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Posted to commits@commons.apache.org by ps...@apache.org on 2015/11/22 20:19:09 UTC
[1/2] [math] Added bootstrap method to KolmogorovSmirnovTest. JIRA:
MATH-1246.
Repository: commons-math
Updated Branches:
refs/heads/master d51092164 -> 23b351c89
Added bootstrap method to KolmogorovSmirnovTest. JIRA: MATH-1246.
Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/7851a3e2
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/7851a3e2
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/7851a3e2
Branch: refs/heads/master
Commit: 7851a3e2bf24c58eea66da70fa42a32f03532620
Parents: d510921
Author: Phil Steitz <ph...@gmail.com>
Authored: Sun Nov 22 12:17:48 2015 -0700
Committer: Phil Steitz <ph...@gmail.com>
Committed: Sun Nov 22 12:17:48 2015 -0700
----------------------------------------------------------------------
src/changes/changes.xml | 3 +
.../stat/inference/KolmogorovSmirnovTest.java | 60 ++++++++++++++++++++
src/test/R/KolmogorovSmirnovTestCases.R | 48 ++++++++++++----
.../inference/KolmogorovSmirnovTestTest.java | 35 ++++++++++++
4 files changed, 134 insertions(+), 12 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/commons-math/blob/7851a3e2/src/changes/changes.xml
----------------------------------------------------------------------
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 1e4ab6a..74341f0 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -54,6 +54,9 @@ If the output is not quite correct, check for invisible trailing spaces!
</release>
<release version="4.0" date="XXXX-XX-XX" description="">
+ <action dev="psteitz" type="update" issue="MATH-1246">
+ Added bootstrap method to 2-sample KolmogorovSmirnovTest.
+ </action>
<action dev="psteitz" type="update" issue="MATH-1287"> <!-- backported to 3.6 -->
Added constructors taking sample data as arguments to enumerated real and integer distributions.
</action>
http://git-wip-us.apache.org/repos/asf/commons-math/blob/7851a3e2/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java b/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java
index 9c8bcb9..a262a28 100644
--- a/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java
+++ b/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java
@@ -22,6 +22,7 @@ import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
+import org.apache.commons.math4.distribution.EnumeratedRealDistribution;
import org.apache.commons.math4.distribution.RealDistribution;
import org.apache.commons.math4.exception.InsufficientDataException;
import org.apache.commons.math4.exception.MathArithmeticException;
@@ -377,6 +378,65 @@ public class KolmogorovSmirnovTest {
}
/**
+ * Estimates the <i>p-value</i> of a two-sample
+ * <a href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test"> Kolmogorov-Smirnov test</a>
+ * evaluating the null hypothesis that {@code x} and {@code y} are samples drawn from the same
+ * probability distribution. This method estimates the p-value by repeatedly sampling sets of size
+ * {@code x.length} and {@code y.length} from the empirical distribution of the combined sample.
+ * When {@code strict} is true, this is equivalent to the algorithm implemented in the R function
+ * ks.boot, described in <pre>
+ * Jasjeet S. Sekhon. 2011. `Multivariate and Propensity Score Matching
+ * Software with Automated Balance Optimization: The Matching package for R.`
+ * Journal of Statistical Software, 42(7): 1-52.
+ * </pre>
+ * @param x first sample
+ * @param y second sample
+ * @param iterations number of bootstrap resampling iterations
+ * @param strict whether or not the null hypothesis is expressed as a strict inequality
+ * @return estimated p-value
+ */
+ public double bootstrap(double[] x, double[] y, int iterations, boolean strict) {
+ final int xLength = x.length;
+ final int yLength = y.length;
+ final double[] combined = new double[xLength + yLength];
+ System.arraycopy(x, 0, combined, 0, xLength);
+ System.arraycopy(y, 0, combined, xLength, yLength);
+ final EnumeratedRealDistribution dist = new EnumeratedRealDistribution(combined);
+ final long d = integralKolmogorovSmirnovStatistic(x, y);
+ int greaterCount = 0;
+ int equalCount = 0;
+ double[] curX;
+ double[] curY;
+ long curD;
+ for (int i = 0; i < iterations; i++) {
+ curX = dist.sample(xLength);
+ curY = dist.sample(yLength);
+ curD = integralKolmogorovSmirnovStatistic(curX, curY);
+ if (curD > d) {
+ greaterCount++;
+ } else if (curD == d) {
+ equalCount++;
+ }
+ }
+ return strict ? greaterCount / (double) iterations :
+ (greaterCount + equalCount) / (double) iterations;
+ }
+
+ /**
+ * Computes {@code bootstrap(x, y, iterations, true)}.
+ * This is equivalent to ks.boot(x,y, nboots=iterations) using the R Matching
+ * package function. See #bootstrap(double[], double[], int, boolean).
+ *
+ * @param x first sample
+ * @param y second sample
+ * @param iterations number of bootstrap resampling iterations
+ * @return estimated p-value
+ */
+ public double bootstrap(double[] x, double[] y, int iterations) {
+ return bootstrap(x, y, iterations, true);
+ }
+
+ /**
* Calculates \(P(D_n < d)\) using the method described in [1] with quick decisions for extreme
* values given in [2] (see above). The result is not exact as with
* {@link #cdfExact(double, int)} because calculations are based on
http://git-wip-us.apache.org/repos/asf/commons-math/blob/7851a3e2/src/test/R/KolmogorovSmirnovTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/KolmogorovSmirnovTestCases.R b/src/test/R/KolmogorovSmirnovTestCases.R
index f66b253..342b6f0 100644
--- a/src/test/R/KolmogorovSmirnovTestCases.R
+++ b/src/test/R/KolmogorovSmirnovTestCases.R
@@ -21,12 +21,20 @@
# into the same directory, launch R from this directory and then enter
# source("<name-of-this-file>")
#
+# NOTE: the 2-sample bootstrap test requires the "Matching" library
+## https://cran.r-project.org/web/packages/Matching/index.html
+## See http://sekhon.berkeley.edu/matching for additional documentation.
+## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
+## Software with Automated Balance Optimization: The Matching package for R.''
+## Journal of Statistical Software, 42(7): 1-52.
