ORC v1.1.1: try catch in ucld scale operator

jordandouglas · Oct 20, 2022 · 1187ce0 · 1187ce0
1 parent e6c3198
commit 1187ce0
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Showing 3 changed files with 87 additions and 79 deletions.
diff --git a/build.xml b/build.xml
@@ -7,7 +7,7 @@
 	</description>
 
 	<!-- set global properties for this build -->
-	<property name="versionORC" value="1.1.0" />
+	<property name="versionORC" value="1.1.1" />
 	<property name="srcORC" location="src" />
 	<property name="docORC" location="doc" />
 	<property name="buildORC" location="build" />
@@ -189,7 +189,6 @@
 		<mkdir dir="${Add_on_dir}/lib" />
 		<mkdir dir="${Add_on_dir}/doc" />
 		<mkdir dir="${Add_on_dir}/examples" />
-		<mkdir dir="${Add_on_dir}/templates" />
 		<mkdir dir="${Add_on_dir}/fxtemplates" />
 
 		<copy todir="${Add_on_dir}">
@@ -211,10 +210,6 @@
 		</copy>
 
 
-		<copy todir="${Add_on_dir}/templates">
-			<fileset file="templates/*.xml" />
-		</copy>
-
 
 		<copy todir="${Add_on_dir}/fxtemplates">
 			<fileset file="fxtemplates/*.xml" />
@@ -279,8 +274,8 @@
 		          productVersion="${version_number}.0"
 		          txtProductVersion="${versionORC}" />
 
-		<copy todir="${Windows_package_dirORC}/templates/">
-			<fileset dir="templates/" />
+		<copy todir="${Windows_package_dirORC}/fxtemplates/">
+			<fileset dir="fxtemplates/" />
 		</copy>
 
 		<zip destfile="${Windows_dirORC}/${CladeAge_name} v${versionORC}.zip">

diff --git a/src/orc/consoperators/UcldScalerOperator.java b/src/orc/consoperators/UcldScalerOperator.java
@@ -80,29 +80,35 @@ public double proposal() {
             LN = (LogNormalDistributionModel) distribution;
         }
 
-        // Step1: calculate rates/quantiles for real rates given the current ucldStdev
-        if (this.usingRates) {
-
-        	// Rates -> quantiles
-	        for (int idx = 0; idx < this.nrates; idx++) {
-	            double r = rates.getValue(idx);
-	            real_rates[idx] = r;
-	            double q = getRateQuantiles(r);
-	            quantiles[idx] = q;
-
+        try {
+
+	        // Step1: calculate rates/quantiles for real rates given the current ucldStdev
+	        if (this.usingRates) {
+
+	        	// Rates -> quantiles
+		        for (int idx = 0; idx < this.nrates; idx++) {
+		            double r = rates.getValue(idx);
+		            real_rates[idx] = r;
+		            double q = getRateQuantiles(r);
+		            quantiles[idx] = q;
+
+		        }
+
+	        }else {
+
+	        	// Quantiles -> rates
+	        	for (int idx = 0; idx < this.nrates; idx++) {
+		            double q = this.quantilesParam.getValue(idx);
+		            quantiles[idx] = q;
+		            double r = getRealRate(q);
+		            real_rates[idx] = r;
+
+		        }
+
 	        }
 
-        }else {
-
-        	// Quantiles -> rates
-        	for (int idx = 0; idx < this.nrates; idx++) {
-	            double q = this.quantilesParam.getValue(idx);
-	            quantiles[idx] = q;
-	            double r = getRealRate(q);
-	            real_rates[idx] = r;
-
-	        }
-
+        }catch(Exception e) {
+        	return Double.NEGATIVE_INFINITY; 
         }
 
         // Step2: use scale operation to propose a new_ucldStdev
@@ -122,15 +128,11 @@ public double proposal() {
         new_stdev = stdev * scale;
         if (new_stdev <= 0) return Double.NEGATIVE_INFINITY;
 
-        // set the new value
-        ucldStdev.setValue(new_stdev);
+
 
         // return the log hastings ratio for scale operation
 
 
-
-
-
         // use mean (M=1) and variance (stdev square) to calculate miu and sigma square of lognormal in log space
         double variance = FastMath.exp(stdev * stdev) -1;
         double new_variance = FastMath.exp(new_stdev * new_stdev) -1; // new sigma square of lognormal
@@ -139,54 +141,65 @@ public double proposal() {
 
