From b76eeb99384cabb77a56da3f09088b6d2202ef1f Mon Sep 17 00:00:00 2001 From: Segei L Kosakovsky Pond Date: Thu, 14 Jan 2021 13:25:42 -0500 Subject: [PATCH 1/2] RELAX constraints fixes --- .../SelectionAnalyses/RELAX.bf | 396 +++++++++++++++++- .../libv3/tasks/estimators.bf | 2 +- src/core/likefunc.cpp | 14 +- 3 files changed, 401 insertions(+), 11 deletions(-) diff --git a/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf b/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf index febb807af..ade5763ef 100644 --- a/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf +++ b/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf @@ -367,11 +367,20 @@ if (relax.model_set == "All") { // run all the models relax.weight_multipliers = parameters.helper.stick_breaking (utility.SwapKeysAndValues(utility.MatrixToDict(relax.distribution["weights"])),None); relax.constrain_parameters = parameters.ConstrainMeanOfSet(relax.distribution["rates"],relax.weight_multipliers,1,"relax"); + + relax.i = 0; for (key, value; in; relax.constrain_parameters[terms.global]){ model.generic.AddGlobal (relax.ge.bsrel_model, value, key); - parameters.SetRange (value, terms.range_almost_01); + relax.i += 1; + if (relax.i < relax.rate_classes) { + parameters.SetRange (value, terms.range_almost_01); + } else { + parameters.SetRange (value, terms.range_gte1); + } + } + relax.distribution["rates"] = Transpose (utility.Values (relax.constrain_parameters[terms.global])); for (relax.i = 1; relax.i < relax.rate_classes; relax.i += 1) { @@ -397,7 +406,8 @@ if (relax.model_set == "All") { // run all the models math.Mean ( utility.Map (selection.io.extract_global_MLE_re (relax.final_partitioned_mg_results, "^" + terms.parameters.omega_ratio + ".+"), "_v_", "_v_[terms.fit.MLE]")); - relax.init_grid_setup (relax.distribution); + + relax.init_grid_setup (relax.distribution); relax.initial_grid = estimators.LHC (relax.initial_ranges,relax.initial_grid.N); relax.initial_grid = utility.Map (relax.initial_grid, "_v_", 'relax._renormalize (_v_, "relax.distribution", relax.initial.test_mean)' @@ -406,8 +416,11 @@ if (relax.model_set == "All") { // run all the models parameters.DeclareGlobalWithRanges ("relax.bl.scaler", 1, 0, 1000); + for (i, v; in; relax.initial_grid) { + v["relax.bl.scaler"] = {terms.id : "relax.bl.scaler", terms.fit.MLE : Random (2,4)}; + } - + relax.grid_search.results = estimators.FitLF (relax.filter_names, relax.trees,{ "0" : {"DEFAULT" : "relax.ge"}}, relax.final_partitioned_mg_results, relax.model_object_map, @@ -429,7 +442,359 @@ if (relax.model_set == "All") { // run all the models } ); + +/*relax.grid_search.results = { + "EFV":{ + "relax.ge": { +{0.04881810356648711} + {0.03987090682724777} + {0.04952731390964531} + {0.04155619114937172} + {0.01811127842789196} + {0.01479191205650485} + {0.01837439200770125} + {0.01541714432400942} + {0.01894057781278376} + {0.01546922059762592} + {0.0192157391301816} + {0.01612308169643694} + {0.02832012582609264} + {0.0231297206498455} + {0.0287315495539327} + {0.02410737976743678} + {0.01664713636441668} + {0.01359611239347263} + {0.01688897946013485} + {0.0141707999760208} + {0.006176006434015015} + {0.005044091414975357} + {0.006265729043506587} + {0.005257297706416126} + {0.006458800294051354} + {0.005275055889649603} + {0.006552631222299025} + {0.005498024708183688} + {0.00965725749346899} + {0.007887311992864245} + {0.009797554358782127} + {0.008220697017259783} + {0.03328033861025202} + {0.02718084446073247} + {0.03376382237225545} + {0.02832973859625429} + {0.01234684337796718} + {0.01008396078440649} + {0.01252621