refactor GLM getXBeta() / getRates() functions so that they perform a…

…s named
beast-dev · Oct 12, 2024 · 2aa3304 · 2aa3304
1 parent 48a9cfb
commit 2aa3304
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Showing 7 changed files with 22 additions and 19 deletions.
diff --git a/src/dr/evomodel/substmodel/GlmSubstitutionModel.java b/src/dr/evomodel/substmodel/GlmSubstitutionModel.java
@@ -71,7 +71,7 @@ public GeneralizedLinearModel getGeneralizedLinearModel() {
     }
 
     protected void setupRelativeRates(double[] rates) {
-        System.arraycopy(glm.getXBeta(),0,rates,0,rates.length);
+        System.arraycopy(glm.getRates(),0,rates,0,rates.length);
     }
 
     @Override

diff --git a/src/dr/evomodel/substmodel/LogAdditiveCtmcRateProvider.java b/src/dr/evomodel/substmodel/LogAdditiveCtmcRateProvider.java
@@ -69,8 +69,8 @@ public Basic(String name, Parameter transformedRateParameter) {
             public Parameter getLogRateParameter() { return transformedRateParameter; }
 
             @Override
-            public double[] getXBeta() { // TODO this function should _not_ exponentiate
-                return transformedRateParameter.getParameterValues();
+            public double[] getXBeta() {
+                return getLogRateParameter().getParameterValues();
             }
 
             @Override

diff --git a/src/dr/evomodelxml/substmodel/GlmSubstitutionModelParser.java b/src/dr/evomodelxml/substmodel/GlmSubstitutionModelParser.java
@@ -65,7 +65,7 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
             glm = new LogAdditiveCtmcRateProvider.DataAugmented.Basic(logRates.getId(), logRates);
         }
 
-        int length = glm.getXBeta().length;
+        int length = glm.getRates().length;
 
         if (length != rateCount) {
             throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + (rateCount) + " dimensions.  However GLM dimension is " + length);

diff --git a/src/dr/inference/distribution/LogGaussianProcessModel.java b/src/dr/inference/distribution/LogGaussianProcessModel.java
@@ -222,14 +222,15 @@ public void precision(double noiseVar) {
     @Override
     public double[] getXBeta() {
         // compute the mean and then exponentiate
-        final int fieldDim = dependentParam.getDimension();
-        double[] rates = new double[fieldDim];
-
-        // here we just exponentiate the log-mean rate into the actual mean rates
-        for (int i = 0; i < fieldDim; i++) {
-            rates[i] = Math.exp(dependentParam.getParameterValue(i));
-        }
-        return rates;
+//        final int fieldDim = dependentParam.getDimension();
+//        double[] rates = new double[fieldDim];
+//
+//        // here we just exponentiate the log-mean rate into the actual mean rates
+//        for (int i = 0; i < fieldDim; i++) {
+//            rates[i] = Math.exp(dependentParam.getParameterValue(i));
+//        }
+//        return rates;
+        return dependentParam.getParameterValues();
     }
 
 }
diff --git a/src/dr/inference/distribution/LogLinearModel.java b/src/dr/inference/distribution/LogLinearModel.java
@@ -48,11 +48,12 @@ public double[] getSuperXBeta() {
 
     @Override
     public double[] getXBeta() {
-        double[] xBeta = super.getXBeta();
-        for(int i = 0; i < xBeta.length; i++) {
-            xBeta[i] = Math.exp(xBeta[i]);
-        }
-        return xBeta;
+//        double[] xBeta = super.getXBeta();
+//        for(int i = 0; i < xBeta.length; i++) {
+//            xBeta[i] = Math.exp(xBeta[i]);
+//        }
+//        return xBeta;
+        return super.getXBeta();
     }
 
     public Parameter getLogRateParameter() {

diff --git a/src/dr/oldevomodel/substmodel/NotUsedGlmSubstitutionModel.java b/src/dr/oldevomodel/substmodel/NotUsedGlmSubstitutionModel.java
@@ -56,7 +56,8 @@ public NotUsedGlmSubstitutionModel(String name, DataType dataType, FrequencyMode
     }
 
     public double[] getRates() {
-        return glm.getXBeta();
+        throw new RuntimeException("No longer supported");
+//        return glm.getXBeta();
     }
 
 

diff --git a/src/dr/oldevomodelxml/substmodel/NotUsedGlmSubstitutionModelParser.java b/src/dr/oldevomodelxml/substmodel/NotUsedGlmSubstitutionModelParser.java
@@ -57,7 +57,7 @@ public Object parseXMLObject(XMLObject xo) throws XMLParseException {
 
         LogLinearModel glm = (LogLinearModel) xo.getChild(GeneralizedLinearModel.class);
 
-        int length = glm.getXBeta().length;
+        int length = glm.getRates().length;
 
         if (length != rateCount) {
             throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + (rateCount) + " dimensions.  However GLM dimension is " + length);