion examples/testing/OUMVNLikelihoodOneTrait_YuleTree_RateCatClock.xml
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Expand Up @@ -55,7 +55,7 @@
<!-- <traitValues id="fixedTraitvalues" spec="parameter.RealParameter">4.1 4.5 5.9</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 sp3" value="4.1 4.5 5.9"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3" value="4.1 4.5 5.9"/>

<!-- (DEPRECATED) Original implementation had my own ColorManager regime mapper -->
<!-- <optimumManager id="optimumManager" spec="contraband.clock.ColorManager" nTraits="1" nColors="1" coalCorrection="false"> -->
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2 changes: 1 addition & 1 deletion examples/testing/OUMVNLikelihoodOneTrait_fixedtree_RateCatClock.xml
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<!-- <traitValues id="fixedTraitvalues" spec="parameter.RealParameter">4.1 4.5 5.9 0.0</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3 sp4" value="4.1 4.5 5.9 0.0"/>

<optimumManager id="optimumManager" spec="contraband.clock.TreeToVCVMat" coalCorrection="false">
<branchRateModel id="rateCatClock" spec="contraband.clock.RateCategoryClockModel" nCat="3">
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2 changes: 1 addition & 1 deletion examples/testing/WNLikelihoodOneTrait.xml
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<!-- <traitValues id="fixedTraitValues" spec="parameter.RealParameter">1.59528080213779 0.329507771815361 -0.820468384118015 0.487429052428485 0.738324705129217 0.575781351653492 -0.305388387156356 1.51178116845085 0.389843236411431 -0.621240580541804 -2.2146998871775 1.12493091814311 -0.0449336090152309 -0.0161902630989461 0.943836210685299 0.821221195098089 0.593901321217509 0.918977371608218 0.782136300731067 0.0745649833651906 -1.98935169586337 0.61982574789471 -0.0561287395290008 -0.155795506705329 -1.47075238389927 -0.47815005510862 0.417941560199702 1.35867955152904 -0.102787727342996 0.387671611559369 -0.0538050405829051 -1.37705955682861 -0.41499456329968 -0.394289953710349 -0.0593133967111857 1.10002537198388 0.763175748457544 -0.164523596253587 -0.253361680136508 0.696963375404737 0.556663198673657 -0.68875569454952 -0.70749515696212 0.36458196213683 0.768532924515416 -0.112346212150228 0.881107726454215 0.398105880367068 -0.612026393250771 0.341119691424425 -1.12936309608079 1.43302370170104 1.98039989850586 -0.367221476466509 -1.04413462631653 0.569719627442413 -0.135054603880824 2.40161776050478 -0.0392400027331692 0.689739362450777 0.0280021587806661 -0.743273208882405 0.188792299514343 -1.80495862889104 1.46555486156289 0.153253338211898 2.17261167036215 0.475509528899663 -0.709946430921815 0.610726353489055 -0.934097631644252 -1.2536334002391 0.291446235517463 -0.443291873218433 0.00110535163162413 0.0743413241516641 -0.589520946188072 -0.568668732818502 -0.135178615123832 1.1780869965732 -1.52356680042976 0.593946187628422 0.332950371213518 1.06309983727636 -0.304183923634301 0.370018809916288 0.267098790772231 -0.54252003099165 1.20786780598317 1.16040261569495 0.700213649514998 1.58683345454085 0.558486425565304 -1.27659220845804 -0.573265414236886 -1.22461261489836 -0.473400636439312 -0.620366677224124 0.0421158731442352 -0.910921648552446</traitValues> -->
<!-- </oneTraitData> -->

