add GeneratorInfo for LPhy Doc #525

phylonco-lphy/examples/SVS.lphy

@@ -5,25 +5,46 @@ b_exp ~ LogNormal(meanlog=-0.98, sdlog=0.35);
 N0_exp ~ LogNormal(meanlog=9.2, sdlog=0.2);
 exponentialPopFunc = exponentialPopFunc(GrowthRate=b_exp, N0=N0_exp);
 
-t50_gom ~ LogNormal(meanlog=4, sdlog=1.2);
+t50_gom ~ LogNormal(meanlog=4, sdlog=0.2);
 b_gom ~ LogNormal(meanlog=-0.98, sdlog=0.35);
 NInf_gomp ~ LogNormal(meanlog=9.2, sdlog=0.12);
 gompertzPopFunc = gompertzPopFunc_t50(NInfinity=NInf_gomp, t50=t50_gom, b=b_gom);
 
-t50_log ~ LogNormal(meanlog=4, sdlog=1.2);
+t50_log ~ LogNormal(meanlog=4, sdlog=0.2);
 b_log ~ LogNormal(meanlog=-0.98, sdlog=0.35);
 Ninf_log ~ LogNormal(meanlog=9.2, sdlog=0.12);
 logisticPopFunc = logisticPopFunc(t50=t50_log, nCarryingCapacity=Ninf_log, b=b_log);
 
-models = [constantPopFunc, exponentialPopFunc, logisticPopFunc, gompertzPopFunc];
+tau_expansion ~ LogNormal(meanlog=4.0, sdlog=0.7);
+r_expansion ~ LogNormal(meanlog=-3.0, sdlog=1.0);
+NC_expansion ~ LogNormal(meanlog=8.0, sdlog=0.7);
+N0_expansion ~ LogNormal(meanlog=5.15, sdlog=0.7);
+expansionPopFunc = expansionPopFunc(tau=tau_expansion, N0=N0_expansion, r=r_expansion, NC=NC_expansion);
+
+models = [constantPopFunc, exponentialPopFunc, logisticPopFunc, gompertzPopFunc, expansionPopFunc];
 I ~ UniformDiscrete(lower=0, upper=length(models)-1);
 SVSmodel = stochasticVariableSelection(indicator=I, models=models);
 tree ~CoalescentPopFunc(n=40, popFunc=SVSmodel);
-D ~ PhyloCTMC(L=2000, Q=jukesCantor(),mu=0.01, tree=tree);
+κ ~ LogNormal(meanlog=1.0, sdlog=0.5);
+π ~ Dirichlet(conc=[2.0,2.0,2.0,2.0]);
+D ~ PhyloCTMC(L=2000, Q=hky(kappa=κ, freq=π), mu=0.00079, tree=tree);
 height = tree.rootAge();
 length = tree.treeLength();
 
 
+
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+
 //π ~ Dirichlet(conc=[30.0, 3.0, 3.0, 3.0, 3.0, 30.0, 3.0, 3.0, 3.0, 3.0, 30.0, 3.0, 3.0, 3.0, 3.0, 30.0]);
 //rates ~ Dirichlet(conc=[1.0, 2.0, 1.0, 1.0, 2.0, 1.0]);
 //Q = gt16(rates=rates, freq=π);

phylonco-lphy/examples/expansionCoal.lphy

@@ -1,15 +1,18 @@
 model {
-tau ~ LogNormal(meanlog=1.0, sdlog=0.2);
-r ~ LogNormal(meanlog=-0.95, sdlog=0.2);
-NC ~ LogNormal(meanlog=6.0, sdlog=0.2);
-N0 ~ LogNormal(meanlog=0.15, sdlog=0.2);
+tau ~ LogNormal(meanlog=4.0, sdlog=0.7);
+r ~ LogNormal(meanlog=-3.0, sdlog=0.5);
+NC ~ LogNormal(meanlog=8.0, sdlog=0.7);
+N0 ~ LogNormal(meanlog=5.15, sdlog=0.7);
 expansionPopFunc = expansionPopFunc(tau=tau, N0=N0, r=r, NC=NC);
 tree ~CoalescentPopFunc(n=40, popFunc=expansionPopFunc);
 D ~ PhyloCTMC(L=1000, Q=jukesCantor(),mu=0.01, tree=tree);
 height = tree.rootAge();
 length = tree.treeLength();
 }
 