349661759} + {0.01051019490766097} + {0.01291219439167226} + {0.01054569641003205} + {0.0130997777090572} + {0.01099144741596503} + {0.0193064315924046} + {0.01576802208506577} + {0.01958690789063199} + {0.01643451308127018} + {0.01964953777584797} + {0.02048009470534294} + {0.008925762616328468} + {0.00728988272051741} + {0.009055432609745021} + {0.00759801529227558} + {0.007623679988342976} + {0.009470072841967696} + {0.007945921677425003} + {0.01395697832125249} + {0.01139899630633314} + {0.01415973985153574} + {0.01188081503812791} + } + }, + "Filters": { +{"relax.filter.default"} + }, + "LF":"iybtBVgK.likelihoodFunction", + "LogL":-3468.628021062044, + "Trees": { +{"((((Pig:0.2002207612790759,Cow:0.2652088954749879)Node3:0.1024483387468423,Horse:0.2271179872916863,Cat:0.2941609243556507)Node2:0.06486663246806917,((RhMonkey:0.003909730323873505,Baboon:0.001860925679316316)Node9:0.02712267964568085,(Human:0,Chimp:0.001921935125106313)Node12:0.01893367713404082)Node8:0.1148290059087238)Node1:0.3005238585248704,Rat:0.07055784179244226,Mouse:0.1259924875975693)"} + }, + "branch length":{ + "0":{ + "Baboon":{ + "MLE":0.001860925679316316, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.00454994471726663, + "constraint":"relax.bl.scaler*0.00421525617283435" + } + }, + "Cat":{ + "MLE":0.2941609243556507, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.7192205248572749, + "constraint":"relax.bl.scaler*0.6663155148959867" + } + }, + "Chimp":{ + "MLE":0.001921935125106313, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.004699112203459599, + "constraint":"relax.bl.scaler*0.004353451075417437" + } + }, + "Cow":{ + "MLE":0.2652088954749879, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.6484331031327714, + "constraint":"relax.bl.scaler*0.6007351320726768" + } + }, + "Horse":{ + "MLE":0.2271179872916863, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.5553012127027491, + "constraint":"relax.bl.scaler*0.5144539131969622" + } + }, + "Human":{ + "MLE":0, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0, + "constraint":"0" + } + }, + "Mouse":{ + "MLE":0.1259924875975693, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.3080503749996349, + "constraint":"relax.bl.scaler*0.2853905542705638" + } + }, + "Node1":{ + "MLE":0.3005238585248704, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.7347778354104789, + "constraint":"relax.bl.scaler*0.6807284481110281" + } + }, + "Node12":{ + "MLE":0.01893367713404082, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.04629265166898581, + "constraint":"relax.bl.scaler*0.04288741904138782" + } + }, + "Node2":{ + "MLE":0.06486663246806917, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.1585982691331329, + "constraint":"relax.bl.scaler*0.146931968300024" + } + }, + "Node3":{ + "MLE":0.1024483387468423, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.2504851659874938, + "constraint":"relax.bl.scaler*0.2320597738529283" + } + }, + "Node8":{ + "MLE":0.1148290059087238, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.2807557736616996, + "constraint":"relax.bl.scaler*0.2601037114792293" + } + }, + "Node9":{ + "MLE":0.02712267964568085, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.06631468109855898, + "constraint":"relax.bl.scaler*0.0614366517002807" + } + }, + "Pig":{ + "MLE":0.2002207612790759, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.4895377634874294, + "constraint":"relax.bl.scaler*0.4535279454154706" + } + }, + "Rat":{ + "MLE":0.07055784179244226, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.1725132191432825, + "constraint":"relax.bl.scaler*0.1598233510683406" + } + }, + "RhMonkey":{ + "MLE":0.003909730323873505, + "relaxation or intensification parameter":{ + "ID":"k", + "MLE":0.5835896398205112, + "constraint":"relax.K" + }, + "synonymous rate":{ + "ID":"t", + "MLE":0.009559251629856012, + "constraint":"relax.bl.scaler*0.008856084401973642" + } + } + } + }, + "global":{ + "Mean scaler variable for relax.ge.omega1":{ + "ID":"relax.ge.omega1_scaler_variable", + "MLE":1 + }, + "Mean scaler variable for relax.ge.omega2":{ + "ID":"relax.ge.omega2_scaler_variable", + "MLE":1 + }, + "Mean scaler variable for relax.ge.omega3":{ + "ID":"relax.ge.omega3_scaler_variable", + "MLE":0.6984561656354166 + }, + "Mixture auxiliary weight for category 1":{ + "ID":"relax.ge.bsrel_mixture_aux_0", + "MLE":1 + }, + "Mixture auxiliary weight for category 2":{ + "ID":"relax.ge.bsrel_mixture_aux_1", + "MLE":0.7992410131933376 + }, + "Substitution rate from nucleotide A to nucleotide C":{ + "ID":"relax.ge.theta_AC", + "MLE":0.5896537813380907 + }, + "Substitution rate from nucleotide A to nucleotide G":{ + "ID":"relax.ge.theta_AG", + "MLE":1, + "constraint":"1" + }, + "Substitution rate from nucleotide A to nucleotide T":{ + "ID":"relax.ge.theta_AT", + "MLE":0.2531352820308571 + }, + "Substitution rate from nucleotide C to nucleotide G":{ + "ID":"relax.ge.theta_CG", + "MLE":0.3871445458988698 + }, + "Substitution rate from nucleotide C to nucleotide T":{ + "ID":"relax.ge.theta_CT", + "MLE":0.9447643279336558 + }, + "Substitution rate from nucleotide G to nucleotide T":{ + "ID":"relax.ge.theta_GT", + "MLE":0.3135181640741386 + }, + "non-synonymous/synonymous rate ratio for category 1":{ + "ID":"relax.ge.omega1", + "MLE":1, + "constraint":"relax.ge.omega1_scaler_variable/relax.scaler_variable" + }, + "non-synonymous/synonymous rate ratio for category 2":{ + "ID":"relax.ge.omega2", + "MLE":1, + "constraint":"relax.ge.omega2_scaler_variable/relax.scaler_variable" + }, + "non-synonymous/synonymous rate ratio for category 3":{ + "ID":"relax.ge.omega3", + "MLE":0.6984561656354166, + "constraint":"relax.ge.omega3_scaler_variable/relax.scaler_variable" + } + }, + "parameters":27 +};*/ + relax.general_descriptive.fit = estimators.FitLF (relax.filter_names, relax.trees, { "0" : {"DEFAULT" : "relax.ge"}}, @@ -1462,6 +1827,31 @@ function relax.init_grid_setup (omega_distro) { //------------------------------------------------------------------------------ +function relax.init_grid_setup_scaled (omega_distro) { + utility.ForEachPair (omega_distro[terms.parameters.rates], "_index_", "_name_", + ' + relax.initial_ranges [_name_] = { + terms.lower_bound : 0, + terms.upper_bound : 1 + }; + + ' + ); + + + utility.ForEachPair (omega_distro[terms.parameters.weights], "_index_", "_name_", + ' + relax.initial_ranges [_name_] = { + terms.lower_bound : 0, + terms.upper_bound : 1 + }; + ' + ); + +} + +//------------------------------------------------------------------------------ + lfunction relax._renormalize (v, distro, mean) { parameters.SetValues (v); diff --git a/res/TemplateBatchFiles/libv3/tasks/estimators.bf b/res/TemplateBatchFiles/libv3/tasks/estimators.bf index 8c865ec51..c3ed1a2a1 100644 --- a/res/TemplateBatchFiles/libv3/tasks/estimators.bf +++ b/res/TemplateBatchFiles/libv3/tasks/estimators.bf @@ -185,7 +185,7 @@ function estimators.SetGlobals2(key2, value) { if (Type(__init_value) != "AssociativeList") { __init_value = (initial_values[terms.global])[key2]; } - + if (Type(__init_value) == "AssociativeList") { if (__init_value[terms.fix]) { diff --git a/src/core/likefunc.cpp b/src/core/likefunc.cpp index 