+#
#------------------------------------------------------------------------------
tol <- 1E-14 # error tolerance for tests
#------------------------------------------------------------------------------
# Function definitions
source("testFunctions") # utility test functions
+require("Matching") # for ks.boot
verifyOneSampleGaussian <- function(data, expectedP, expectedD, mean, sigma, exact, tol, desc) {
results <- ks.test(data, "pnorm", mean, sigma, exact = exact)
@@ -34,12 +42,12 @@ verifyOneSampleGaussian <- function(data, expectedP, expectedD, mean, sigma, exa
displayPadded(c(desc," p-value test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
- }
+ }
if (assertEquals(expectedD, results$statistic, tol, "D statistic value")) {
displayPadded(c(desc," D statistic test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " D statistic test"), FAILED, WIDTH)
- }
+ }
}
verifyOneSampleUniform <- function(data, expectedP, expectedD, min, max, exact, tol, desc) {
@@ -48,12 +56,12 @@ verifyOneSampleUniform <- function(data, expectedP, expectedD, min, max, exact,
displayPadded(c(desc," p-value test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
- }
+ }
if (assertEquals(expectedD, results$statistic, tol, "D statistic value")) {
displayPadded(c(desc," D statistic test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " D statistic test"), FAILED, WIDTH)
- }
+ }
}
verifyTwoSampleLargeSamples <- function(sample1, sample2, expectedP, expectedD, tol, desc) {
@@ -62,12 +70,12 @@ verifyTwoSampleLargeSamples <- function(sample1, sample2, expectedP, expectedD,
displayPadded(c(desc," p-value test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
- }
+ }
if (assertEquals(expectedD, results$statistic, tol, "D statistic value")) {
displayPadded(c(desc," D statistic test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " D statistic test"), FAILED, WIDTH)
- }
+ }
}
verifyTwoSampleSmallSamplesExact <- function(sample1, sample2, expectedP, expectedD, tol, desc) {
@@ -76,14 +84,22 @@ verifyTwoSampleSmallSamplesExact <- function(sample1, sample2, expectedP, expect
displayPadded(c(desc," p-value test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
- }
+ }
if (assertEquals(expectedD, results$statistic, tol, "D statistic value")) {
displayPadded(c(desc," D statistic test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " D statistic test"), FAILED, WIDTH)
- }
+ }
}
+verifyTwoSampleBootstrap <- function(sample1, sample2, expectedP, tol, desc) {
+ results <- ks.boot(sample1, sample2,nboots=10000 )
+ if (assertEquals(expectedP, results$ks.boot.pvalue, tol, "p-value")) {
+ displayPadded(c(desc, " p-value test"), SUCCEEDED, WIDTH)
+ } else {
+ displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
+ }
+}
cat("KolmogorovSmirnovTest test cases\n")
@@ -100,7 +116,7 @@ gaussian <- c(0.26055895, -0.63665233, 1.51221323, 0.61246988, -0.03013003, -1.7
0.25165971, -0.04125231, -0.23756244, -0.93389975, 0.75551407, 0.08347445, -0.27482228, -0.4717632,
-0.1867746, -0.1166976, 0.5763333, 0.1307952, 0.7630584, -0.3616248, 2.1383790,-0.7946630,
0.0231885, 0.7919195, 1.6057144, -0.3802508, 0.1229078, 1.5252901, -0.8543149, 0.3025040)
-
+
shortGaussian <- gaussian[1:50]
gaussian2 <- c(2.88041498038308, -0.632349445671017, 0.402121295225571, 0.692626364613243, 1.30693446815426,
@@ -137,10 +153,14 @@ uniform <- c(0.7930305, 0.6424382, 0.8747699, 0.7156518, 0.1845909, 0.2022326,
0.85201008, 0.02945562, 0.26200374, 0.11382818, 0.17238856, 0.36449473, 0.69688273, 0.96216330,
0.4859432,0.4503438, 0.1917656, 0.8357845, 0.9957812, 0.4633570, 0.8654599, 0.4597996,
0.68190289, 0.58887855, 0.09359396, 0.98081979, 0.73659533, 0.89344777, 0.18903099, 0.97660425)
-
+
smallSample1 <- c(6, 7, 9, 13, 19, 21, 22, 23, 24)
smallSample2 <- c(10, 11, 12, 16, 20, 27, 28, 32, 44, 54)
-
+bootSample1 <- c(0, 2, 4, 6, 8, 8, 10, 15, 22, 30, 33, 36, 38)
+bootSample2 <- c(9, 17, 20, 33, 40, 51, 60, 60, 72, 90, 101)
+roundingSample1 <- c(2,4,6,8,9,10,11,12,13)
+roundingSample2 <- c(0,1,3,5,7)
+
shortUniform <- uniform[1:20]
verifyOneSampleGaussian(gaussian, 0.3172069207622391, 0.0932947561266756, 0, 1,
@@ -167,6 +187,10 @@ verifyTwoSampleLargeSamples(gaussian, gaussian2, 0.0319983962391632, 0.202352941
verifyTwoSampleSmallSamplesExact(smallSample1, smallSample2, 0.105577085453247, .5, tol,
"Two sample small samples exact")
+verifyTwoSampleBootstrap(bootSample1, bootSample2, 0.0059, 1E-3, "Two sample bootstrap - isolated failures possible")
+verifyTwoSampleBootstrap(gaussian, gaussian2, 0.0237, 1E-2, "Two sample bootstrap - isolated failures possible")
+verifyTwoSampleBootstrap(roundingSample1, roundingSample2, 0.06303, 1E-2, "Two sample bootstrap - isolated failures possible")
+
displayDashes(WIDTH)
-
+
http://git-wip-us.apache.org/repos/asf/commons-math/blob/7851a3e2/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java b/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java
index 28db893..bd1b1cb 100644
--- a/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java
+++ b/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java
@@ -533,6 +533,41 @@ public class KolmogorovSmirnovTestTest {
}
/**
+ * Test an example with ties in the data. Reference data is R 3.2.0,
+ * ks.boot implemented in Matching (Version 4.8-3.4, Build Date: 2013/10/28)
+ */
+ @Test
+ public void testBootstrapSmallSamplesWithTies() {
+ final double[] x = {0, 2, 4, 6, 8, 8, 10, 15, 22, 30, 33, 36, 38};
+ final double[] y = {9, 17, 20, 33, 40, 51, 60, 60, 72, 90, 101};
+ final KolmogorovSmirnovTest test = new KolmogorovSmirnovTest(new Well19937c(2000));
+ Assert.assertEquals(0.0059, test.bootstrap(x, y, 10000, false), 1E-3);
+ }
+
+ /**
+ * Reference data is R 3.2.0, ks.boot implemented in
+ * Matching (Version 4.8-3.4, Build Date: 2013/10/28)
+ */
+ @Test
+ public void testBootstrapLargeSamples() {
+ final KolmogorovSmirnovTest test = new KolmogorovSmirnovTest(new Well19937c(1000));
+ Assert.assertEquals(0.0237, test.bootstrap(gaussian, gaussian2, 10000), 1E-2);
+ }
+
+ /**
+ * Test an example where D-values are close (subject to rounding).
+ * Reference data is R 3.2.0, ks.boot implemented in
+ * Matching (Version 4.8-3.4, Build Date: 2013/10/28)
+ */
+ @Test
+ public void testBootstrapRounding() {
+ final double[] x = {2,4,6,8,9,10,11,12,13};
+ final double[] y = {0,1,3,5,7};
+ final KolmogorovSmirnovTest test = new KolmogorovSmirnovTest(new Well19937c(1000));
+ Assert.assertEquals(0.06303, test.bootstrap(x, y, 10000, false), 1E-2);
+ }
+
+ /**
* Verifies the inequality exactP(criticalValue, n, m, true) < alpha < exactP(criticalValue, n,
* m, false).
*
[2/2] [math] Removed trailing spaces.
Posted by ps...@apache.org.
Removed trailing spaces.
Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/23b351c8
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/23b351c8
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/23b351c8
Branch: refs/heads/master
Commit: 23b351c89461009a3f772c07edd47a9a2a0b9e7b
Parents: 7851a3e
Author: Phil Steitz <ph...@gmail.com>
Authored: Sun Nov 22 12:18:46 2015 -0700
Committer: Phil Steitz <ph...@gmail.com>
Committed: Sun Nov 22 12:18:46 2015 -0700
----------------------------------------------------------------------
src/test/R/ChiSquareDistributionTestCases.R | 8 +--
src/test/R/FDistributionTestCases.R | 8 +--
src/test/R/GammaDistributionTestCases.R | 8 +--
.../R/KolmogorovSmirnovDistributionTestCases.R | 6 +-
src/test/R/LevyDistributionTestCases.R | 4 +-
src/test/R/README.txt | 72 ++++++++++----------
src/test/R/TDistributionTestCases.R | 8 +--
src/test/R/TTestCases | 20 +++---
src/test/R/WeibullDistributionTestCases.R | 8 +--
src/test/R/anovaTestCases | 8 +--
src/test/R/binomialTestCases | 8 +--
src/test/R/cauchyTestCases.R | 6 +-
src/test/R/chiSquareTestCases | 20 +++---
src/test/R/correlationTestCases | 16 ++---
src/test/R/covarianceTestCases | 16 ++---
src/test/R/descriptiveTestCases | 6 +-
src/test/R/exponentialTestCases | 8 +--
src/test/R/geometricTestCases | 10 +--
src/test/R/hypergeometricTestCases | 12 ++--
src/test/R/multipleOLSRegressionTestCases | 32 ++++-----
src/test/R/normalTestCases | 8 +--
src/test/R/pascalTestCases | 6 +-
src/test/R/poissonTestCases | 12 ++--
src/test/R/regressionTestCases | 24 +++----
src/test/R/testAll | 2 +-
src/test/R/testFunctions | 6 +-
src/test/R/zipfTestCases | 6 +-
27 files changed, 174 insertions(+), 174 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/ChiSquareDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/ChiSquareDistributionTestCases.R b/src/test/R/ChiSquareDistributionTestCases.R
index 78929ef..3df58ba 100644
--- a/src/test/R/ChiSquareDistributionTestCases.R
+++ b/src/test/R/ChiSquareDistributionTestCases.R
@@ -40,7 +40,7 @@ verifyDistribution <- function(points, expected, df, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -56,7 +56,7 @@ verifyDensity <- function(points, expected, df, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -72,7 +72,7 @@ verifyQuantiles <- function(points, expected, df, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -83,7 +83,7 @@ distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.95
densityValues <- c(0.0115379817652, 0.0415948507811, 0.0665060119842, 0.0919455953114, 0.121472591024,
0.000433630076361, 0.00412780610309, 0.00999340341045, 0.0193246438937, 0.0368460089216)
distributionPoints <- c(0.210212602629, 0.554298076728, 0.831211613487, 1.14547622606, 1.61030798696,
- 20.5150056524, 15.0862724694, 12.8325019940, 11.0704976935, 9.23635689978)
+ 20.5150056524, 15.0862724694, 12.8325019940, 11.0704976935, 9.23635689978)
verifyQuantiles(distributionValues, distributionPoints, df, tol)
verifyDistribution(distributionPoints, distributionValues, df, tol)
verifyDensity(distributionPoints, densityValues, df, tol)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/FDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/FDistributionTestCases.R b/src/test/R/FDistributionTestCases.R
index e5f3656..ee7c199 100644
--- a/src/test/R/FDistributionTestCases.R
+++ b/src/test/R/FDistributionTestCases.R
@@ -40,7 +40,7 @@ verifyDistribution <- function(points, expected, numeratorDf, denominatorDf, tol
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -56,7 +56,7 @@ verifyDensity <- function(points, expected, numeratorDf, denominatorDf, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -72,7 +72,7 @@ verifyQuantiles <- function(points, expected, numeratorDf, denominatorDf, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -84,7 +84,7 @@ distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.95
densityValues <- c(0.0689156576706, 0.236735653193, 0.364074131941, 0.481570789649, 0.595880479994,
0.000133443915657, 0.00286681303403, 0.00969192007502, 0.0242883861471, 0.0605491314658)
distributionPoints <- c(0.0346808448626, 0.0937009113303, 0.143313661184, 0.202008445998, 0.293728320107,
- 20.8026639595, 8.74589525602, 5.98756512605, 4.38737418741, 3.10751166664)
+ 20.8026639595, 8.74589525602, 5.98756512605, 4.38737418741, 3.10751166664)
verifyQuantiles(distributionValues, distributionPoints, numeratorDf, denominatorDf, tol)
verifyDistribution(distributionPoints, distributionValues, numeratorDf, denominatorDf, tol)
verifyDensity(distributionPoints, densityValues, numeratorDf, denominatorDf, tol)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/GammaDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/GammaDistributionTestCases.R b/src/test/R/GammaDistributionTestCases.R
index 7cbefda..2ed7c95 100644
--- a/src/test/R/GammaDistributionTestCases.R
+++ b/src/test/R/GammaDistributionTestCases.R
@@ -40,7 +40,7 @@ verifyDistribution <- function(points, expected, alpha, beta, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -56,7 +56,7 @@ verifyDensity <- function(points, expected, alpha, beta, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -72,7 +72,7 @@ verifyQuantiles <- function(points, expected, alpha, beta, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -84,7 +84,7 @@ distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.95
densityValues <- c(0.00427280075546, 0.0204117166709, 0.0362756163658, 0.0542113174239, 0.0773195272491,
0.000394468852816, 0.00366559696761, 0.00874649473311, 0.0166712508128, 0.0311798227954)
distributionPoints <- c(0.857104827257, 1.64649737269, 2.17973074725, 2.7326367935, 3.48953912565,
- 26.1244815584, 20.0902350297, 17.5345461395, 15.5073130559, 13.3615661365)
+ 26.1244815584, 20.0902350297, 17.5345461395, 15.5073130559, 13.3615661365)
verifyQuantiles(distributionValues, distributionPoints, shape, scale, tol)
verifyDistribution(distributionPoints, distributionValues, shape, scale, tol)
verifyDensity(distributionPoints, densityValues, shape, scale, tol)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/KolmogorovSmirnovDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/KolmogorovSmirnovDistributionTestCases.R b/src/test/R/KolmogorovSmirnovDistributionTestCases.R
index d458dcc..19f74b7 100644
--- a/src/test/R/KolmogorovSmirnovDistributionTestCases.R
+++ b/src/test/R/KolmogorovSmirnovDistributionTestCases.R
@@ -21,16 +21,16 @@ ps <- c(0.005, 0.02, 0.031111, 0.04)
for (n in ns) {
for (p in ps) {
res <- .C("pkolmogorov2x", p = as.double(p), n = as.integer(n), PACKAGE = "stats")$p
-
+
cat("/* formatC(.C(\"pkolmogorov2x\", p = as.double(", p, "), n = as.integer(", n, "), PACKAGE = \"stats\")$p, 40) gives\n", sep = "")
cat(" * ", formatC(res, digits = 40), "\n", sep = "")
cat(" */\n")
-
+
cat("dist = new KolmogorovSmirnovDistributionImpl(", n, ");\n", sep = "")
#cat("Assert.assertEquals(", formatC(res, digits = 40), ", dist.cdf(", p, ", true), TOLERANCE);\n", sep = "")
cat("Assert.assertEquals(", formatC(res, digits = 40), ", dist.cdf(", p, ", false), TOLERANCE);\n", sep = "")
cat("\n")
-
+
#cat("System.out.println(\"", formatC(res, digits = 20), " - \" + dist.cdf(", p, ", false) + \" = \" + (", res, " - dist.cdf(", p, ", false)));\n", sep = "")
}
}
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/LevyDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/LevyDistributionTestCases.R b/src/test/R/LevyDistributionTestCases.R
index 9e9238e..ed7c367 100644
--- a/src/test/R/LevyDistributionTestCases.R
+++ b/src/test/R/LevyDistributionTestCases.R
@@ -47,7 +47,7 @@ verifyDistribution <- function(points, expected, m, s, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -64,7 +64,7 @@ verifyDensity <- function(points, expected, m, s, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/README.txt
----------------------------------------------------------------------
diff --git a/src/test/R/README.txt b/src/test/R/README.txt
index c6549bc..eb83ecc 100644
--- a/src/test/R/README.txt
+++ b/src/test/R/README.txt
@@ -17,34 +17,34 @@
INTRODUCTION
-The purpose of the R programs included in this directory is to validate
-the target values used in Apache commons math unit tests. Success running the
-R and commons-math tests on a platform (OS and R version) means that R and
-commons-math give results for the test cases that are close in value. The
-tests include configurable tolerance levels; but care must be taken in changing
-these, since in most cases the pre-set tolerance is close to the number of
-decimal digits used in expressing the expected values (both here and in the
+The purpose of the R programs included in this directory is to validate
+the target values used in Apache commons math unit tests. Success running the
+R and commons-math tests on a platform (OS and R version) means that R and
+commons-math give results for the test cases that are close in value. The
+tests include configurable tolerance levels; but care must be taken in changing
+these, since in most cases the pre-set tolerance is close to the number of
+decimal digits used in expressing the expected values (both here and in the
corresponding commons-math unit tests).
-Of course it is always possible that both R and commons-math give incorrect
-values for test cases, so these tests should not be interpreted as definitive
-in any absolute sense. The value of developing and running the tests is really
-to generate questions (and answers!) when the two systems give different
+Of course it is always possible that both R and commons-math give incorrect
+values for test cases, so these tests should not be interpreted as definitive
+in any absolute sense. The value of developing and running the tests is really
+to generate questions (and answers!) when the two systems give different
results.
-Contributions of additional test cases (both R and Junit code) or just
-R programs to validate commons-math tests that are not covered here would be
+Contributions of additional test cases (both R and Junit code) or just
+R programs to validate commons-math tests that are not covered here would be
greatly appreciated.
SETUP
0) Download and install R. You can get R here
http://www.r-project.org/
-Follow the install instructions and make sure that you can launch R from this
-(i.e., either explitly add R to your OS path or let the install package do it
-for you).