+
+
+
 tau ~ LogNormal(meanlog=1.0, sdlog=0.2);
 r ~ LogNormal(meanlog=-0.95, sdlog=0.2);
 NC ~ LogNormal(meanlog=6.0, sdlog=0.2);

phylonco-lphy/examples/gomp_f0_jc69.lphy

@@ -9,4 +9,5 @@ model {
   tree ~ CoalescentPopFunc(n=40, popFunc=gompertzPopFunc);
   D ~ PhyloCTMC(L=L, Q=jukesCantor(), mu=0.01, tree=tree);
   //height = tree.rootAge();
-}
+}
+

phylonco-lphy/examples/gomp_t50_gt16.lphy

@@ -6,9 +6,9 @@ model {
 rates ~ Dirichlet(conc=[1.0, 2.0, 1.0, 1.0, 2.0, 1.0]);
 Q = gt16(rates=rates, freq=π);
 
-t50 ~ LogNormal(meanlog=0.3, sdlog=0.1);
-b ~ LogNormal(meanlog=2, sdlog=0.5);
-NInfinity ~ LogNormal(meanlog=4.5, sdlog=0.5);
+t50 ~ LogNormal(meanlog=4, sdlog=1.2);
+b ~ LogNormal(meanlog=-0.98, sdlog=0.35);
+NInfinity ~ LogNormal(meanlog=9.2, sdlog=0.12);
 
 gompertzPopFunc = gompertzPopFunc_t50(NInfinity=NInfinity,t50=t50, b=b);
 ψ ~ CoalescentPopFunc(n=40, popFunc=gompertzPopFunc);
@@ -18,4 +18,6 @@ delta ~ Beta(alpha=1.5, beta=4.5);
 E ~ GT16ErrorModel(delta=delta, epsilon=epsilon, alignment=A);
 D = unphase(alignment=E);
 height = ψ.rootAge();
-}
+}
+
+

phylonco-lphy/examples/gomp_t50_jc69.lphy

@@ -2,13 +2,23 @@ data {
   L = 1000;
 }
 model {
-  t50 ~ LogNormal(meanlog=0.3, sdlog=0.1);
-  b ~ LogNormal(meanlog=2, sdlog=0.5);
-  NInfinity ~ LogNormal(meanlog=4.5, sdlog=0.5);
+  t50 =8.9;
+   b =0.226;
+  NInfinity =150.0;
   gompertzPopFunc = gompertzPopFunc_t50(NInfinity=NInfinity,t50=t50, b=b);
-  //n0 = gompertzPopFunc.getN0();
-  //f0=n0/NInfinity;
   tree ~ CoalescentPopFunc(n=40, popFunc=gompertzPopFunc);
   D ~ PhyloCTMC(tree=tree, L=L, Q=jukesCantor(), mu=1e-2);
   height = tree.rootAge();
-}
+  length = tree.treeLength();
+}
+
+
+t50 ~ LogNormal(meanlog=4.0, sdlog=0.5);
+   b ~ LogNormal(meanlog=-0.98, sdlog=0.5);
+  NInfinity ~ LogNormal(meanlog=9.2, sdlog=1.7);
+
+
+  //n0 = gompertzPopFunc.getN0();
+  //f0=n0/NInfinity;
+
+  b ~ LogNormal(meanlog=0.4, sdlog=0.35);

phylonco-lphybeast/src/main/java/phylonco/lphybeast/spi/LBPhylonco.java

@@ -77,7 +77,7 @@ public List<Class<? extends Generator>> getExcludedGenerator() {
                 SampleBranch.class, SubstituteClade.class, SubsampledTree.class, LabelClade.class,
                 MRCA.class,
                 PopulationFunctionCoalescent.class,
-                SVSFunction.class,
+                SVSPopulationFunction.class,
                 GompertzPopulationFunction_f0.class,
                 GompertzPopulationFunction_t50.class,
                 ExponentialPopulationFunction.class,
@@ -90,7 +90,7 @@ public List<Class<? extends Generator>> getExcludedGenerator() {
     @Override
     public List<Class> getExcludedValueType() {
         return Arrays.asList(TimeTreeNode.class,
-                SVSPopulationFunction.class);
+                SVSPopulation.class);
     }
 
