From 7b8394410ca59f4337b2df3caee0f24f715b8c2d Mon Sep 17 00:00:00 2001
From: stepan <stepan.sindelar@oracle.com>
Date: Wed, 21 Dec 2016 14:34:55 +0100
Subject: [PATCH] Externals for logis distribution: dlogis, qlogis, plogis
---
.../oracle/truffle/r/library/stats/Logis.java | 137 ++++++++++++++++++
.../foreign/CallAndExternalFunctions.java | 10 +-
mx.fastr/copyrights/overrides | 2 +-
3 files changed, 147 insertions(+), 2 deletions(-)
create mode 100644 com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java
new file mode 100644
index 0000000000..45328c4693
--- /dev/null
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java
@@ -0,0 +1,137 @@
+/*
+ * 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) 1998--2008, The R Core Team
+ * Copyright (c) 2016, 2016, Oracle and/or its affiliates
+ *
+ * All rights reserved.
+ */
+/*
+ * Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka
+ * Copyright (C) 2000 The R Core Team
+ */
+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 Logis {
+ private Logis() {
+ // only static members
+ }
+
+ public static final class DLogis implements Function3_1 {
+ @Override
+ public double evaluate(double x, double location, double scale, boolean giveLog) {
+ if (Double.isNaN(x) || Double.isNaN(location) || Double.isNaN(scale)) {
+ return x + location + scale;
+ }
+ if (scale <= 0.0) {
+ return RMath.mlError();
+ }
+
+ x = TOMS708.fabs((x - location) / scale);
+ double e = Math.exp(-x);
+ double f = 1.0 + e;
+ return giveLog ? -(x + Math.log(scale * f * f)) : e / (scale * f * f);
+ }
+ }
+
+ public static final class QLogis implements Function3_2 {
+ @Override
+ public double evaluate(double p, double location, double scale, boolean lowerTail, boolean logP) {
+ if (Double.isNaN(p) || Double.isNaN(location) || Double.isNaN(scale)) {
+ return p + location + scale;
+ }
+
+ try {
+ DPQ.rqp01boundaries(p, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, lowerTail, logP);
+ } catch (EarlyReturn e) {
+ return e.result;
+ }
+
+ if (scale < 0.) {
+ return RMath.mlError();
+ }
+ if (scale == 0.) {
+ return location;
+ }
+
+ /* p := logit(p) = Math.log( p / (1-p) ) : */
+ if (logP) {
+ if (lowerTail) {
+ p = p - DPQ.rlog1exp(p);
+ } else {
+ p = DPQ.rlog1exp(p) - p;
+ }
+ } else {
+ p = Math.log(lowerTail ? (p / (1. - p)) : ((1. - p) / p));
+ }
+
+ return location + scale * p;
+ }
+ }
+
+ public static final class PLogis implements Function3_2 {
+ @Override
+ public double evaluate(double x, double location, double scale, boolean lowerTail, boolean logP) {
+ if (Double.isNaN(x) || Double.isNaN(location) || Double.isNaN(scale)) {
+ return x + location + scale;
+ }
+ if (scale <= 0.0) {
+ return RMath.mlError();
+ }
+
+ x = (x - location) / scale;
+ if (Double.isNaN(x)) {
+ return RMath.mlError();
+ }
+
+ try {
+ DPQ.rpboundsinf01(x, lowerTail, logP);
+ } catch (EarlyReturn earlyReturn) {
+ return earlyReturn.result;
+ }
+
+ if (logP) {
+ // Math.log(1 / (1 + Math.exp( +- x ))) = -Math.log(1 + Math.exp( +- x))
+ return -log1pexp(lowerTail ? -x : x);
+ } else {
+ return 1 / (1 + Math.exp(lowerTail ? -x : x));
+ }
+ }
+
+ private static double log1pexp(double x) {
+ if (x <= 18.) {
+ return RMath.log1p(Math.exp(x));
+ }
+ if (x > 33.3) {
+ return x;
+ }
+ // else: 18.0 < x <= 33.3 :
+ return x + Math.exp(-x);
+ }
+ }
+
+ public static final class RLogis extends RandFunction2_Double {
+ @Override
+ public double execute(double location, double scale, RandomNumberProvider rand) {
+ if (Double.isNaN(location) || !Double.isFinite(scale)) {
+ return RMath.mlError();
+ }
+
+ if (scale == 0. || !Double.isFinite(location)) {
+ return location;
+ } else {
+ double u = rand.unifRand();
+ return location + scale * Math.log(u / (1. - u));
+ }
+ }
+ }
+}
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java
index 2c2f2c7983..001e044000 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/foreign/CallAndExternalFunctions.java
@@ -68,6 +68,9 @@ 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.Logis;
+import com.oracle.truffle.r.library.stats.Logis.DLogis;
+import com.oracle.truffle.r.library.stats.Logis.RLogis;
import com.oracle.truffle.r.library.stats.Pbeta;
import com.oracle.truffle.r.library.stats.Pbinom;
import com.oracle.truffle.r.library.stats.Pf;
@@ -78,7 +81,6 @@ import com.oracle.truffle.r.library.stats.RBeta;
import com.oracle.truffle.r.library.stats.RChisq;
import com.oracle.truffle.r.library.stats.RGamma;
import com.oracle.truffle.r.library.stats.RHyper;
-import com.oracle.truffle.r.library.stats.RLogis;
import com.oracle.truffle.r.library.stats.RMultinomNodeGen;
import com.oracle.truffle.r.library.stats.RNbinomMu;
import com.oracle.truffle.r.library.stats.RNchisq;
@@ -338,6 +340,12 @@ public class CallAndExternalFunctions {
return StatsFunctionsFactory.Function3_2NodeGen.create(new QLNorm());
case "plnorm":
return StatsFunctionsFactory.Function3_2NodeGen.create(new PLNorm());
+ case "dlogis":
+ return StatsFunctionsFactory.Function3_1NodeGen.create(new DLogis());
+ case "qlogis":
+ return StatsFunctionsFactory.Function3_2NodeGen.create(new Logis.QLogis());
+ case "plogis":
+ return StatsFunctionsFactory.Function3_2NodeGen.create(new Logis.PLogis());
case "rmultinom":
return RMultinomNodeGen.create();
case "Approx":
diff --git a/mx.fastr/copyrights/overrides b/mx.fastr/copyrights/overrides
index 0467373d31..1c597c2f2f 100644
--- a/mx.fastr/copyrights/overrides
+++ b/mx.fastr/copyrights/overrides
@@ -68,7 +68,7 @@ com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/SNorm.java,g
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/SExp.java,gnu_r_ihaka_core.copyright
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RGamma.java,gnu_r_ihaka_core.copyright
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RNbinomMu.java,gnu_r_ihaka_core.copyright
-com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RLogis.java,gnu_r_ihaka_core.copyright
+com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java,gnu_r_ihaka_core.copyright
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Rf.java,gnu_r_ihaka_core.copyright
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RChisq.java,gnu_r_ihaka_core.copyright
com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Exp.java,gnu_r_ihaka_core.copyright
--
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