694f78322..c67efc222 100644 --- a/src/core/likefunc.cpp +++ b/src/core/likefunc.cpp @@ -2675,7 +2675,7 @@ void _LikelihoodFunction::CheckDependentBounds (void) { lowerBounds.theData[index] = cornholio->GetLowerBound(); upperBounds.theData[index] = cornholio->GetUpperBound(); - //fprintf (stderr, "_LikelihoodFunction::CheckDependentBounds variable %s (%d), current value %g, range %g to %g\n", cornholio->theName->sData, index, currentValues.theData[index], lowerBounds.theData[index], upperBounds.theData[index]); + //fprintf (stderr, "_LikelihoodFunction::CheckDependentBounds variable %s (%d), current value %g, range %g to %g\n", cornholio->theName->get_str(), index, currentValues.theData[index], lowerBounds.theData[index], upperBounds.theData[index]); bool badApple = currentValues.theData[index]upperBounds.theData[index]; if (badApple) { @@ -2734,7 +2734,7 @@ void _LikelihoodFunction::CheckDependentBounds (void) { SetIthIndependent (index,temp); } - //fprintf (stderr, "\n%s\n", _String((_String*)dependancies.toStr()).sData); + //fprintf (stderr, "\n%s\n", _String((_String*)dependancies.toStr()).get_str()); // now we can go through the dependant variables which are out of bounds one at a time // and attempt to move them back in. @@ -2863,16 +2863,16 @@ void _LikelihoodFunction::CheckDependentBounds (void) { tagged.ReorderList(); - // fprintf (stderr, "Tagged the following variables %s\n", _String((_String*)_aux.toStr()).sData); + //fprintf (stderr, "Tagged the following variables %s\n", _String((_String*)_aux.toStr()).get_str()); for (index = 0; index10?10:GetIthIndependentBound (index,true))-dependancies(0,index)); + dependancies.Store (1,index,(GetIthIndependentBound (index,false)>10?10:GetIthIndependentBound (index,false))-dependancies(0,index)); dependancies.Store (2,index,GetIthIndependent (index)); } - // fprintf (stderr, "\n%s\n", _String((_String*)dependancies.toStr()).sData); + //fprintf (stderr, "\n%s\n", _String((_String*)dependancies.toStr()).get_str()); for (i = 0L; i < 10000L; i++) { @@ -2880,14 +2880,14 @@ void _LikelihoodFunction::CheckDependentBounds (void) { for (long v = 0L; v < _aux.lLength; v++) { index = _aux.get(v); SetIthIndependent (index,dependancies(0,index)+genrand_real2()*dependancies(1,index)); - //fprintf (stderr, "[%d] %s => %g\n", index, GetIthIndependentName(index)->sData, GetIthIndependent(index)); + //fprintf (stderr, "[%d] %s => %g (%g - %g)\n", index, GetIthIndependentName(index)->get_str(), GetIthIndependent(index), dependancies(0,index), dependancies(1,index)); } for (j = 0; j < nonConstantDep->lLength; j++) { // check whether any of the dependent variables are out of bounds long j_corrected = nonConstantIndices.get(j); currentValues.theData[j_corrected] = LocateVar(nonConstantDep->list_data[j])->Compute()->Value(); - //fprintf (stderr, "[%d] %g (%g, %g)\n", j, j_corrected, currentValues.theData[j_corrected], lowerBounds.theData[j_corrected], upperBounds[j_corrected]); if (currentValues.theData[j_corrected]upperBounds.theData[j_corrected]) { + //fprintf (stderr, "[%d] %s => %g (%g, %g)\n", j, LocateVar(nonConstantDep->list_data[j])->GetName()->get_str(), j_corrected, currentValues.theData[j_corrected], lowerBounds.theData[j_corrected], upperBounds[j_corrected]); //fprintf (stderr, "===| CHECK FAILED\n"); badConstraint = nonConstantDep->list_data[j]; break; From baac141a78cb59401331bbc8b8fe8d1fd066bf86 Mon Sep 17 00:00:00 2001 From: Segei L Kosakovsky Pond Date: Thu, 14 Jan 2021 13:25:59 -0500 Subject: [PATCH 2/2] RELAX constraints fixes --- .../SelectionAnalyses/RELAX.bf | 351 ------------------ 1 file changed, 