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From pste...@apache.org
Subject svn commit: r922691 - in /commons/proper/math/trunk/src/test/R: ChiSquareDistributionTestCases.R FDistributionTestCases.R GammaDistributionTestCases.R WeibullDistributionTestCases.R exponentialTestCases testAll
Date Sat, 13 Mar 2010 23:32:37 GMT
Author: psteitz
Date: Sat Mar 13 23:32:37 2010
New Revision: 922691

URL: http://svn.apache.org/viewvc?rev=922691&view=rev
Log:
Added Wiebull, Gamma, F, ChiSquare verification tests, added density test for exponential.

Added:
    commons/proper/math/trunk/src/test/R/ChiSquareDistributionTestCases.R   (with props)
    commons/proper/math/trunk/src/test/R/FDistributionTestCases.R   (with props)
    commons/proper/math/trunk/src/test/R/GammaDistributionTestCases.R   (with props)
    commons/proper/math/trunk/src/test/R/WeibullDistributionTestCases.R   (with props)
Modified:
    commons/proper/math/trunk/src/test/R/exponentialTestCases
    commons/proper/math/trunk/src/test/R/testAll

Added: commons/proper/math/trunk/src/test/R/ChiSquareDistributionTestCases.R
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/R/ChiSquareDistributionTestCases.R?rev=922691&view=auto
==============================================================================
--- commons/proper/math/trunk/src/test/R/ChiSquareDistributionTestCases.R (added)
+++ commons/proper/math/trunk/src/test/R/ChiSquareDistributionTestCases.R Sat Mar 13 23:32:37
2010
@@ -0,0 +1,97 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#------------------------------------------------------------------------------
+# R source file to validate ChiSquare distribution tests in
+# org.apache.commons.math.distribution.ChiSquareDistributionTest
+#
+# To run the test, install R, put this file and testFunctions
+# into the same directory, launch R from this directory and then enter
+# source("<name-of-this-file>")
+#
+#-----------------------------------------------------------------------------
+tol <- 1E-9
+
+# Function definitions
+source("testFunctions")           # utility test functions
+
+# function to verify distribution computations
+verifyDistribution <- function(points, expected, df, tol) {
+ rDistValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDistValues[i] <- pchisq(point, df, log = FALSE)
+    }
+    output <- c("Distribution test df = ", df)
+    if (assertEquals(expected, rDistValues, tol, "Distribution Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify density computations
+verifyDensity <- function(points, expected, df, tol) {
+ rDensityValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDensityValues[i] <- dchisq(point, df, log = FALSE)
+    }
+    output <- c("Density test df = ", df)
+    if (assertEquals(expected, rDensityValues, tol, "Density Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify quantiles
+verifyQuantiles <- function(points, expected, df, tol) {
+	rQuantileValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rQuantileValues[i] <- qchisq(point, df, log = FALSE)
+    }
+    output <- c("Quantile test df = ", df)
+    if (assertEquals(expected, rQuantileValues, tol, "Quantile Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }    
+}
+
+#--------------------------------------------------------------------------
+cat("ChiSquare Distribution test cases\n")
+
+df <- 5
+distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.950, 0.900)
+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)
             
+verifyQuantiles(distributionValues, distributionPoints, df, tol)
+verifyDistribution(distributionPoints, distributionValues, df, tol)
+verifyDensity(distributionPoints, densityValues, df, tol)
+
+df <- .1
+distributionPoints <- c(1.16892641146e-60, 1.16892641146e-40, 1.06313237798e-32, 1.11477509638e-26,
1.16892641146e-20,
+                5.47291719746, 2.17525480018, 1.13434752351, 0.531864604852, 0.152634227818)
+verifyQuantiles(distributionValues, distributionPoints, df, tol)
+verifyDistribution(distributionPoints, distributionValues, df, tol)
+
+displayDashes(WIDTH)

