From 8308f20726241ef099c46de83e655e9a28f7693a Mon Sep 17 00:00:00 2001
From: Michael Haupt <michael.haupt@oracle.com>
Date: Thu, 30 Jan 2014 22:37:31 +0100
Subject: [PATCH] fix bug in cor implementation
---
.../truffle/r/nodes/builtin/base/Cor.java | 2 +-
.../truffle/r/nodes/builtin/base/Cov.java | 2 +-
.../truffle/r/nodes/builtin/base/Covcor.java | 111 +++++++++++++++++-
.../truffle/r/test/ExpectedTestOutput.test | 8 ++
.../oracle/truffle/r/test/all/AllTests.java | 10 +-
.../truffle/r/test/failing/FailingTests.java | 5 -
.../r/test/simple/TestSimpleBuiltins.java | 2 +-
7 files changed, 123 insertions(+), 17 deletions(-)
diff --git a/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cor.java b/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cor.java
index 5fb1932a0c..5c7430e071 100644
--- a/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cor.java
+++ b/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cor.java
@@ -37,6 +37,6 @@ public abstract class Cor extends RBuiltinNode {
@Specialization
@SuppressWarnings("unused")
public RDoubleVector dimWithDimensions(RDoubleVector vector1, RMissing vector2) {
- return Covcor.cor(vector1, vector1, false, this.getEncapsulatingSourceSection());
+ return Covcor.cor(vector1, null, false, this.getEncapsulatingSourceSection());
}
}
diff --git a/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cov.java b/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cov.java
index b765919ea7..c054f2581b 100644
--- a/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cov.java
+++ b/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Cov.java
@@ -37,6 +37,6 @@ public abstract class Cov extends RBuiltinNode {
@Specialization
@SuppressWarnings("unused")
public RDoubleVector dimWithDimensions(RDoubleVector vector1, RMissing vector2) {
- return Covcor.cov(vector1, vector1, false, this.getEncapsulatingSourceSection());
+ return Covcor.cov(vector1, null, false, this.getEncapsulatingSourceSection());
}
}
diff --git a/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Covcor.java b/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Covcor.java
index 73bb82050b..36bf738ef1 100644
--- a/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Covcor.java
+++ b/com.oracle.truffle.r.nodes/src/com/oracle/truffle/r/nodes/builtin/base/Covcor.java
@@ -12,6 +12,7 @@
package com.oracle.truffle.r.nodes.builtin.base;
import com.oracle.truffle.api.*;
+import com.oracle.truffle.api.CompilerDirectives.SlowPath;
import com.oracle.truffle.r.runtime.*;
import com.oracle.truffle.r.runtime.data.*;
import com.oracle.truffle.r.runtime.data.model.*;
@@ -32,7 +33,7 @@ public class Covcor {
return corcov(x, y, iskendall, false, source);
}
- @com.oracle.truffle.api.CompilerDirectives.SlowPath
+ @SlowPath
private static RDoubleVector corcov(RDoubleVector x, RDoubleVector y, boolean iskendall, boolean cor, SourceSection source) {
boolean ansmat;
boolean naFail;
@@ -51,7 +52,9 @@ public class Covcor {
ncx = 1;
}
- if (isMatrix(y)) {
+ if (y == null) {
+ ncy = ncx;
+ } else if (isMatrix(y)) {
if (nrows(y) != n) {
error("incompatible dimensions");
}
@@ -82,8 +85,13 @@ public class Covcor {
double[] ym = new double[ncy];
RIntVector ind = RDataFactory.createIntVector(n);
- complete2(n, ncx, ncy, x, y, ind, naFail);