351 deletions(-) diff --git a/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf b/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf index ade5763ef..75eb6b5de 100644 --- a/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf +++ b/res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf @@ -443,357 +443,6 @@ if (relax.model_set == "All") { // run all the models ); -/*relax.grid_search.results = { - "EFV":{ - "relax.ge": { -{0.04881810356648711} - {0.03987090682724777} - {0.04952731390964531} - {0.04155619114937172} - {0.01811127842789196} - {0.01479191205650485} - {0.01837439200770125} - {0.01541714432400942} - {0.01894057781278376} - {0.01546922059762592} - {0.0192157391301816} - {0.01612308169643694} - {0.02832012582609264} - {0.0231297206498455} - {0.0287315495539327} - {0.02410737976743678} - {0.01664713636441668} - {0.01359611239347263} - {0.01688897946013485} - {0.0141707999760208} - {0.006176006434015015} - {0.005044091414975357} - {0.006265729043506587} - {0.005257297706416126} - {0.006458800294051354} - {0.005275055889649603} - {0.006552631222299025} - {0.005498024708183688} - {0.00965725749346899} - {0.007887311992864245} - {0.009797554358782127} - {0.008220697017259783} - {0.03328033861025202} - {0.02718084446073247} - {0.03376382237225545} - {0.02832973859625429} - {0.01234684337796718} - {0.01008396078440649} - {0.01252621349661759} - {0.01051019490766097} - {0.01291219439167226} - {0.01054569641003205} - {0.0130997777090572} - {0.01099144741596503} - {0.0193064315924046} - {0.01576802208506577} - {0.01958690789063199} - {0.01643451308127018} - {0.01964953777584797} - {0.02048009470534294} - {0.008925762616328468} - {0.00728988272051741} - {0.009055432609745021} - {0.00759801529227558} - {0.007623679988342976} - {0.009470072841967696} - {0.007945921677425003} - {0.01395697832125249} - {0.01139899630633314} - {0.01415973985153574} - {0.01188081503812791} - } - }, - "Filters": { -{"relax.filter.default"} - }, - "LF":"iybtBVgK.likelihoodFunction", - "LogL":-3468.628021062044, - "Trees": { -{"((((Pig:0.2002207612790759,Cow:0.2652088954749879)Node3:0.1024483387468423,Horse:0.2271179872916863,Cat:0.2941609243556507)Node2:0.06486663246806917,((RhMonkey:0.003909730323873505,Baboon:0.001860925679316316)Node9:0.02712267964568085,(Human:0,Chimp:0.001921935125106313)Node12:0.01893367713404082)Node8:0.1148290059087238)Node1:0.3005238585248704,Rat:0.07055784179244226,Mouse:0.1259924875975693)"} - }, - "branch length":{ - "0":{ - "Baboon":{ - "MLE":0.001860925679316316, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.00454994471726663, - "constraint":"relax.bl.scaler*0.00421525617283435" - } - }, - "Cat":{ - "MLE":0.2941609243556507, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.7192205248572749, - "constraint":"relax.bl.scaler*0.6663155148959867" - } - }, - "Chimp":{ - "MLE":0.001921935125106313, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.004699112203459599, - "constraint":"relax.bl.scaler*0.004353451075417437" - } - }, - "Cow":{ - "MLE":0.2652088954749879, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.6484331031327714, - "constraint":"relax.bl.scaler*0.6007351320726768" - } - }, - "Horse":{ - "MLE":0.2271179872916863, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.5553012127027491, - "constraint":"relax.bl.scaler*0.5144539131969622" - } - }, - "Human":{ - "MLE":0, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0, - "constraint":"0" - } - }, - "Mouse":{ - "MLE":0.1259924875975693, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.3080503749996349, - "constraint":"relax.bl.scaler*0.2853905542705638" - } - }, - "Node1":{ - "MLE":0.3005238585248704, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.7347778354104789, - "constraint":"relax.bl.scaler*0.6807284481110281" - } - }, - "Node12":{ - "MLE":0.01893367713404082, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.04629265166898581, - "constraint":"relax.bl.scaler*0.04288741904138782" - } - }, - "Node2":{ - "MLE":0.06486663246806917, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.1585982691331329, - "constraint":"relax.bl.scaler*0.146931968300024" - } - }, - "Node3":{ - "MLE":0.1024483387468423, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.2504851659874938, - "constraint":"relax.bl.scaler*0.2320597738529283" - } - }, - "Node8":{ - "MLE":0.1148290059087238, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.2807557736616996, - "constraint":"relax.bl.scaler*0.2601037114792293" - } - }, - "Node9":{ - "MLE":0.02712267964568085, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.06631468109855898, - "constraint":"relax.bl.scaler*0.0614366517002807" - } - }, - "Pig":{ - "MLE":0.2002207612790759, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.4895377634874294, - "constraint":"relax.bl.scaler*0.4535279454154706" - } - }, - "Rat":{ - "MLE":0.07055784179244226, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.1725132191432825, - "constraint":"relax.bl.scaler*0.1598233510683406" - } - }, - "RhMonkey":{ - "MLE":0.003909730323873505, - "relaxation or intensification parameter":{ - "ID":"k", - "MLE":0.5835896398205112, - "constraint":"relax.K" - }, - "synonymous rate":{ - "ID":"t", - "MLE":0.009559251629856012, - "constraint":"relax.bl.scaler*0.008856084401973642" - } - } - } - }, - "global":{ - "Mean scaler variable for relax.ge.omega1":{ - "ID":"relax.ge.omega1_scaler_variable", - "MLE":1 - }, - "Mean scaler variable for relax.ge.omega2":{ - "ID":"relax.ge.omega2_scaler_variable", - "MLE":1 - }, - "Mean scaler variable for relax.ge.omega3":{ - "ID":"relax.ge.omega3_scaler_variable", - "MLE":0.6984561656354166 - }, - "Mixture auxiliary weight for category 1":{ - "ID":"relax.ge.bsrel_mixture_aux_0", - "MLE":1 - }, - "Mixture auxiliary weight for category 2":{ - "ID":"relax.ge.bsrel_mixture_aux_1", - "MLE":0.7992410131933376 - }, - "Substitution rate from nucleotide A to nucleotide C":{ - "ID":"relax.ge.theta_AC", - "MLE":0.5896537813380907 - }, - "Substitution rate from nucleotide A to nucleotide G":{ - "ID":"relax.ge.theta_AG", - "MLE":1, - "constraint":"1" - }, - "Substitution rate from nucleotide A to nucleotide T":{ - "ID":"relax.ge.theta_AT", - "MLE":0.2531352820308571 - }, - "Substitution rate from nucleotide C to nucleotide G":{ - "ID":"relax.ge.theta_CG", - "MLE":0.3871445458988698 - }, - "Substitution rate from nucleotide C to nucleotide T":{ - "ID":"relax.ge.theta_CT", - "MLE":0.9447643279336558 - }, - "Substitution rate from nucleotide G to nucleotide T":{ - "ID":"relax.ge.theta_GT", - "MLE":0.3135181640741386 - }, - "non-synonymous/synonymous rate ratio for category 1":{ - "ID":"relax.ge.omega1", - "MLE":1, - "constraint":"relax.ge.omega1_scaler_variable/relax.scaler_variable" - }, - "non-synonymous/synonymous rate ratio for category 2":{ - "ID":"relax.ge.omega2", - "MLE":1, - "constraint":"relax.ge.omega2_scaler_variable/relax.scaler_variable" - }, - "non-synonymous/synonymous rate ratio for category 3":{ - "ID":"relax.ge.omega3", - "MLE":0.6984561656354166, - "constraint":"relax.ge.omega3_scaler_variable/relax.scaler_variable" - } - }, - "parameters":27 -};*/ - relax.general_descriptive.fit = estimators.FitLF (relax.filter_names, relax.trees,