Implement {x}lnorm functions and df

com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Df.java

+/*
+ * This material is distributed under the GNU General Public License
+ * Version 2. You may review the terms of this license at
+ * http://www.gnu.org/licenses/gpl-2.0.html
+ *
+ * Copyright (c) 2000--2014, The R Core Team
+ * Copyright (c) 2016, Oracle and/or its affiliates
+ *
+ * All rights reserved.
+ */
+// Acknowledgement from GnuR header:
+// Author: Catherine Loader, catherine@research.bell-labs.com, October 23, 2000.
+package com.oracle.truffle.r.library.stats;
+
+import static com.oracle.truffle.r.library.stats.Dbinom.dbinomRaw;
+import static com.oracle.truffle.r.library.stats.GammaFunctions.dgamma;
+
+import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_1;
+
+public final class Df implements Function3_1 {
+    @Override
+    public double evaluate(double x, double m, double n, boolean giveLog) {
+        double p;
+        double q;
+        double f;
+        double dens;
+
+        if (Double.isNaN(x) || Double.isNaN(m) || Double.isNaN(n)) {
+            return x + m + n;
+        }
+
+        if (m <= 0 || n <= 0) {
+            return RMath.mlError();
+        }
+        if (x < 0.) {
+            return DPQ.rd0(giveLog);
+        }
+        if (x == 0.) {
+            return m > 2 ? DPQ.rd0(giveLog) : (m == 2 ? DPQ.rd1(giveLog) : Double.POSITIVE_INFINITY);
+        }
+        if (!Double.isFinite(m) && !Double.isFinite(n)) { /* both +Inf */
+            if (x == 1.) {
+                return Double.POSITIVE_INFINITY;
+            } else {
+                return DPQ.rd0(giveLog);
+            }
+        }
+        if (!Double.isFinite(n)) {
+            /* must be +Inf by now */
+            return dgamma(x, m / 2, 2. / m, giveLog);
+        }
+        if (m > 1e14) { /* includes +Inf: code below is inaccurate there */
+            dens = dgamma(1. / x, n / 2, 2. / n, giveLog);
+            return giveLog ? dens - 2 * Math.log(x) : dens / (x * x);
+        }
+
+        f = 1. / (n + x * m);
+        q = n * f;
+        p = x * m * f;
+
+        if (m >= 2) {
+            f = m * q / 2;
+            dens = dbinomRaw((m - 2) / 2, (m + n - 2) / 2, p, q, giveLog);
+        } else {
+            f = m * m * q / (2 * p * (m + n));
+            dens = dbinomRaw(m / 2, (m + n) / 2, p, q, giveLog);
+        }
+        return (giveLog ? Math.log(f) + dens : f * dens);
+    }
+}