+Follow the install instructions and make sure that you can launch R from this
+(i.e., either explitly add R to your OS path or let the install package do it
+for you).
-1) Launch R from this directory and type
+1) Launch R from this directory and type
> source("testAll")
to an R prompt. This should produce output to the console similar to this:
@@ -69,26 +69,26 @@ Distribution test mu = 0, sigma = 0.1..................................SUCCEEDED
WORKING WITH THE TESTS
-The R distribution comes with online manuals that you can view by launching
+The R distribution comes with online manuals that you can view by launching
a browser instance and then entering
> help.start()
-at an R prompt. Poking about in the test case files and the online docs should
-bring you up to speed fairly quickly. Here are some basic things to get
-you started. I should note at this point that I am by no means an expert R
-programmer, so some things may not be implemented in the the nicest way.
+at an R prompt. Poking about in the test case files and the online docs should
+bring you up to speed fairly quickly. Here are some basic things to get
+you started. I should note at this point that I am by no means an expert R
+programmer, so some things may not be implemented in the the nicest way.
Comments / suggestions for improvement are welcome!
All of the test cases use some basic functions and global constants (screen
-width and success / failure strings) defined in "testFunctions." The
-R "source" function is used to "import" these functions into each of the test
-programs. The "testAll" program pulls together and executes all of the
+width and success / failure strings) defined in "testFunctions." The
+R "source" function is used to "import" these functions into each of the test
+programs. The "testAll" program pulls together and executes all of the
individual test programs. You can execute any one of them by just entering
> source(<program-name>).
-The "assertEquals" function in the testFunctions file mimics the similarly
+The "assertEquals" function in the testFunctions file mimics the similarly
named function used by Junit:
assertEquals <- function(expected, observed, tol, message) {
@@ -102,11 +102,11 @@ assertEquals <- function(expected, observed, tol, message) {
}
}
-The <expected> and <observed> arguments can be scalar values, vectors or
+The <expected> and <observed> arguments can be scalar values, vectors or
matrices. If the arguments are vectors or matrices, corresponding entries
are compared.
-The standard pattern used throughout the tests looks like this (from
+The standard pattern used throughout the tests looks like this (from
binomialTestCases):
Start by defining a "verification function" -- in this example a function to
@@ -129,11 +129,11 @@ verifyDensity <- function(points, expected, n, p, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
The displayPadded function just displays its first and second arguments with
-enough dots in between to make the whole string WIDTH characters long. It is
+enough dots in between to make the whole string WIDTH characters long. It is
defined in testFunctions.
Then call this function with different parameters corresponding to the different
@@ -143,7 +143,7 @@ size <- 10.0
probability <- 0.70
densityPoints <- c(-1,0,1,2,3,4,5,6,7,8,9,10,11)
-densityValues <- c(0, 0.0000, 0.0001, 0.0014, 0.0090, 0.0368, 0.1029,
+densityValues <- c(0, 0.0000, 0.0001, 0.0014, 0.0090, 0.0368, 0.1029,
0.2001, 0.2668, 0.2335, 0.1211, 0.0282, 0)
...
verifyDensity(densityPoints, densityValues, size, probability, tol)
@@ -153,16 +153,16 @@ produce one line of output to the console:
Density test n = 10, p = 0.7...........................................SUCCEEDED
-If you modify the value of tol set at the top of binomialTestCases to make the
-test more sensitive than the number of digits specified in the densityValues
+If you modify the value of tol set at the top of binomialTestCases to make the
+test more sensitive than the number of digits specified in the densityValues
vector, it will fail, producing the following output, showing the failure and
the expected and observed values:
-FAILURE: Density Values
+FAILURE: Density Values
EXPECTED: 0 0 1e-04 0.0014 0.009 0.0368 0.1029 0.2001 0.2668 0.2335 0.1211 /
- 0.0282 0
+ 0.0282 0
OBSERVED: 0 5.9049e-06 0.000137781 0.0014467005 0.009001692 0.036756909 /
-0.1029193452 0.200120949 0.266827932 0.2334744405 0.121060821 0.0282475249 0
+0.1029193452 0.200120949 0.266827932 0.2334744405 0.121060821 0.0282475249 0
Density test n = 10, p = 0.7..............................................FAILED
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/TDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/TDistributionTestCases.R b/src/test/R/TDistributionTestCases.R
index 723e958..6f91269 100644
--- a/src/test/R/TDistributionTestCases.R
+++ b/src/test/R/TDistributionTestCases.R
@@ -40,7 +40,7 @@ verifyDistribution <- function(points, expected, df, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -56,7 +56,7 @@ verifyDensity <- function(points, expected, df, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -72,7 +72,7 @@ verifyQuantiles <- function(points, expected, df, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -83,7 +83,7 @@ distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.95
densityValues <- c(0.000756494565517, 0.0109109752919, 0.0303377878006, 0.0637967988952, 0.128289492005,
0.000756494565517, 0.0109109752919, 0.0303377878006, 0.0637967988952, 0.128289492005)
distributionPoints <- c(-5.89342953136, -3.36492999891, -2.57058183564, -2.01504837333, -1.47588404882,
- 5.89342953136, 3.36492999891, 2.57058183564, 2.01504837333, 1.47588404882)
+ 5.89342953136, 3.36492999891, 2.57058183564, 2.01504837333, 1.47588404882)
verifyQuantiles(distributionValues, distributionPoints, df, tol)
verifyDistribution(distributionPoints, distributionValues, df, tol)
verifyDensity(distributionPoints, densityValues, df, tol)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/TTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/TTestCases b/src/test/R/TTestCases
index 6aa5e2d..38adf7b 100644
--- a/src/test/R/TTestCases
+++ b/src/test/R/TTestCases
@@ -27,14 +27,14 @@
# Arguments
# x a numeric vector of data values.
# y an optional numeric vector data values.
-# alternative a character string specifying the alternative hypothesis,
+# alternative a character string specifying the alternative hypothesis,
# must be one of "two.sided" (default), "greater" or "less". You can specify
# just the initial letter.
# mu a number indicating the true value of the mean (or difference in means
# if you are performing a two sample test).
# paired a logical indicating whether you want a paired t-test.
# var.equal a logical variable indicating whether to treat the two
-# variances as being equal.
+# variances as being equal.