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Added: commons/proper/math/trunk/src/test/R/FDistributionTestCases.R
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/R/FDistributionTestCases.R?rev=922691&view=auto
==============================================================================
--- commons/proper/math/trunk/src/test/R/FDistributionTestCases.R (added)
+++ commons/proper/math/trunk/src/test/R/FDistributionTestCases.R Sat Mar 13 23:32:37 2010
@@ -0,0 +1,92 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#------------------------------------------------------------------------------
+# R source file to validate F distribution tests in
+# org.apache.commons.math.distribution.TDistributionTest
+#
+# To run the test, install R, put this file and testFunctions
+# into the same directory, launch R from this directory and then enter
+# source("<name-of-this-file>")
+#
+#-----------------------------------------------------------------------------
+tol <- 1E-9
+
+# Function definitions
+source("testFunctions")           # utility test functions
+
+# function to verify distribution computations
+verifyDistribution <- function(points, expected, numeratorDf, denominatorDf, tol) {
+ rDistValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDistValues[i] <- pf(point, numeratorDf, denominatorDf, log = FALSE)
+    }
+    output <- c("Distribution test numerator df = ", numeratorDf, " denominator df = ",
denominatorDf)
+    if (assertEquals(expected, rDistValues, tol, "Distribution Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify density computations
+verifyDensity <- function(points, expected, numeratorDf, denominatorDf, tol) {
+ rDensityValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDensityValues[i] <- df(point, numeratorDf, denominatorDf, log = FALSE)
+    }
+    output <- c("Density test numerator df = ", numeratorDf, " denominator df = ", denominatorDf)
+    if (assertEquals(expected, rDensityValues, tol, "Density Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify quantiles
+verifyQuantiles <- function(points, expected, numeratorDf, denominatorDf, tol) {
+	rQuantileValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rQuantileValues[i] <- qf(point, numeratorDf, denominatorDf, log = FALSE)
+    }
+    output <- c("Quantile test numerator df = ", numeratorDf, " denominator df = ", denominatorDf)
+    if (assertEquals(expected, rQuantileValues, tol, "Quantile Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }    
+}
+
+#--------------------------------------------------------------------------
+cat("F Distribution test cases\n")
+
+numeratorDf <- 5
+denominatorDf <- 6
+distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.950, 0.900)
+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)
             
+verifyQuantiles(distributionValues, distributionPoints, numeratorDf, denominatorDf, tol)
+verifyDistribution(distributionPoints, distributionValues, numeratorDf, denominatorDf, tol)
+verifyDensity(distributionPoints, densityValues, numeratorDf, denominatorDf, tol)
+
+displayDashes(WIDTH)

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Added: commons/proper/math/trunk/src/test/R/GammaDistributionTestCases.R
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/R/GammaDistributionTestCases.R?rev=922691&view=auto
==============================================================================
--- commons/proper/math/trunk/src/test/R/GammaDistributionTestCases.R (added)
+++ commons/proper/math/trunk/src/test/R/GammaDistributionTestCases.R Sat Mar 13 23:32:37
2010
@@ -0,0 +1,92 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#------------------------------------------------------------------------------
+# R source file to validate Gamma distribution tests in
+# org.apache.commons.math.distribution.GammaDistributionTest
+#
+# To run the test, install R, put this file and testFunctions
+# into the same directory, launch R from this directory and then enter
+# source("<name-of-this-file>")
+#
+#-----------------------------------------------------------------------------
+tol <- 1E-9
+
+# Function definitions
+source("testFunctions")           # utility test functions
+
+# function to verify distribution computations
+verifyDistribution <- function(points, expected, alpha, beta, tol) {
+ rDistValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDistValues[i] <- pgamma(point, shape=alpha, scale=beta, log = FALSE)
+    }
+    output <- c("Distribution test shape = ", shape, " scale = ", scale)
+    if (assertEquals(expected, rDistValues, tol, "Distribution Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify density computations
+verifyDensity <- function(points, expected, alpha, beta, tol) {
+ rDensityValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDensityValues[i] <- dgamma(point, shape=alpha, scale=beta, log = FALSE)
+    }
+    output <- c("Density test shape = ", shape, " scale = ", scale)
+    if (assertEquals(expected, rDensityValues, tol, "Density Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify quantiles
+verifyQuantiles <- function(points, expected, alpha, beta, tol) {
+	rQuantileValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rQuantileValues[i] <- qgamma(point, shape=alpha, scale=beta, log = FALSE)
+    }
+    output <- c("Quantile test shape = ", shape, " scale = ", scale)
+    if (assertEquals(expected, rQuantileValues, tol, "Quantile Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }    
+}
+
+#--------------------------------------------------------------------------
+cat("Gamma Distribution test cases\n")
+
+shape <- 4
+scale <- 2
+distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.950, 0.900)
+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)
             