com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/LogNormal.java

+/*
+ * This material is distributed under the GNU General Public License
+ * Version 2. You may review the terms of this license at
+ * http://www.gnu.org/licenses/gpl-2.0.html
+ *
+ * Copyright (C) 1998 Ross Ihaka
+ * Copyright (c) 2000--2014, The R Core Team
+ * Copyright (c) 2005, The R Foundation
+ * Copyright (c) 2016, Oracle and/or its affiliates
+ *
+ * All rights reserved.
+ */
+package com.oracle.truffle.r.library.stats;
+
+import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
+import com.oracle.truffle.r.library.stats.RandGenerationFunctions.RandFunction2_Double;
+import com.oracle.truffle.r.library.stats.RandGenerationFunctions.RandomNumberProvider;
+import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_1;
+import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_2;
+
+public final class LogNormal {
+    private LogNormal() {
+        // only static members
+    }
+
+    public static final class RLNorm implements RandFunction2_Double {
+        private final Rnorm rnorm = new Rnorm();
+
+        @Override
+        public double evaluate(double meanlog, double sdlog, RandomNumberProvider rand) {
+            if (Double.isNaN(meanlog) || !Double.isFinite(sdlog) || sdlog < 0.) {
+                return RMath.mlError();
+            }
+            return Math.exp(rnorm.evaluate(meanlog, sdlog, rand));
+        }
+    }
+
+    public static final class DLNorm implements Function3_1 {
+        @Override
+        public double evaluate(double x, double meanlog, double sdlog, boolean giveLog) {
+            if (Double.isNaN(x) || Double.isNaN(meanlog) || Double.isNaN(sdlog)) {
+                return x + meanlog + sdlog;
+            }
+            if (sdlog <= 0) {
+                if (sdlog < 0) {
+                    return RMath.mlError();
+                }
+                // sdlog == 0 :
+                return (Math.log(x) == meanlog) ? Double.POSITIVE_INFINITY : DPQ.rd0(giveLog);
+            }
+            if (x <= 0) {
+                return DPQ.rd0(giveLog);
+            }
+
+            double y = (Math.log(x) - meanlog) / sdlog;
+            return (giveLog ? -(MathConstants.M_LN_SQRT_2PI + 0.5 * y * y + Math.log(x * sdlog)) : MathConstants.M_1_SQRT_2PI * Math.exp(-0.5 * y * y) / (x * sdlog));
+            /* M_1_SQRT_2PI = 1 / Math.sqrt(2 * pi) */
+        }
+    }
+
+    public static final class QLNorm implements Function3_2 {
+        private final Qnorm qnorm = new Qnorm();
+
+        @Override
+        public double evaluate(double p, double meanlog, double sdlog, boolean lowerTail, boolean logP) {
+            if (Double.isNaN(p) || Double.isNaN(meanlog) || Double.isNaN(sdlog)) {
+                return p + meanlog + sdlog;
+            }
+            try {
+                DPQ.rqp01boundaries(p, 0, Double.POSITIVE_INFINITY, lowerTail, logP);
+            } catch (EarlyReturn e) {
+                return e.result;
+            }
+            return Math.exp(qnorm.evaluate(p, meanlog, sdlog, lowerTail, logP));
+        }
+    }
+
+    public static final class PLNorm implements Function3_2 {
+        private final Pnorm pnorm = new Pnorm();
+
+        @Override
+        public double evaluate(double x, double meanlog, double sdlog, boolean lowerTail, boolean logP) {
+            if (Double.isNaN(x) || Double.isNaN(meanlog) || Double.isNaN(sdlog)) {
+                return x + meanlog + sdlog;
+            }
+            if (sdlog < 0) {
+                return RMath.mlError();
+            }
+            if (x > 0) {
+                return pnorm.evaluate(Math.log(x), meanlog, sdlog, lowerTail, logP);
+            }
+            return DPQ.rdt0(lowerTail, logP);
+        }
+    }
+}

com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pnorm.java

@@ -41,11 +41,11 @@ public final class Pnorm implements StatsFunctions.Function3_2 {
                 return Double.NaN;
             }
             /* sigma = 0 : */
-            return (x < mu) ? DPQ.rd0(logP) : DPQ.rd1(logP);
+            return (x < mu) ? DPQ.rdt0(lowerTail, logP) : DPQ.rdt1(lowerTail, logP);
         }
         double p = (x - mu) / sigma;
         if (!Double.isFinite(p)) {
-            return (x < mu) ? DPQ.rd0(logP) : DPQ.rd1(logP);
+            return (x < mu) ? DPQ.rdt0(lowerTail, logP) : DPQ.rdt1(lowerTail, logP);
         }
 
         PnormBoth pnormBoth = new PnormBoth(p);

com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java

@@ -52,6 +52,7 @@ import com.oracle.truffle.r.library.stats.CutreeNodeGen;
 import com.oracle.truffle.r.library.stats.DBeta;
 import com.oracle.truffle.r.library.stats.DPois;
 import com.oracle.truffle.r.library.stats.Dbinom;
+import com.oracle.truffle.r.library.stats.Df;
 import com.oracle.truffle.r.library.stats.DoubleCentreNodeGen;
 import com.oracle.truffle.r.library.stats.Dt;
 import com.oracle.truffle.r.library.stats.Exp.DExp;
@@ -63,6 +64,10 @@ import com.oracle.truffle.r.library.stats.GammaFunctions.QgammaFunc;
 import com.oracle.truffle.r.library.stats.Geom;
 import com.oracle.truffle.r.library.stats.Geom.DGeom;
 import com.oracle.truffle.r.library.stats.Geom.RGeom;
+import com.oracle.truffle.r.library.stats.LogNormal;
+import com.oracle.truffle.r.library.stats.LogNormal.DLNorm;
+import com.oracle.truffle.r.library.stats.LogNormal.PLNorm;
+import com.oracle.truffle.r.library.stats.LogNormal.QLNorm;
 import com.oracle.truffle.r.library.stats.Pbeta;
 import com.oracle.truffle.r.library.stats.Pbinom;
 import com.oracle.truffle.r.library.stats.Pf;
@@ -299,6 +304,8 @@ public class CallAndExternalFunctions {
                     return StatsFunctionsFactory.Function3_2NodeGen.create(new Cauchy.QCauchy());
                 case "pf":
                     return StatsFunctionsFactory.Function3_2NodeGen.create(new Pf());
+                case "df":
+                    return StatsFunctionsFactory.Function3_1NodeGen.create(new Df());
                 case "dgamma":
                     return StatsFunctionsFactory.Function3_1NodeGen.create(new DGamma());
                 case "dchisq":
@@ -321,6 +328,14 @@ public class CallAndExternalFunctions {
                     return StatsFunctionsFactory.Function3_1NodeGen.create(new DBeta());
                 case "dt":
                     return StatsFunctionsFactory.Function2_1NodeGen.create(new Dt());
+                case "rlnorm":
+                    return RandGenerationFunctionsFactory.Function2_DoubleNodeGen.create(new LogNormal.RLNorm());
+                case "dlnorm":
+                    return StatsFunctionsFactory.Function3_1NodeGen.create(new DLNorm());
+                case "qlnorm":
+                    return StatsFunctionsFactory.Function3_2NodeGen.create(new QLNorm());
+                case "plnorm":
+                    return StatsFunctionsFactory.Function3_2NodeGen.create(new PLNorm());
                 case "rmultinom":
                     return RMultinomNodeGen.create();
                 case "Approx":