# If TRUE then the pooled variance is used to estimate the variance,
# otherwise the Welch (or Satterthwaite) approximation to the degrees
# of freedom is used.
@@ -54,14 +54,14 @@ verifyTest <- function(out,expectedP, expectedT,
displayPadded(output, SUCCEEDED, 80)
} else {
displayPadded(output, FAILED, 80)
- }
- output <- c("t test test statistic")
+ }
+ output <- c("t test test statistic")
if (assertEquals(expectedT, out$statistic, tol,
"Ttest t statistic")) {
displayPadded(output, SUCCEEDED, 80)
} else {
displayPadded(output, FAILED, 80)
- }
+ }
displayDashes(WIDTH)
}
@@ -71,14 +71,14 @@ sample1 <- c(93.0, 103.0, 95.0, 101.0, 91.0, 105.0, 96.0, 94.0, 101.0, 88.0,
out <- t.test(sample1, mu=100.0)
expectedP <- 0.0136390585873
expectedT<- -2.81976445346
-verifyTest(out,expectedP, expectedT, tol)
+verifyTest(out,expectedP, expectedT, tol)
cat("One-sample, one-sided TTest test cases \n")
sample1 <- c(2, 0, 6, 6, 3, 3, 2, 3, -6, 6, 6, 6, 3, 0, 1, 1, 0, 2, 3, 3)
out <- t.test(sample1, mu=0.0, alternative="g")
expectedP <- 0.000521637019637
expectedT<- 3.86485535541
-verifyTest(out,expectedP, expectedT, tol)
+verifyTest(out,expectedP, expectedT, tol)
cat("Homoscedastic TTest test cases \n")
sample1 <- c(2, 4, 6, 8, 10, 97)
@@ -87,10 +87,10 @@ out <- t.test(sample1,sample2,var.equal = TRUE)
expectedP <- 0.4833963785
expectedT<- 0.73096310086
verifyTest(out,expectedP, expectedT, tol)
-
+
cat("Heteroscedastic TTest test cases \n")
sample1 <- c(7, -4, 18, 17, -3, -5, 1, 10, 11, -2)
-sample2 <- c(-1, 12, -1, -3, 3, -5, 5, 2, -11, -1, -3)
+sample2 <- c(-1, 12, -1, -3, 3, -5, 5, 2, -11, -1, -3)
out <- t.test(sample1,sample2,var.equal = FALSE)
expectedP <- 0.128839369622
expectedT<- 1.60371728768
@@ -103,4 +103,4 @@ out <- t.test(sample1,sample2,var.equal = FALSE)
expectedP <- 0.198727388935
expectedT<- -2.2360679775
verifyTest(out,expectedP, expectedT, tol)
-
+
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/WeibullDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/WeibullDistributionTestCases.R b/src/test/R/WeibullDistributionTestCases.R
index fadc625..7228641 100644
--- a/src/test/R/WeibullDistributionTestCases.R
+++ b/src/test/R/WeibullDistributionTestCases.R
@@ -40,7 +40,7 @@ verifyDistribution <- function(points, expected, alpha, beta, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -56,7 +56,7 @@ verifyDensity <- function(points, expected, alpha, beta, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -72,7 +72,7 @@ verifyQuantiles <- function(points, expected, alpha, beta, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -84,7 +84,7 @@ distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.95
densityValues <- c(0.180535929306, 0.262801138133, 0.301905425199, 0.330899152971, 0.353441418887, 0.000788590320203,
0.00737060094841, 0.0177576041516, 0.0343043442574, 0.065664589369)
distributionPoints <- c(0.00664355180993, 0.0454328283309, 0.0981162737374, 0.176713524579, 0.321946865392,
- 10.5115496887, 7.4976304671, 6.23205600701, 5.23968436955, 4.20790282578)
+ 10.5115496887, 7.4976304671, 6.23205600701, 5.23968436955, 4.20790282578)
verifyQuantiles(distributionValues, distributionPoints, shape, scale, tol)
verifyDistribution(distributionPoints, distributionValues, shape, scale, tol)
verifyDensity(distributionPoints, densityValues, shape, scale, tol)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/anovaTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/anovaTestCases b/src/test/R/anovaTestCases
index 077ba09..1c1dd7c 100644
--- a/src/test/R/anovaTestCases
+++ b/src/test/R/anovaTestCases
@@ -43,13 +43,13 @@ verifyAnova <- function(frame, expectedP, expectedF, frameName) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
output <- c("F-value test frame = ", frameName)
if (assertEquals(expectedF,f,tol,"F value")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -63,10 +63,10 @@ class=c(rep("classA", length(classA)),
rep("classB", length(classB)),
rep("classC", length(classC))))
-verifyAnova(threeClasses,6.959446e-06, 24.67361709460624, "Three classes")
+verifyAnova(threeClasses,6.959446e-06, 24.67361709460624, "Three classes")
twoClasses = data.frame(val = c(classA, classB),
class=c(rep("classA", length(classA)), rep("classB", length(classB))))
verifyAnova(twoClasses, 0.904212960464, 0.0150579150579, "Two classes")
-displayDashes(WIDTH)
\ No newline at end of file
+displayDashes(WIDTH)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/binomialTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/binomialTestCases b/src/test/R/binomialTestCases
index 6b1871c..144a221 100644
--- a/src/test/R/binomialTestCases
+++ b/src/test/R/binomialTestCases
@@ -46,7 +46,7 @@ verifyDensity <- function(points, expected, n, p, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify distribution computations
@@ -63,7 +63,7 @@ verifyDistribution <- function(points, expected, n, p, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -73,7 +73,7 @@ size <- 10.0
probability <- 0.70
densityPoints <- c(-1,0,1,2,3,4,5,6,7,8,9,10,11)
-densityValues <- c(0, 0.0000, 0.0001, 0.0014, 0.0090, 0.0368, 0.1029,
+densityValues <- c(0, 0.0000, 0.0001, 0.0014, 0.0090, 0.0368, 0.1029,
0.2001, 0.2668, 0.2335, 0.1211, 0.0282, 0)
distributionValues <- c(0, 0.0000, 0.0001, 0.0016, 0.0106, 0.0473,
0.1503, 0.3504, 0.6172, 0.8507, 0.9718, 1, 1)
@@ -98,7 +98,7 @@ if (assertEquals(inverseCumValues, rInverseCumValues-1, tol,
displayPadded(output, SUCCEEDED, 80)
} else {
displayPadded(output, FAILED, 80)
-}
+}
# Degenerate cases
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/cauchyTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/cauchyTestCases.R b/src/test/R/cauchyTestCases.R
index b046ca5..d0fe442 100644
--- a/src/test/R/cauchyTestCases.R
+++ b/src/test/R/cauchyTestCases.R
@@ -42,7 +42,7 @@ verifyDistribution <- function(points, expected, median, scale, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -59,7 +59,7 @@ verifyDensity <- function(points, expected, median, scale, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -76,7 +76,7 @@ verifyQuantiles <- function(points, expected, median, scale, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/chiSquareTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/chiSquareTestCases b/src/test/R/chiSquareTestCases
index 747b5e8..be6eb84 100644
--- a/src/test/R/chiSquareTestCases
+++ b/src/test/R/chiSquareTestCases
@@ -38,16 +38,16 @@ verifyTable <- function(counts, expectedP, expectedStat, tol, desc) {
displayPadded(c(desc," p-value test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
- }
+ }
if (assertEquals(expectedStat, results$statistic, tol,
"ChiSquare Statistic")) {
displayPadded(c(desc, " chi-square statistic test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " chi-square statistic test"), FAILED, WIDTH)
- }
+ }
}
-verifyHomogeneity <- function(obs, exp, expectedP, expectedStat,
+verifyHomogeneity <- function(obs, exp, expectedP, expectedStat,
tol, desc) {
results <- chisq.test(obs,p=exp,rescale.p=TRUE)
chi <- results$statistic
@@ -56,13 +56,13 @@ verifyHomogeneity <- function(obs, exp, expectedP, expectedStat,
displayPadded(c(desc, " p-value test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " p-value test"), FAILED, WIDTH)
- }
+ }
if (assertEquals(expectedStat, chi, tol,
"ChiSquare Statistic")) {
displayPadded(c(desc, " chi-square statistic test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " chi-square statistic test"), FAILED, WIDTH)