+verifyQuantiles(distributionValues, distributionPoints, shape, scale, tol)
+verifyDistribution(distributionPoints, distributionValues, shape, scale, tol)
+verifyDensity(distributionPoints, densityValues, shape, scale, tol)
+
+displayDashes(WIDTH)

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Added: commons/proper/math/trunk/src/test/R/WeibullDistributionTestCases.R
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/R/WeibullDistributionTestCases.R?rev=922691&view=auto
==============================================================================
--- commons/proper/math/trunk/src/test/R/WeibullDistributionTestCases.R (added)
+++ commons/proper/math/trunk/src/test/R/WeibullDistributionTestCases.R Sat Mar 13 23:32:37
2010
@@ -0,0 +1,92 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#------------------------------------------------------------------------------
+# R source file to validate Weibull distribution tests in
+# org.apache.commons.math.distribution.GammaDistributionTest
+#
+# To run the test, install R, put this file and testFunctions
+# into the same directory, launch R from this directory and then enter
+# source("<name-of-this-file>")
+#
+#-----------------------------------------------------------------------------
+tol <- 1E-9
+
+# Function definitions
+source("testFunctions")           # utility test functions
+
+# function to verify distribution computations
+verifyDistribution <- function(points, expected, alpha, beta, tol) {
+ rDistValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDistValues[i] <- pweibull(point, shape=alpha, scale=beta, log = FALSE)
+    }
+    output <- c("Distribution test shape = ", shape, " scale = ", scale)
+    if (assertEquals(expected, rDistValues, tol, "Distribution Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify density computations
+verifyDensity <- function(points, expected, alpha, beta, tol) {
+ rDensityValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDensityValues[i] <- dweibull(point, shape=alpha, scale=beta, log = FALSE)
+    }
+    output <- c("Density test shape = ", shape, " scale = ", scale)
+    if (assertEquals(expected, rDensityValues, tol, "Density Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify quantiles
+verifyQuantiles <- function(points, expected, alpha, beta, tol) {
+	rQuantileValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rQuantileValues[i] <- qweibull(point, shape=alpha, scale=beta, log = FALSE)
+    }
+    output <- c("Quantile test shape = ", shape, " scale = ", scale)
+    if (assertEquals(expected, rQuantileValues, tol, "Quantile Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }    
+}
+
+#--------------------------------------------------------------------------
+cat("Weibull Distribution test cases\n")
+
+shape <- 1.2
+scale <- 2.1
+distributionValues <- c(0.001, 0.01, 0.025, 0.05, 0.1, 0.999, 0.990, 0.975, 0.950, 0.900)
+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)
             
+verifyQuantiles(distributionValues, distributionPoints, shape, scale, tol)
+verifyDistribution(distributionPoints, distributionValues, shape, scale, tol)
+verifyDensity(distributionPoints, densityValues, shape, scale, tol)
+
+displayDashes(WIDTH)