- sd0 = covComplete2(n, ncx, ncy, x, y, xm, ym, ind, answerData, cor, iskendall);
+ if (y == null) {
+ complete1(n, ncx, x, ind, naFail);
+ sd0 = covComplete1(n, ncx, x, xm, ind, answerData, cor, iskendall);
+ } else {
+ complete2(n, ncx, ncy, x, y, ind, naFail);
+ sd0 = covComplete2(n, ncx, ncy, x, y, xm, ym, ind, answerData, cor, iskendall);
+ }
if (sd0) { /* only in cor() */
RError.warning(source, RError.SD_ZERO);
@@ -108,6 +116,26 @@ public class Covcor {
return x.getDimensions()[0];
}
+ private static void complete1(int n, int ncx, RDoubleVector x, RIntVector ind, boolean naFail) {
+ int i;
+ int j;
+ for (i = 0; i < n; i++) {
+ ind.updateDataAt(i, 1, check);
+ }
+ for (j = 0; j < ncx; j++) {
+ // z = &x[j * n];
+ for (i = 0; i < n; i++) {
+ if (Double.isNaN(x.getDataAt(j * n + i))) {
+ if (naFail) {
+ error("missing observations in cov/cor");
+ } else {
+ ind.updateDataAt(i, 0, check);
+ }
+ }
+ }
+ }
+ }
+
private static void complete2(int n, int ncx, int ncy, RDoubleVector x, RDoubleVector y, RIntVector ind, boolean naFail) {
int i;
int j;
@@ -141,6 +169,81 @@ public class Covcor {
}
}
+ private static boolean covComplete1(int n, int ncx, RDoubleVector x, double[] xm, RIntVector indInput, double[] ans, boolean cor, boolean kendall) {
+ int n1 = -1;
+ int nobs;
+ boolean isSd0 = false;
+
+ /* total number of complete observations */
+ nobs = 0;
+ for (int k = 0; k < n; k++) {
+ if (indInput.getDataAt(k) != 0) {
+ nobs++;
+ }
+ }
+ if (nobs <= 1) { /* too many missing */
+ for (int i = 0; i < ans.length; i++) {
+ ans[i] = RRuntime.DOUBLE_NA;
+ }
+ return isSd0;
+ }
+
+ RIntVector ind = indInput;
+ if (nobs == ind.getLength()) {
+ // No values of ind are zeroed.
+ ind = null;
+ }
+
+ if (!kendall) {
+ mean(x, xm, ind, n, ncx, nobs);
+ n1 = nobs - 1;
+ }
+ for (int i = 0; i < ncx; i++) {
+ if (!kendall) {
+ double xxm = xm[i];
+ for (int j = 0; j <= i; j++) {
+ double yym = xm[j];
+ double sum = 0.0;
+ for (int k = 0; k < n; k++) {
+ if (ind == null || ind.getDataAt(k) != 0) {
+ sum += (x.getDataAt(i * n + k) - xxm) * (x.getDataAt(j * n + k) - yym);
+ }
+ }
+ double r = sum / n1;
+ ans[i + j * ncx] = r;
+ ans[j + i * ncx] = r;
+ }
+ } else { /* Kendall's tau */
+ throw new UnsupportedOperationException("kendall's unsupported");
+ }
+ }
+
+ if (cor) {
+ for (int i = 0; i < ncx; i++) {
+ xm[i] = Math.sqrt(ans[i + i * ncx]);
+ }
+ for (int i = 0; i < ncx; i++) {
+ for (int j = 0; j < i; j++) {
+ if (xm[i] == 0 || xm[j] == 0) {
+ isSd0 = true;
+ ans[i + j * ncx] = RRuntime.DOUBLE_NA;
+ ans[j + i * ncx] = RRuntime.DOUBLE_NA;
+ } else {
+ double sum = ans[i + j * ncx] / (xm[i] * xm[j]);
+ if (sum > 1.0) {
+ sum = 1.0;
+ }
+ ans[i + j * ncx] = sum;
+ ans[j + i * ncx] = sum;
+ }
+ }
+ ans[i + i * ncx] = 1.0;
+ }
+ }
+
+ return isSd0;
+ }
+
private static boolean covComplete2(int n, int ncx, int ncy, RDoubleVector x, RDoubleVector y, double[] xm, double[] ym, RIntVector indInput, double[] ans, boolean cor, boolean kendall) {
int n1 = -1;
int nobs;
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test
index 18c6f6335e..c95e78ca32 100644
--- a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/ExpectedTestOutput.test
@@ -3654,6 +3654,14 @@ a1 a2
#{ cor(c(1,2,3),c(1,2,3)) }
[1] 1