- }
+ }
}
cat("ChiSquareTest test cases\n")
@@ -85,17 +85,17 @@ verifyHomogeneity(observed, expected, 0, 114875.90421929007, tol,
"testChiSquareLargeTestStatistic")
counts <- matrix(c(40, 22, 43, 91, 21, 28, 60, 10, 22), nc = 3);
-verifyTable(counts, 0.000144751460134, 22.709027688, tol,
+verifyTable(counts, 0.000144751460134, 22.709027688, tol,
"testChiSquareIndependence1")
counts <- matrix(c(10, 15, 30, 40, 60, 90), nc = 3);
-verifyTable(counts, 0.918987499852, 0.168965517241, tol,
+verifyTable(counts, 0.918987499852, 0.168965517241, tol,
"testChiSquareIndependence2")
-
+
counts <- matrix(c(40, 0, 4, 91, 1, 2, 60, 2, 0), nc = 3);
-verifyTable(counts, 0.0462835770603, 9.67444662263, tol,
+verifyTable(counts, 0.0462835770603, 9.67444662263, tol,
"testChiSquareZeroCount")
displayDashes(WIDTH)
-
+
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/correlationTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/correlationTestCases b/src/test/R/correlationTestCases
index caacd5f..07fdb27 100644
--- a/src/test/R/correlationTestCases
+++ b/src/test/R/correlationTestCases
@@ -37,7 +37,7 @@ verifyPearsonsCorrelation <- function(matrix, expectedCorrelation, name) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# Verify Spearman's correlation
@@ -48,7 +48,7 @@ verifySpearmansCorrelation <- function(matrix, expectedCorrelation, name) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# Verify Kendall's correlation
@@ -59,7 +59,7 @@ verifyKendallsCorrelation <- function(matrix, expectedCorrelation, name) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify p-values
@@ -133,16 +133,16 @@ expectedCorrelation <- matrix(c(
0.4172451498349454, 0.993952846232926, 1.0000000000000000),
nrow = 7, ncol = 7, byrow = TRUE)
verifyPearsonsCorrelation(longley, expectedCorrelation, "longley")
-
+
expectedPValues <- c(
4.38904690369668e-10,
8.36353208910623e-12, 7.8159700933611e-14,
- 0.0472894097790304, 0.01030636128354301, 0.01316878049026582,
+ 0.0472894097790304, 0.01030636128354301, 0.01316878049026582,
0.0749178049642416, 0.06971758330341182, 0.0830166169296545, 0.510948586323452,
- 3.693245043123738e-09, 4.327782576751815e-11, 1.167954621905665e-13, 0.00331028281967516, 0.1652293725106684,
+ 3.693245043123738e-09, 4.327782576751815e-11, 1.167954621905665e-13, 0.00331028281967516, 0.1652293725106684,
3.95834476307755e-10, 1.114663916723657e-13, 1.332267629550188e-15, 0.00466039138541463, 0.1078477071581498, 7.771561172376096e-15)
verifyPValues(longley, expectedPValues, "longley")
-
+
# Spearman's
expectedCorrelation <- matrix(c(
1, 0.982352941176471, 0.985294117647059, 0.564705882352941, 0.2264705882352941, 0.976470588235294,
@@ -218,7 +218,7 @@ expectedCorrelation <- matrix(c(
44.7,46.6,16,29,50.43,
42.8,27.7,22,29,58.33),
nrow = 47, ncol = 5, byrow = TRUE)
-
+
# Pearson's
expectedCorrelation <- matrix(c(
1, 0.3530791836199747, -0.6458827064572875, -0.663788857035069, 0.463684700651794,
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/covarianceTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/covarianceTestCases b/src/test/R/covarianceTestCases
index 3d8d603..eca5d0b 100644
--- a/src/test/R/covarianceTestCases
+++ b/src/test/R/covarianceTestCases
@@ -37,7 +37,7 @@ verifyCovariance <- function(matrix, expectedCovariance, name) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -79,11 +79,11 @@ expectedCovariance <- matrix(c(
16240.93333333333, 5.092333333333334e+01, 470977.900000000,
2973.033333333333, 1382.433333333333, 32917.40000000, 22.66666666666667),
nrow = 7, ncol = 7, byrow = TRUE)
-
+
verifyCovariance(longley, expectedCovariance, "longley")
-
+
# Swiss Fertility
-
+
fertility <- matrix(c(80.2,17.0,15,12,9.96,
83.1,45.1,6,9,84.84,
92.5,39.7,5,5,93.40,
@@ -132,7 +132,7 @@ expectedCovariance <- matrix(c(
44.7,46.6,16,29,50.43,
42.8,27.7,22,29,58.33),
nrow = 47, ncol = 5, byrow = TRUE)
-
+
expectedCovariance <- matrix(c(
156.0424976873265, 100.1691489361702, -64.36692876965772, -79.7295097132285, 241.5632030527289,
100.169148936170251, 515.7994172062905, -124.39283071230344, -139.6574005550416, 379.9043755781684,
@@ -140,7 +140,7 @@ expectedCovariance <- matrix(c(
-79.7295097132285, -139.6574005550416, 53.57585568917669, 92.4560592044403, -61.6988297872340,
241.5632030527289, 379.9043755781684, -190.56061054579092, -61.6988297872340, 1739.2945371877890),
nrow = 5, ncol = 5, byrow = TRUE)
-
+
verifyCovariance(fertility, expectedCovariance, "swiss fertility")
-
- displayDashes(WIDTH)
\ No newline at end of file
+
+ displayDashes(WIDTH)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/descriptiveTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/descriptiveTestCases b/src/test/R/descriptiveTestCases
index c724567..f6a6183 100644
--- a/src/test/R/descriptiveTestCases
+++ b/src/test/R/descriptiveTestCases
@@ -38,7 +38,7 @@ verifyMean <- function(values, expectedMean, tol, desc) {
displayPadded(c(desc," mean test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " mean test"), FAILED, WIDTH)
- }
+ }
}
verifySigma <- function(values, expectedSigma, tol, desc) {
@@ -47,7 +47,7 @@ verifySigma <- function(values, expectedSigma, tol, desc) {
displayPadded(c(desc," std test"), SUCCEEDED, WIDTH)
} else {
displayPadded(c(desc, " std test"), FAILED, WIDTH)
- }
+ }
}
cat("Descriptive test cases\n")
@@ -80,4 +80,4 @@ expectedSigma <- 0.000429123454003053
verifyMean(values, expectedMean, tol, "Mavro")
verifySigma(values, expectedSigma, tol, "Mavro")
-displayDashes(WIDTH)
+displayDashes(WIDTH)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/exponentialTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/exponentialTestCases b/src/test/R/exponentialTestCases
index 25f801a..c73e6dd 100644
--- a/src/test/R/exponentialTestCases
+++ b/src/test/R/exponentialTestCases
@@ -42,7 +42,7 @@ verifyDistribution <- function(points, expected, mean, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -58,7 +58,7 @@ verifyDensity <- function(points, expected, mean, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify quantiles
@@ -74,7 +74,7 @@ verifyQuantiles <- function(points, expected, mean, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
@@ -98,6 +98,6 @@ if (assertEquals(0.0905214480757, pexp(.75, 1/mean) - pexp(.25, 1/mean), tol, "P
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
-}
+}
displayDashes(WIDTH)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/geometricTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/geometricTestCases b/src/test/R/geometricTestCases
index 0c2293f..96ca82e 100644
--- a/src/test/R/geometricTestCases
+++ b/src/test/R/geometricTestCases
@@ -22,7 +22,7 @@
# source("<name-of-this-file>")
#
# R functions used
-# dgeom(x, prob, log = FALSE) <- density
+# dgeom(x, prob, log = FALSE) <- density
# pgeom(q, prob, lower.tail = TRUE, log.p = FALSE) <- distribution
# qgeom(p, prob, lower.tail = TRUE, log.p = FALSE) <- quantiles
#------------------------------------------------------------------------------
@@ -46,7 +46,7 @@ verifyDensity <- function(points, expected, prob, tol, log = FALSE) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify distribution computations
@@ -63,7 +63,7 @@ verifyDistribution <- function(points, expected, prob, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -79,7 +79,7 @@ densityValues <- c(0, 0.4, 0.24, 0.144, 0.0864, 0.05184, 0.031104, 0.0186624, 0.