 }

phylonco-lphybeast/src/main/java/phylonco/lphybeast/tobeast/generators/PopFuncCoalescentToBEAST.java

@@ -4,6 +4,7 @@
 import beast.base.evolution.tree.TreeIntervals;
 import lphy.base.evolution.coalescent.PopulationFunction;
 import lphy.base.evolution.coalescent.PopulationFunctionCoalescent;
+import lphy.base.evolution.coalescent.populationmodel.SVSPopulation;
 import lphy.base.evolution.coalescent.populationmodel.SVSPopulationFunction;
 import lphy.core.model.Value;
 import lphybeast.BEASTContext;
@@ -29,7 +30,7 @@ public beast.base.evolution.tree.coalescent.Coalescent generatorToBEAST(Populati
 
         beast.base.evolution.tree.coalescent.PopulationFunction populationFunction;
 
-        if (beastObj instanceof SVSPopulationFunction) {
+        if (beastObj instanceof SVSPopulation) {
             populationFunction = convertSVSPopulationFunction((SVSPopulationFunction) beastObj, context);
         } else if (beastObj instanceof beast.base.evolution.tree.coalescent.PopulationFunction) {
             populationFunction = (beast.base.evolution.tree.coalescent.PopulationFunction) beastObj;
@@ -58,7 +59,7 @@ public beast.base.evolution.tree.coalescent.Coalescent generatorToBEAST(Populati
     }
 
     private beast.base.evolution.tree.coalescent.PopulationFunction convertSVSPopulationFunction(SVSPopulationFunction svsPopFunc, BEASTContext context) {
-        PopulationFunction model = svsPopFunc.getModel();
+        PopulationFunction model = (PopulationFunction) svsPopFunc.getModels();
         Value<PopulationFunction> modelValue = new Value<>(model, null);
 
         Object beastObj = context.getBEASTObject(modelValue);

phylonco-lphybeast/src/main/java/phylonco/lphybeast/tobeast/values/SVSPopulationFunctionToBEAST.java

@@ -2,7 +2,7 @@
 
 import beast.base.inference.parameter.IntegerParameter;
 import lphy.base.evolution.coalescent.PopulationFunction;
-import lphy.base.evolution.coalescent.populationmodel.SVSFunction;
+import lphy.base.evolution.coalescent.populationmodel.SVSPopulation;
 import lphy.base.evolution.coalescent.populationmodel.SVSPopulationFunction;
 import lphy.core.model.GraphicalModelNode;
 import lphy.core.model.Value;
@@ -13,14 +13,14 @@
 
 import java.util.ArrayList;
 
-public class SVSPopulationFunctionToBEAST implements ValueToBEAST<SVSPopulationFunction, StochasticVariableSelection> {
+public class SVSPopulationFunctionToBEAST implements ValueToBEAST<SVSPopulation, StochasticVariableSelection> {
 
     @Override
-    public StochasticVariableSelection valueToBEAST(Value<SVSPopulationFunction> lphyPopFuncVal, BEASTContext context) {
+    public StochasticVariableSelection valueToBEAST(Value<SVSPopulation> lphyPopFuncVal, BEASTContext context) {
 
         StochasticVariableSelection beastPopFunc = new StochasticVariableSelection();
 
-        SVSFunction gen = (SVSFunction) lphyPopFuncVal.getGenerator();
+        SVSPopulationFunction gen = (SVSPopulationFunction) lphyPopFuncVal.getGenerator();
 
         IntegerParameter indicatorParam = context.getAsIntegerParameter(gen.getIndicator());
 
@@ -68,7 +68,7 @@ public StochasticVariableSelection valueToBEAST(Value<SVSPopulationFunction> lph
 
     @Override
     public Class getValueClass() {
-        return SVSPopulationFunction.class;
+        return SVSPopulation.class;
     }
 
     @Override