A few trivial changes

beast-dev · Jul 17, 2023 · e436a42 · e436a42
1 parent 39bafa4
commit e436a42
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Showing 3 changed files with 2 additions and 3 deletions.
diff --git a/src/dr/evomodel/siteratemodel/GammaSiteRateDelegate.java b/src/dr/evomodel/siteratemodel/GammaSiteRateDelegate.java
@@ -236,8 +236,6 @@ public static void setQuadratureRates(double[] categoryRates, double[] categoryP
             categoryProportions[i + offset] = coefficients[i]/GammaFunction.gamma(alpha);
         }
 
-        double nothing;
-
     }
 
     /**

diff --git a/src/dr/evomodelxml/siteratemodel/GammaSiteRateModelParser.java b/src/dr/evomodelxml/siteratemodel/GammaSiteRateModelParser.java
@@ -131,6 +131,7 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
         DiscretizedSiteRateModel siteRateModel = new DiscretizedSiteRateModel(SiteModel.SITE_MODEL, muParam, muWeight, delegate);
 
         siteRateModel.setSubstitutionModel(substitutionModel);
+        siteRateModel.addModel(substitutionModel);
 
         return siteRateModel;
     }

diff --git a/src/dr/math/GeneralisedGaussLaguerreQuadrature.java b/src/dr/math/GeneralisedGaussLaguerreQuadrature.java
@@ -109,7 +109,7 @@ private void setupArrays(){
                 throw new RuntimeException("Too many iterations");
             }
             abscissae[i] = z;
-            coefficients[i] = -Math.exp(GammaFunction.lnGamma(alpha+noPoints) - GammaFunction.lnGamma((double)noPoints))/
+            coefficients[i] = -Math.exp(GammaFunction.lnGamma(alpha+noPoints) - GammaFunction.lnGamma(noPoints))/
                     (pp*noPoints*p2);
 
         }