0.000313456656384, 0.0001880739938304, 0.00011284439629824, 6.7706637778944e-05,
4.06239826673664e-05, 2.43743896004198e-05, 1.46246337602519e-05, 8.77478025615113e-06,
5.26486815369068e-06, 3.15892089221441e-06, 1.89535253532865e-06, 1.13721152119719e-06,
- 6.82326912718312e-07, 4.09396147630988e-07, 2.45637688578593e-07)
+ 6.82326912718312e-07, 4.09396147630988e-07, 2.45637688578593e-07)
logDensityValues <- c(-Inf, -0.916290731874155, -1.42711635564015, -1.93794197940614, -2.44876760317213,
-2.95959322693812, -3.47041885070411, -3.9812444744701, -4.49207009823609,
-5.00289572200208, -5.51372134576807, -6.02454696953406, -6.53537259330005,
@@ -116,6 +116,6 @@ if (assertEquals(inverseCumValues, rInverseCumValues-1, tol,
displayPadded(output, SUCCEEDED, 80)
} else {
displayPadded(output, FAILED, 80)
-}
+}
displayDashes(WIDTH)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/hypergeometricTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/hypergeometricTestCases b/src/test/R/hypergeometricTestCases
index a1d4ee9..04bc8a0 100644
--- a/src/test/R/hypergeometricTestCases
+++ b/src/test/R/hypergeometricTestCases
@@ -22,7 +22,7 @@
# source("<name-of-this-file>")
#
# R functions used
-# dhyper(x, m, n, k, log = FALSE) <- density
+# dhyper(x, m, n, k, log = FALSE) <- density
# phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) <- distribution
# qhyper(p, m, n, k, lower.tail = TRUE, log.p = FALSE) <- quantiles
#------------------------------------------------------------------------------
@@ -41,13 +41,13 @@ verifyDensity <- function(points, expected, good, bad, selected, tol, log = FALS
i <- i + 1
rDensityValues[i] <- dhyper(point, good, bad, selected, log)
}
- output <- c("Density test good = ", good, ", bad = ", bad,
+ output <- c("Density test good = ", good, ", bad = ", bad,
", selected = ",selected)
if (assertEquals(expected,rDensityValues,tol,"Density Values")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify distribution computations
@@ -65,7 +65,7 @@ verifyDistribution <- function(points, expected, good, bad, selected, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -98,7 +98,7 @@ for (point in inverseCumPoints) {
rInverseCumValues[i] <- qhyper(point, good, bad, selected)
}
-output <- c("Inverse Distribution test good = ", good, ", bad = ", bad,
+output <- c("Inverse Distribution test good = ", good, ", bad = ", bad,
", selected = ", selected)
# R defines quantiles from the right, need to subtract one
if (assertEquals(inverseCumValues, rInverseCumValues-1, tol,
@@ -106,7 +106,7 @@ if (assertEquals(inverseCumValues, rInverseCumValues-1, tol,
displayPadded(output, SUCCEEDED, 80)
} else {
displayPadded(output, FAILED, 80)
-}
+}
# Degenerate cases
good <- 5
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/multipleOLSRegressionTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/multipleOLSRegressionTestCases b/src/test/R/multipleOLSRegressionTestCases
index 1fe983d..458426f 100644
--- a/src/test/R/multipleOLSRegressionTestCases
+++ b/src/test/R/multipleOLSRegressionTestCases
@@ -44,13 +44,13 @@ verifyRegression <- function(model, expectedBeta, expectedResiduals,
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
output <- c("Residuals test dataset = ", modelName)
if (assertEquals(expectedResiduals,residuals,tol,"Residuals")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
output <- c("Errors test dataset = ", modelName)
if (assertEquals(expectedErrors,errors,tol,"Errors")) {
displayPadded(output, SUCCEEDED, WIDTH)
@@ -95,13 +95,13 @@ expectedStdError <- NaN
expectedRSquare <- 1
expectedAdjRSquare <- NaN
verifyRegression(model, expectedBeta, expectedResiduals, expectedErrors,
- expectedStdError, expectedRSquare, expectedAdjRSquare, "perfect fit")
+ expectedStdError, expectedRSquare, expectedAdjRSquare, "perfect fit")
# Longley
#
# Data Source: J. Longley (1967) "An Appraisal of Least Squares Programs for the
-# Electronic Computer from the Point of View of the User",
-# Journal of the American Statistical Association,
+# Electronic Computer from the Point of View of the User",
+# Journal of the American Statistical Association,
# vol. 62. September, pp. 819-841.
#
# Certified values (and data) are from NIST:
@@ -154,16 +154,16 @@ expectedRSquare <- 0.995479004577296
expectedAdjRSquare <- 0.992465007628826
verifyRegression(model, expectedBeta, expectedResiduals, expectedErrors,
-expectedStdError, expectedRSquare, expectedAdjRSquare, "Longley")
+expectedStdError, expectedRSquare, expectedAdjRSquare, "Longley")
# Model with no intercept
model <- lm(y ~ 0 + x1 + x2 + x3 + x4 + x5 + x6)
-estimates <- matrix(c(-52.99357013868291, 129.54486693117232,
+estimates <- matrix(c(-52.99357013868291, 129.54486693117232,
0.07107319907358, 0.03016640003786,
- -0.42346585566399, 0.41773654056612,
+ -0.42346585566399, 0.41773654056612,
-0.57256866841929, 0.27899087467676,
- -0.41420358884978, 0.32128496193363,
+ -0.41420358884978, 0.32128496193363,
48.41786562001326, 17.68948737819961),
nrow = 6, ncol = 2, byrow = TRUE)
@@ -171,7 +171,7 @@ expectedBeta <- estimates[,1]
expectedErrors <- estimates[,2]
expectedResiduals <- c(279.90274927293092, -130.32465380836874, 90.73228661967445,
-401.31252201634948, -440.46768772620027, -543.54512853774793, 201.32111639536299,
- 215.90889365977932, 73.09368242049943, 913.21694494481869, 424.82484953610174,
+ 215.90889365977932, 73.09368242049943, 913.21694494481869, 424.82484953610174,
-8.56475876776709, -361.32974610842876, 27.34560497213464, 151.28955976355002,
-492.49937355336846)
expectedStdError <- 475.1655079819517
@@ -179,7 +179,7 @@ expectedRSquare <- 0.9999670130706
expectedAdjRSquare <- 0.999947220913
verifyRegression(model, expectedBeta, expectedResiduals, expectedErrors,
-expectedStdError, expectedRSquare, expectedAdjRSquare, "Longley No Intercept")
+expectedStdError, expectedRSquare, expectedAdjRSquare, "Longley No Intercept")
# Swiss Fertility (R dataset named "swiss")
@@ -272,23 +272,23 @@ expectedRSquare <- 0.649789742860228
expectedAdjRSquare <- 0.6164363850373927
verifyRegression(model, expectedBeta, expectedResiduals, expectedErrors,
-expectedStdError, expectedRSquare, expectedAdjRSquare, "Swiss Fertility")
+expectedStdError, expectedRSquare, expectedAdjRSquare, "Swiss Fertility")
# model with no intercept
model <- lm(y ~ 0 + x1 + x2 + x3 + x4)
estimates <- matrix(c(0.52191832900513, 0.10470063765677,
2.36588087917963, 0.41684100584290,
- -0.94770353802795, 0.43370143099691,
+ -0.94770353802795, 0.43370143099691,
0.30851985863609, 0.07694953606522),
nrow = 4, ncol = 2, byrow = TRUE)
expectedBeta <- estimates[,1]
expectedErrors <- estimates[,2]
-expectedResiduals <- c(44.138759883538249, 27.720705122356215, 35.873200836126799,
+expectedResiduals <- c(44.138759883538249, 27.720705122356215, 35.873200836126799,
34.574619581211977, 26.600168342080213, 15.074636243026923, -12.704904871199814,
- 1.497443824078134, 2.691972687079431, 5.582798774291231, -4.422986561283165,
+ 1.497443824078134, 2.691972687079431, 5.582798774291231, -4.422986561283165,
-9.198581600334345, 4.481765170730647, 2.273520207553216, -22.649827853221336,
-17.747900013943308, 20.298314638496436, 6.861405135329779, -8.684712790954924,
-10.298639278062371, -9.896618896845819, 4.568568616351242, -15.313570491727944,
@@ -304,6 +304,6 @@ expectedRSquare <- 0.946350722085
expectedAdjRSquare <- 0.9413600915813
verifyRegression(model, expectedBeta, expectedResiduals, expectedErrors,
-expectedStdError, expectedRSquare, expectedAdjRSquare, "Swiss Fertility No Intercept")
+expectedStdError, expectedRSquare, expectedAdjRSquare, "Swiss Fertility No Intercept")
displayDashes(WIDTH)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/normalTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/normalTestCases b/src/test/R/normalTestCases
index ae54a96..7be2e75 100644
--- a/src/test/R/normalTestCases
+++ b/src/test/R/normalTestCases
@@ -44,7 +44,7 @@ verifyDistribution <- function(points, expected, mu, sigma, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify density computations