<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyEnhancedRealParameter" keys="sp1 sp2 sp3 sp4 sp5 sp6 sp7 sp8 sp9 sp10 sp11 sp12 sp13 sp14 sp15 sp16 sp17 sp18 sp19 sp20 sp21 sp22 sp23 sp24 sp25 sp26 sp27 sp28 sp29 sp30 sp31 sp32 sp33 sp34 sp35 sp36 sp37 sp38 sp39 sp40 sp41 sp42 sp43 sp44 sp45 sp46 sp47 sp48 sp49 sp50 sp51 sp52 sp53 sp54 sp55 sp56 sp57 sp58 sp59 sp60 sp61 sp62 sp63 sp64 sp65 sp66 sp67 sp68 sp69 sp70 sp71 sp72 sp73 sp74 sp75 sp76 sp77 sp78 sp79 sp80 sp81 sp82 sp83 sp84 sp85 sp86 sp87 sp88 sp89 sp90 sp91 sp92 sp93 sp94 sp95 sp96 sp97 sp98 sp99 sp100" value="1.59528080213779 0.329507771815361 -0.820468384118015 0.487429052428485 0.738324705129217 0.575781351653492 -0.305388387156356 1.51178116845085 0.389843236411431 -0.621240580541804 -2.2146998871775 1.12493091814311 -0.0449336090152309 -0.0161902630989461 0.943836210685299 0.821221195098089 0.593901321217509 0.918977371608218 0.782136300731067 0.0745649833651906 -1.98935169586337 0.61982574789471 -0.0561287395290008 -0.155795506705329 -1.47075238389927 -0.47815005510862 0.417941560199702 1.35867955152904 -0.102787727342996 0.387671611559369 -0.0538050405829051 -1.37705955682861 -0.41499456329968 -0.394289953710349 -0.0593133967111857 1.10002537198388 0.763175748457544 -0.164523596253587 -0.253361680136508 0.696963375404737 0.556663198673657 -0.68875569454952 -0.70749515696212 0.36458196213683 0.768532924515416 -0.112346212150228 0.881107726454215 0.398105880367068 -0.612026393250771 0.341119691424425 -1.12936309608079 1.43302370170104 1.98039989850586 -0.367221476466509 -1.04413462631653 0.569719627442413 -0.135054603880824 2.40161776050478 -0.0392400027331692 0.689739362450777 0.0280021587806661 -0.743273208882405 0.188792299514343 -1.80495862889104 1.46555486156289 0.153253338211898 2.17261167036215 0.475509528899663 -0.709946430921815 0.610726353489055 -0.934097631644252 -1.2536334002391 0.291446235517463 -0.443291873218433 0.00110535163162413 0.0743413241516641 -0.589520946188072 -0.568668732818502 -0.135178615123832 1.1780869965732 -1.52356680042976 0.593946187628422 0.332950371213518 1.06309983727636 -0.304183923634301 0.370018809916288 0.267098790772231 -0.54252003099165 1.20786780598317 1.16040261569495 0.700213649514998 1.58683345454085 0.558486425565304 -1.27659220845804 -0.573265414236886 -1.22461261489836 -0.473400636439312 -0.620366677224124 0.0421158731442352 -0.910921648552446"/>
<oneTraitData id="oneTraitData" spec="outercore.parameter.KeyRealParameter" keys="sp1 sp2 sp3 sp4 sp5 sp6 sp7 sp8 sp9 sp10 sp11 sp12 sp13 sp14 sp15 sp16 sp17 sp18 sp19 sp20 sp21 sp22 sp23 sp24 sp25 sp26 sp27 sp28 sp29 sp30 sp31 sp32 sp33 sp34 sp35 sp36 sp37 sp38 sp39 sp40 sp41 sp42 sp43 sp44 sp45 sp46 sp47 sp48 sp49 sp50 sp51 sp52 sp53 sp54 sp55 sp56 sp57 sp58 sp59 sp60 sp61 sp62 sp63 sp64 sp65 sp66 sp67 sp68 sp69 sp70 sp71 sp72 sp73 sp74 sp75 sp76 sp77 sp78 sp79 sp80 sp81 sp82 sp83 sp84 sp85 sp86 sp87 sp88 sp89 sp90 sp91 sp92 sp93 sp94 sp95 sp96 sp97 sp98 sp99 sp100" value="1.59528080213779 0.329507771815361 -0.820468384118015 0.487429052428485 0.738324705129217 0.575781351653492 -0.305388387156356 1.51178116845085 0.389843236411431 -0.621240580541804 -2.2146998871775 1.12493091814311 -0.0449336090152309 -0.0161902630989461 0.943836210685299 0.821221195098089 0.593901321217509 0.918977371608218 0.782136300731067 0.0745649833651906 -1.98935169586337 0.61982574789471 -0.0561287395290008 -0.155795506705329 -1.47075238389927 -0.47815005510862 0.417941560199702 1.35867955152904 -0.102787727342996 0.387671611559369 -0.0538050405829051 -1.37705955682861 -0.41499456329968 -0.394289953710349 -0.0593133967111857 1.10002537198388 0.763175748457544 -0.164523596253587 -0.253361680136508 0.696963375404737 0.556663198673657 -0.68875569454952 -0.70749515696212 0.36458196213683 0.768532924515416 -0.112346212150228 0.881107726454215 0.398105880367068 -0.612026393250771 0.341119691424425 -1.12936309608079 1.43302370170104 1.98039989850586 -0.367221476466509 -1.04413462631653 0.569719627442413 -0.135054603880824 2.40161776050478 -0.0392400027331692 0.689739362450777 0.0280021587806661 -0.743273208882405 0.188792299514343 -1.80495862889104 1.46555486156289 0.153253338211898 2.17261167036215 0.475509528899663 -0.709946430921815 0.610726353489055 -0.934097631644252 -1.2536334002391 0.291446235517463 -0.443291873218433 0.00110535163162413 0.0743413241516641 -0.589520946188072 -0.568668732818502 -0.135178615123832 1.1780869965732 -1.52356680042976 0.593946187628422 0.332950371213518 1.06309983727636 -0.304183923634301 0.370018809916288 0.267098790772231 -0.54252003099165 1.20786780598317 1.16040261569495 0.700213649514998 1.58683345454085 0.558486425565304 -1.27659220845804 -0.573265414236886 -1.22461261489836 -0.473400636439312 -0.620366677224124 0.0421158731442352 -0.910921648552446"/>

