| # 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 Hypergeometric distribution tests in |
| # org.apache.commons.math.distribution.HypergeometricDistributionTest |
| # |
| # 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>") |
| # |
| # R functions used |
| # 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 |
| #------------------------------------------------------------------------------ |
| tol <- 1E-6 # error tolerance for tests |
| #------------------------------------------------------------------------------ |
| # Function definitions |
| |
| source("testFunctions") # utility test functions |
| |
| # function to verify density computations |
| |
| verifyDensity <- function(points, expected, good, bad, selected, tol) { |
| rDensityValues <- rep(0, length(points)) |
| i <- 0 |
| for (point in points) { |
| i <- i + 1 |
| rDensityValues[i] <- dhyper(point, good, bad, selected) |
| } |
| 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 |
| |
| verifyDistribution <- function(points, expected, good, bad, selected, tol) { |
| rDistValues <- rep(0, length(points)) |
| i <- 0 |
| for (point in points) { |
| i <- i + 1 |
| rDistValues[i] <- phyper(point, good, bad, selected) |
| } |
| output <- c("Distribution test good = ", good, ", bad = ", |
| bad, ", selected = ",selected) |
| if (assertEquals(expected,rDistValues,tol,"Distribution Values")) { |
| displayPadded(output, SUCCEEDED, WIDTH) |
| } else { |
| displayPadded(output, FAILED, WIDTH) |
| } |
| } |
| |
| #-------------------------------------------------------------------------- |
| cat("Hypergeometric test cases\n") |
| |
| good <- 5 |
| bad <- 5 |
| selected <- 5 |
| |
| densityPoints <- c(-1, 0, 1, 2, 3, 4, 5, 10) |
| densityValues <- c(0, 0.003968, 0.099206, 0.396825, 0.396825, 0.099206, |
| 0.003968, 0) |
| distributionValues <- c(0, .003968, .103175, .50000, .896825, .996032, |
| 1.00000, 1) |
| #Eliminate p=1 case because it will mess up adjustement below |
| inverseCumPoints <- c(0, 0.001, 0.010, 0.025, 0.050, 0.100, 0.999, |
| 0.990, 0.975, 0.950, 0.900) |
| inverseCumValues <- c(-1, -1, 0, 0, 0, 0, 4, 3, 3, 3, 3) |
| |
| verifyDensity(densityPoints, densityValues, good, bad, selected, tol) |
| verifyDistribution(densityPoints, distributionValues, good, bad, selected, tol) |
| |
| i <- 0 |
| rInverseCumValues <- rep(0,length(inverseCumPoints)) |
| for (point in inverseCumPoints) { |
| i <- i + 1 |
| rInverseCumValues[i] <- qhyper(point, good, bad, selected) |
| } |
| |
| 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, |
| "Inverse Dist Values")) { |
| displayPadded(output, SUCCEEDED, 80) |
| } else { |
| displayPadded(output, FAILED, 80) |
| } |
| |
| # Degenerate cases |
| good <- 5 |
| bad <- 0 |
| selected <- 3 |
| densityPoints <- c(-1, 0, 1, 3, 10) |
| densityValues <- c(0, 0, 0, 1, 0) |
| distributionValues <- c(0, 0, 0, 1, 1) |
| verifyDensity(densityPoints, densityValues, good, bad, selected, tol) |
| verifyDistribution(densityPoints, distributionValues, good, bad, selected, tol) |
| |
| good <- 0 |
| bad <- 5 |
| selected <- 3 |
| densityPoints <- c(-1, 0, 1, 3, 10) |
| densityValues <- c(0, 1, 0, 0, 0) |
| distributionValues <- c(0, 1, 1, 1, 1) |
| verifyDensity(densityPoints, densityValues, good, bad, selected, tol) |
| verifyDistribution(densityPoints, distributionValues, good, bad, selected, tol) |
| |
| good <- 3 |
| bad <- 2 |
| selected <- 5 |
| densityPoints <- c(-1, 0, 1, 3, 10) |
| densityValues <- c(0, 0, 0, 1, 0) |
| distributionValues <- c(0, 0, 0, 1, 1) |
| verifyDensity(densityPoints, densityValues, good, bad, selected, tol) |
| verifyDistribution(densityPoints, distributionValues, good, bad, selected, tol) |
| |
| displayDashes(WIDTH) |