@@ -61,7 +61,7 @@ verifyDensity <- function(points, expected, mu, sigma, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -94,7 +94,7 @@ distributionPoints <- c(mu - 2 *sigma, mu - sigma, mu, mu + sigma,
mu + 2 * sigma, mu + 3 * sigma, mu + 4 * sigma,
mu + 5 * sigma)
densityValues <- c(0.0539909665132, 0.241970724519, 0.398942280401, 0.241970724519, 0.0539909665132,
- 0.00443184841194, 0.000133830225765, 1.48671951473e-06)
+ 0.00443184841194, 0.000133830225765, 1.48671951473e-06)
verifyDistribution(distributionPoints, distributionValues, mu, sigma, tol)
verifyDensity(distributionPoints, densityValues, mu, sigma, tol)
@@ -104,7 +104,7 @@ distributionPoints <- c(mu - 2 *sigma, mu - sigma, mu, mu + sigma,
mu + 2 * sigma, mu + 3 * sigma, mu + 4 * sigma,
mu + 5 * sigma)
densityValues <- c(0.539909665132, 2.41970724519, 3.98942280401, 2.41970724519,
- 0.539909665132, 0.0443184841194, 0.00133830225765, 1.48671951473e-05)
+ 0.539909665132, 0.0443184841194, 0.00133830225765, 1.48671951473e-05)
verifyDistribution(distributionPoints, distributionValues, mu, sigma, tol)
verifyDensity(distributionPoints, densityValues, mu, sigma, tol)
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/pascalTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/pascalTestCases b/src/test/R/pascalTestCases
index a8c6c31..0e7e68e 100644
--- a/src/test/R/pascalTestCases
+++ b/src/test/R/pascalTestCases
@@ -46,7 +46,7 @@ verifyDensity <- function(points, expected, size, p, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify distribution computations
@@ -63,7 +63,7 @@ verifyDistribution <- function(points, expected, size, p, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------
@@ -100,7 +100,7 @@ if (assertEquals(inverseCumValues, rInverseCumValues-1, tol,
displayPadded(output, SUCCEEDED, 80)
} else {
displayPadded(output, FAILED, 80)
-}
+}
# Degenerate cases
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/poissonTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/poissonTestCases b/src/test/R/poissonTestCases
index 200aa75..2b5bbb7 100644
--- a/src/test/R/poissonTestCases
+++ b/src/test/R/poissonTestCases
@@ -46,7 +46,7 @@ verifyDensity <- function(points, expected, lambda, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify distribution computations
@@ -63,14 +63,14 @@ verifyDistribution <- function(points, expected, lambda, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify normal approximation
verifyNormalApproximation <- function(expected, lambda, lower, upper, tol) {
rValue <- pnorm(upper, mean=lambda, sd=sqrt(lambda), lower.tail = TRUE,
- log.p = FALSE) -
+ log.p = FALSE) -
pnorm(lower, mean=lambda, sd=sqrt(lambda), lower.tail = TRUE,
log.p = FALSE)
output <- c("Normal approx. test lambda = ", lambda, " upper = ",
@@ -79,7 +79,7 @@ verifyNormalApproximation <- function(expected, lambda, lower, upper, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
cat("Poisson distribution test cases\n")
@@ -112,5 +112,5 @@ displayDashes(WIDTH)
-
-
+
+
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/regressionTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/regressionTestCases b/src/test/R/regressionTestCases
index c4465ca..d8b3c73 100644
--- a/src/test/R/regressionTestCases
+++ b/src/test/R/regressionTestCases
@@ -58,19 +58,19 @@ if (assertEquals(4.596e-07, significance, tol, "Significance")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
-}
-
+}
+
output <- "InfData conf interval test"
ci<-confint(model)
# ci[1,1] = lower 2.5% bound for intercept, ci[1,2] = upper 97.5% for intercept
# ci[2,1] = lower 2.5% bound for slope, ci[2,2] = upper 97.5% for slope
halfWidth <- ci[2,2] - slope
-if (assertEquals(0.0270713794287, halfWidth, tol,
+if (assertEquals(0.0270713794287, halfWidth, tol,
"Slope conf. interval half-width")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
-}
+}
#------------------------------------------------------------------------------
# Norris dataset from NIST examples
@@ -123,37 +123,37 @@ if (assertEquals(0.261829133982, significance, tol, "Significance")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
-}
+}
output <- "InfData2 conf interval test"
ci<-confint(model)
# ci[1,1] = lower 2.5% bound for intercept, ci[1,2] = upper 97.5% for intercept
# ci[2,1] = lower 2.5% bound for slope, ci[2,2] = upper 97.5% for slope
halfWidth <- ci[2,2] - slope
-if (assertEquals(2.97802204827, halfWidth, tol,
+if (assertEquals(2.97802204827, halfWidth, tol,
"Slope conf. interval half-width")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
-}
+}
#------------------------------------------------------------------------------
# Correlation example
x <- c(101.0, 100.1, 100.0, 90.6, 86.5, 89.7, 90.6, 82.8, 70.1, 65.4,
61.3, 62.5, 63.6, 52.6, 59.7, 59.5, 61.3)
y <- c(99.2, 99.0, 100.0, 111.6, 122.2, 117.6, 121.1, 136.0, 154.2, 153.6,
- 158.5, 140.6, 136.2, 168.0, 154.3, 149.0, 165.5)
+ 158.5, 140.6, 136.2, 168.0, 154.3, 149.0, 165.5)
output <- "Correlation test"
-if (assertEquals(-0.94663767742, cor(x,y, method="pearson"), tol,
+if (assertEquals(-0.94663767742, cor(x,y, method="pearson"), tol,
"Correlation coefficient")) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
}
-
+
displayDashes(WIDTH)
-
-
+
+
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/testAll
----------------------------------------------------------------------
diff --git a/src/test/R/testAll b/src/test/R/testAll
index bf77f6d..9af417b 100644
--- a/src/test/R/testAll
+++ b/src/test/R/testAll
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to run all commons-math R verification tests
-#
+#
# To run the test, install R, put this file and all other o.a.c.math R
# verification tests and the testfunctions utilities file into the same
# directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/testFunctions
----------------------------------------------------------------------
diff --git a/src/test/R/testFunctions b/src/test/R/testFunctions
index 92f62ea..744b554 100644
--- a/src/test/R/testFunctions
+++ b/src/test/R/testFunctions
@@ -60,7 +60,7 @@ assertEquals <- function(expected, observed, tol, message) {
cat("OBSERVED: ",observed,"\n")
cat("DIFF: ",observed - expected,"\n")
cat("TOLERANCE: ",tol,"\n")
- }
+ }
return(!failed)
}
#------------------------------------------------------------------------------
@@ -73,12 +73,12 @@ displayDashes <- function(n) {
return(1)
}
#------------------------------------------------------------------------------
-# Displays <start>......<end> with enough dots in between to make <n> cols,
+# Displays <start>......<end> with enough dots in between to make <n> cols,
# followed by a new line character. Blows up if <start><end> is longer than
# <n> cols by itself.
#
# Expects <start> and <end> to be strings (character vectors).
-#
+#
displayPadded <- function(start, end, n) {
len = sum(nchar(start)) + sum(nchar(end))
cat(start, rep(".", n - len), end, "\n",sep='')
http://git-wip-us.apache.org/repos/asf/commons-math/blob/23b351c8/src/test/R/zipfTestCases
----------------------------------------------------------------------
diff --git a/src/test/R/zipfTestCases b/src/test/R/zipfTestCases
index f198548..318fffa 100644
--- a/src/test/R/zipfTestCases
+++ b/src/test/R/zipfTestCases
@@ -22,7 +22,7 @@
# source("<name-of-this-file>")
#
# R functions used
-# dzipf(x, N, s, log = FALSE) <- density
+# dzipf(x, N, s, log = FALSE) <- density
# pzipf(q, N, s) <- distribution
#------------------------------------------------------------------------------
tol <- 1E-6 # error tolerance for tests
@@ -46,7 +46,7 @@ verifyDensity <- function(points, expected, N, s, tol, log = FALSE) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
# function to verify distribution computations
@@ -63,7 +63,7 @@ verifyDistribution <- function(points, expected, N, s, tol) {
displayPadded(output, SUCCEEDED, WIDTH)
} else {
displayPadded(output, FAILED, WIDTH)
- }
+ }
}
#--------------------------------------------------------------------------