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Modified: commons/proper/math/trunk/src/test/R/exponentialTestCases
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/R/exponentialTestCases?rev=922691&r1=922690&r2=922691&view=diff
==============================================================================
--- commons/proper/math/trunk/src/test/R/exponentialTestCases (original)
+++ commons/proper/math/trunk/src/test/R/exponentialTestCases Sat Mar 13 23:32:37 2010
@@ -21,11 +21,8 @@
 # into the same directory, launch R from this directory and then enter
 # source("<name-of-this-file>")
 #
-# R functions used
-# pexp(q, rate = 1, lower.tail = TRUE, log.p = FALSE) <- distribution
-# qexp(p, rate = 1, lower.tail = TRUE, log.p = FALSE) <- quantiles
 #------------------------------------------------------------------------------
-tol <- 1E-7
+tol <- 1E-9
 
 # Function definitions
 
@@ -48,6 +45,39 @@ verifyDistribution <- function(points, e
     }       
 }
 
+# function to verify density computations
+verifyDensity <- function(points, expected, mean, tol) {
+ rDensityValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rDensityValues[i] <- dexp(point, 1/mean)
+    }
+    output <- c("Density test mean = ", mean)
+    if (assertEquals(expected, rDensityValues, tol, "Density Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }       
+}
+
+# function to verify quantiles
+verifyQuantiles <- function(points, expected, mean, tol) {
+	rQuantileValues <- rep(0, length(points))
+    i <- 0
+    for (point in points) {
+        i <- i + 1
+        rQuantileValues[i] <- qexp(point, 1/mean, log = FALSE)
+    }
+    output <- c("Quantile test mean = ", mean)
+    if (assertEquals(expected, rQuantileValues, tol, "Quantile Values")) {
+        displayPadded(output, SUCCEEDED, WIDTH)
+    } else {
+        displayPadded(output, FAILED, WIDTH)
+    }    
+}
+
+
 #--------------------------------------------------------------------------
 cat("Exponential test cases\n")
 
@@ -55,13 +85,16 @@ mean <- 5
 
 distributionValues <- c(0, 0, 0.001, 0.01, 0.025, 0.05, 0.1, 0.999,
                 0.990, 0.975, 0.950, 0.900)
-distributionPoints <- c(-2, 0, 0.005002502, 0.05025168, 0.1265890, 0.2564665, 0.5268026,

-                34.53878, 23.02585, 18.44440, 14.97866, 11.51293)
-
+densityValues <- c(0.2, 0.2, 0.1998, 0.198, 0.195, 0.19, 0.18, 0.000200000000000,
+                0.00200000000002, 0.00499999999997, 0.00999999999994, 0.0199999999999)
+distributionPoints <- c(0, 0, 0.00500250166792, 0.0502516792675, 0.126589039921, 0.256466471938,
+                0.526802578289, 34.5387763949, 23.0258509299, 18.4443972706, 14.9786613678,
11.5129254650)
 verifyDistribution(distributionPoints, distributionValues, mean, tol)
+verifyQuantiles(distributionValues, distributionPoints, mean, tol)
+verifyDensity(distributionPoints, densityValues, mean, tol)
 
 output <- "Probability test P(.25 < X < .75)"
-if (assertEquals(0.0905214, pexp(.75, 1/mean) - pexp(.25, 1/mean), tol, "Probability value"))
{
+if (assertEquals(0.0905214480757, pexp(.75, 1/mean) - pexp(.25, 1/mean), tol, "Probability
value")) {
     displayPadded(output, SUCCEEDED, WIDTH)
 } else {
     displayPadded(output, FAILED, WIDTH)

Modified: commons/proper/math/trunk/src/test/R/testAll
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/R/testAll?rev=922691&r1=922690&r2=922691&view=diff
==============================================================================
--- commons/proper/math/trunk/src/test/R/testAll (original)
+++ commons/proper/math/trunk/src/test/R/testAll Sat Mar 13 23:32:37 2010
@@ -36,6 +36,10 @@ source("exponentialTestCases")
 source("cauchyTestCases.R")
 source("pascalTestCases")
 source("TDistributionTestCases.R")
+source("FDistributionTestCases.R")
+source("GammaDistributionTestCases.R")
+source("WeibullDistributionTestCases.R")
+source("ChiSquareDistributionTestCases.R")
 
 # regression
 source("regressionTestCases")



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