+##com.oracle.truffle.r.test.simple.TestSimpleBuiltins.testCor
+#{ cor(cbind(c(1,1,1), c(1,1,1))) }
+ [,1] [,2]
+[1,] 1 NA
+[2,] NA 1
+Warning message:
+In cor(cbind(c(1, 1, 1), c(1, 1, 1))) : the standard deviation is zero
+
##com.oracle.truffle.r.test.simple.TestSimpleBuiltins.testCor
#{ cor(cbind(c(3,2,1), c(1,2,3))) }
[,1] [,2]
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/all/AllTests.java b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/all/AllTests.java
index b761810493..b290d2b34a 100644
--- a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/all/AllTests.java
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/all/AllTests.java
@@ -5548,6 +5548,11 @@ public class AllTests extends TestBase {
assertEval("{ cor(cbind(c(3,2,1), c(1,2,3))) }");
}
+ @Test
+ public void TestSimpleBuiltins_testCor_a9306c39144eb95725c311083b3248ba() {
+ assertEval("{ cor(cbind(c(1,1,1), c(1,1,1))) }");
+ }
+
@Test
public void TestSimpleBuiltins_testCorIgnore_564c5ee2d2eea4a4b168dca5e6fa9e4f() {
assertEval("{ cor(cbind(c(1:9,0/0), 101:110)) }");
@@ -5558,11 +5563,6 @@ public class AllTests extends TestBase {
assertEval("{ round( cor(cbind(c(10,5,4,1), c(2,5,10,5))), digits=5 ) }");
}
- @Test
- public void TestSimpleBuiltins_testCorIgnore_a9306c39144eb95725c311083b3248ba() {
- assertEval("{ cor(cbind(c(1,1,1), c(1,1,1))) }");
- }
-
@Test
public void TestSimpleBuiltins_testCov_4b96d1c7c503defdec6ebab5b659625c() {
assertEval("{ cov(c(1,2,3),c(1,2,3)) }");
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/failing/FailingTests.java b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/failing/FailingTests.java
index db64573384..4946aa2d34 100644
--- a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/failing/FailingTests.java
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/failing/FailingTests.java
@@ -1798,11 +1798,6 @@ public class FailingTests extends TestBase {
assertEval("{ round( cor(cbind(c(10,5,4,1), c(2,5,10,5))), digits=5 ) }");
}
- @Ignore
- public void TestSimpleBuiltins_testCorIgnore_a9306c39144eb95725c311083b3248ba() {
- assertEval("{ cor(cbind(c(1,1,1), c(1,1,1))) }");
- }
-
@Ignore
public void TestSimpleBuiltins_testCrossprod_7f9549017d66ad3dd1583536fa7183d7() {
assertEval("{ x <- 1:6 ; crossprod(x) }");
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/simple/TestSimpleBuiltins.java b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/simple/TestSimpleBuiltins.java
index b49278cdf2..80a1d34b20 100644
--- a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/simple/TestSimpleBuiltins.java
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/simple/TestSimpleBuiltins.java
@@ -1777,6 +1777,7 @@ public class TestSimpleBuiltins extends TestBase {
assertEval("{ cor(c(1,2,3),c(1,2,3)) }");
assertEval("{ as.integer(cor(c(1,2,3),c(1,2,5))*10000000) }");
assertEval("{ cor(cbind(c(3,2,1), c(1,2,3))) }");
+ assertEval("{ cor(cbind(c(1, 1, 1), c(1, 1, 1))) }");
}
@Test
@@ -1784,7 +1785,6 @@ public class TestSimpleBuiltins extends TestBase {
public void testCorIgnore() {
assertEval("{ cor(cbind(c(1:9,0/0), 101:110)) }");
assertEval("{ round( cor(cbind(c(10,5,4,1), c(2,5,10,5))), digits=5 ) }");
- assertEval("{ cor(cbind(c(1,1,1), c(1,1,1))) }");
}
@Test
--
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