prior problem in birthDeathOnRootAgeAndTaxa.lphy #492

LinguaPhylo · Jun 11, 2024 · d767faf · d767faf
1 parent 07b829b
commit d767faf
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/examples/birth-death/birthDeathOnRootAgeAndTaxa.lphy b/examples/birth-death/birthDeathOnRootAgeAndTaxa.lphy
@@ -17,8 +17,8 @@ model{
   // Conditioned on root age and on number of taxa
   ψ ~ BirthDeath(lambda=λ, mu=death_rate, rootAge=root_time, taxa=taxa);
 
-  ucln_mean ~ Exp(mean=2.0);
-  ucln_sigma ~ Exp(mean=3.0);
+  ucln_mean ~ Normal(mean=-4.5, sd=0.5);
+  ucln_sigma ~ Exp(mean=0.5);
   branch_rates ~ LogNormal(meanlog=ucln_mean, sdlog=ucln_sigma, replicates=2*n - 2);
 
   D ~ PhyloCTMC(tree=ψ, Q=Q, branchRates=branch_rates, L=L);

diff --git a/lphy-base/src/main/java/lphy/base/evolution/likelihood/AbstractPhyloCTMC.java b/lphy-base/src/main/java/lphy/base/evolution/likelihood/AbstractPhyloCTMC.java
@@ -48,11 +48,15 @@ public abstract class AbstractPhyloCTMC implements GenerativeDistribution<Alignm
     protected Value<Double[]> rootFreqs;
     protected SortedMap<String, Integer> idMap = new TreeMap<>();
     protected double[][] transProb;
+    /**
+     * <code>e^{Qt} = Ee^{At}E^-1</code>, where A is a diagonal matrix of eigenvalues (Eval),
+     * E is the matrix of right eigenvectors (Evec), and E^-1 is the matrix of left eigenvectors (Ievc).
+     */
     private EigenDecomposition decomposition;
-    private double[][] Ievc;
-    private double[][] Evec;
-    private double[][] iexp;
-    private double[] Eval;
+    private double[][] Ievc; // inverse Eigen vectors
+    private double[][] Evec; // Eigen vectors
+    private double[][] iexp; // intermediate matrix
+    private double[] Eval; // Eigenvalues
 
 
     public AbstractPhyloCTMC(Value<TimeTree> tree, Value<Number> clockRate, Value<Double[]> freq,