         // Step3: calculate the new rates or quantiles under the proposed new_ucldStdev
 
-        // Rates
-        if (this.usingRates) {
-	       for (int idx = 0; idx < this.nrates; idx++) {
-	            double r_ = getRealRate(quantiles[idx]);
-
-	            // to avoid numerical issues
-	            if (r_== 0.0 || r_ == Double.POSITIVE_INFINITY) {
-	                return Double.NEGATIVE_INFINITY;
-	            }
-
-	            // partial derivative of icdf_s'(cdf_s(r)) / r
-	            hastingsRatio = hastingsRatio + getDicdf(real_rates[idx],quantiles[idx],miu,new_miu,stdev,new_stdev);
+
+        try {
+
+	        // Rates
+	        if (this.usingRates) {
+		       for (int idx = 0; idx < this.nrates; idx++) {
+		            double r_ = getRealRate(quantiles[idx]);
+
+		            // to avoid numerical issues
+		            if (r_== 0.0 || r_ == Double.POSITIVE_INFINITY) {
+		                return Double.NEGATIVE_INFINITY;
+		            }
+
+		            // partial derivative of icdf_s'(cdf_s(r)) / r
+		            hastingsRatio = hastingsRatio + getDicdf(real_rates[idx],quantiles[idx],miu,new_miu,stdev,new_stdev);
+
+		            rates.setValue(idx, r_);
+		        }
+
+		    // Quantiles
+	        }else {
+
+	        	// Step3: calculate the new quantiles such that the rates remain constant
+
+	        	for (int idx = 0; idx < this.nrates; idx++) {
+
+	        		// Original quantile
+	        		double q = this.quantilesParam.getArrayValue(idx);
+
+	        		// Original rate (want the new rate to be the same)
+					double r = real_rates[idx];
+
+					// Propose q_ such that the rate is constant
+					double q_ = this.getRateQuantiles(r);
+	        		if (q_ <= 0 || q_ >= 1) return Double.NEGATIVE_INFINITY;
+	        		quantilesParam.setValue(idx, q_);
+
+
+	        		// logHR
+	        		double logHRBranch = this.getQuantHR(q, miu, new_miu, stdev, new_stdev);
+
+
+	        		//System.out.println(stdev + " -> " + new_stdev + "; " + q + " -> " + q_ + "; HR: " + logHRBranch);
+	        		hastingsRatio += logHRBranch;
+
+	        	}
+
 
-	            rates.setValue(idx, r_);
-	        }
-
-	    // Quantiles
-        }else {
-
-        	// Step3: calculate the new quantiles such that the rates remain constant
-
-        	for (int idx = 0; idx < this.nrates; idx++) {
-
-        		// Original quantile
-        		double q = this.quantilesParam.getArrayValue(idx);
-
-        		// Original rate (want the new rate to be the same)
-				double r = real_rates[idx];
-
-				// Propose q_ such that the rate is constant
-				double q_ = this.getRateQuantiles(r);
-        		if (q_ <= 0 || q_ >= 1) return Double.NEGATIVE_INFINITY;
-        		quantilesParam.setValue(idx, q_);
-
-
-        		// logHR
-        		double logHRBranch = this.getQuantHR(q, miu, new_miu, stdev, new_stdev);
-
-
-        		//System.out.println(stdev + " -> " + new_stdev + "; " + q + " -> " + q_ + "; HR: " + logHRBranch);
-        		hastingsRatio += logHRBranch;
-
-        	}
 
-
-
+	        }
+
+        }catch(Exception e) {
+        	return Double.NEGATIVE_INFINITY;
         }
 
+
+        // set the new value
+        ucldStdev.setValue(new_stdev);
+
         //System.out.println("HR " + hastingsRatio);
 
         return hastingsRatio;

diff --git a/version.xml b/version.xml
@@ -1,4 +1,4 @@
-<package name='ORC' version='1.1.0'>
+<package name='ORC' version='1.1.1'>
 	<depends on='BEAST.base' atleast='2.7.0'/>
 	<depends on='BEAST.app' atleast='2.7.0'/>
 	<depends on='BEASTLabs' atleast='2.0.0'/>