com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/stats/TestRandGenerationFunctions.java

@@ -31,7 +31,7 @@ import com.oracle.truffle.r.test.TestBase;
  * tests for its specific corner cases if those are not covered here.
  */
 public class TestRandGenerationFunctions extends TestBase {
-    private static final String[] FUNCTION2_NAMES = {"rnorm", "runif", "rgamma", "rbeta", "rcauchy", "rf", "rlogis", "rweibull", "rchisq", "rwilcox"};
+    private static final String[] FUNCTION2_NAMES = {"rnorm", "runif", "rgamma", "rbeta", "rcauchy", "rf", "rlogis", "rweibull", "rchisq", "rwilcox", "rlnorm"};
     private static final String[] FUNCTION2_PARAMS = {
                     "10, 10, 10",
                     "20, c(-1, 0, 0.2, 2:5), c(-1, 0, 0.1, 0.9, 3)",

com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/stats/TestStatFunctions.java

@@ -30,7 +30,7 @@ import com.oracle.truffle.r.test.TestBase;
  * Common tests for functions implemented using {@code StatsFunctions} infrastructure.
  */
 public class TestStatFunctions extends TestBase {
-    private static final String[] FUNCTION3_1_NAMES = {"dgamma", "dbeta", "dcauchy"};
+    private static final String[] FUNCTION3_1_NAMES = {"dgamma", "dbeta", "dcauchy", "dlnorm"};
     private static final String[] FUNCTION3_1_PARAMS = {
                     "10, 10, 10, log=TRUE",
                     "3, 3, 3, log=FALSE",
@@ -80,7 +80,7 @@ public class TestStatFunctions extends TestBase {
         assertEval(Output.IgnoreWhitespace, template("set.seed(1); %0(%1)", FUNCTION2_2_NAMES, new String[]{"rep(c(1, 0, 0.1), 5), c(NA, 0, NaN, 1/0, -1/0)"}));
     }
 
-    private static final String[] FUNCTION3_2_NAMES = {"pbeta", "pcauchy", "qcauchy"};
+    private static final String[] FUNCTION3_2_NAMES = {"pbeta", "pcauchy", "qcauchy", "qlnorm", "plnorm"};
     private static final String[] FUNCTION3_2_PARAMS = {
                     "0, 10, 10",
                     "c(-1, 0, 0.2, 2), c(-1, 0, 0.1, 0.9, 3), rep(c(-1, 0, 1, 0.1, -0.1, 0.0001), 20)",

mx.fastr/copyrights/overrides

@@ -61,6 +61,7 @@ com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/SplineFuncti
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/StatsFunctions.java,gnu_r_gentleman_ihaka.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RandGenerationFunctions.java,gnu_r_gentleman_ihaka.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMath.java,gnu_r_ihaka.copyright
+com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/LogNormal.java,gnu_r_ihaka.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/MathConstants.java,gnu_r_ihaka.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/TOMS708.java,gnu_r.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/SNorm.java,gnu_r_ihaka_core.copyright
@@ -73,6 +74,7 @@ com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RChisq.java,
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Exp.java,gnu_r_ihaka_core.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Geom.java,gnu_r_ihaka_core.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dt.java,gnu_r.core.copyright
+com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Df.java,gnu_r.core.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DBeta.java,gnu_r.core.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DPois.java,gnu_r.core.copyright
 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RNchisq.java,gnu_r.copyright