<sigmaSqs id="WNVars" spec="parameter.RealParameter">1.0</sigmaSqs>

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6 changes: 3 additions & 3 deletions src/contraband/mvnlikelihood/BMMVNLikelihoodOneTrait.java
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Expand Up @@ -10,7 +10,7 @@
import beast.core.State;
import beast.core.parameter.RealParameter;
import beast.core.Input.Validate;
import outercore.parameter.KeyEnhancedRealParameter;
import outercore.parameter.KeyRealParameter;

/**
* @author Fabio K. Mendes
Expand All @@ -27,7 +27,7 @@ public class BMMVNLikelihoodOneTrait extends MVNProcessOneTrait {

final public Input<RealParameter> sigmasqInput = new Input<>("sigmaSq", "Sigma^2, the variance of the process.", Validate.REQUIRED); // OPTIONAL because BMMVNShift has ColorManager instead
final public Input<RealParameter> rootValueInput = new Input<>("rootValue", "rootValue, or y_0, the root value and the expected value at the tips.", Validate.REQUIRED);
final public Input<KeyEnhancedRealParameter> oneTraitInput = new Input<>("oneTraitData", "continuous data values for one trait.", Validate.REQUIRED);
final public Input<KeyRealParameter> oneTraitInput = new Input<>("oneTraitData", "continuous data values for one trait.", Validate.REQUIRED);
// final public Input<OneValueContTraits> oneTraitInput = new Input<>("oneTraitData", "continuous data values for one trait.", Validate.REQUIRED); // original implementation (for the above line) with OneValueContTraits data wrapper

private boolean dirty;
Expand Down Expand Up @@ -134,7 +134,7 @@ protected void populateOneTraitDataVector() {
// }

String[] spNamesInPhyloTMatOrder = getSpNamesInPhyloTMatOrder();
KeyEnhancedRealParameter oneTraitValues = oneTraitInput.get();
KeyRealParameter oneTraitValues = oneTraitInput.get();
int i = 0;
for (String spName: spNamesInPhyloTMatOrder) {
oneTraitDataVec.setEntry(i, oneTraitValues.getValue(spName));
Expand Down
6 changes: 3 additions & 3 deletions src/contraband/mvnlikelihood/BMMVNShiftLikelihoodOneTrait.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
import beast.core.Input;
import beast.core.Input.Validate;
import beast.core.parameter.RealParameter;
import outercore.parameter.KeyEnhancedRealParameter;
import outercore.parameter.KeyRealParameter;

/**
* @author Fabio K. Mendes
Expand All @@ -30,7 +30,7 @@ public class BMMVNShiftLikelihoodOneTrait extends MVNShiftProcessOneTrait {

final public Input<RealParameter> rootValueInput = new Input<>("rootValue", "rootValue, or y_0, the root value and the expected value at the tips.", Validate.REQUIRED);
final public Input<TreeToVCVMat> rateManagerInput = new Input<>("rateManager", "color manager object that paints branches with their own rates.", Validate.REQUIRED);
final public Input<KeyEnhancedRealParameter> oneTraitInput = new Input<>("oneTraitData", "continuous data values for one trait.", Validate.REQUIRED);
final public Input<KeyRealParameter> oneTraitInput = new Input<>("oneTraitData", "continuous data values for one trait.", Validate.REQUIRED);
// final public Input<OneValueContTraits> oneTraitInput = new Input<>("oneTraitData", "continuous data values for one trait.", Validate.REQUIRED); // original implementation (for the above line) with OneValueContTraits data wrapper

/*
Expand Down Expand Up @@ -189,7 +189,7 @@ protected void populateOneTraitDataVector() {
// }

String[] spNamesInPhyloTMatOrder = rateManager.getSpNamesInVCVMatOrder();
KeyEnhancedRealParameter oneTraitValues = oneTraitInput.get();
KeyRealParameter oneTraitValues = oneTraitInput.get();
int i = 0;
for (String spName: spNamesInPhyloTMatOrder) {
oneTraitDataVec.setEntry(i, oneTraitValues.getValue(spName));
Expand Down
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