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authorAlexeyKhudyakov <>2020-01-05 14:07:00 (GMT)
committerhdiff <hdiff@hdiff.luite.com>2020-01-05 14:07:00 (GMT)
commite9ccb87dd3e65aa519cacb94f15e2b1a17fb0d19 (patch)
treea02a27c387b484e49ad7a50a9ad17c1bd0c4ade6
parentf2a6161de5c407782f2313fdf64655f9cbcc861d (diff)
version 0.15.2.0HEAD0.15.2.0master
-rw-r--r--Statistics/ConfidenceInt.hs2
-rw-r--r--Statistics/Distribution/Exponential.hs4
-rw-r--r--Statistics/Distribution/Geometric.hs16
-rw-r--r--Statistics/Sample/Histogram.hs2
-rwxr-xr-xchangelog.md13
-rw-r--r--statistics.cabal11
-rw-r--r--tests/Tests/Correlation.hs9
-rw-r--r--tests/Tests/Distribution.hs156
-rw-r--r--tests/Tests/Function.hs6
-rw-r--r--tests/Tests/Helpers.hs12
-rw-r--r--tests/Tests/KDE.hs14
-rw-r--r--tests/Tests/Matrix.hs10
-rw-r--r--tests/Tests/NonParametric.hs25
-rw-r--r--tests/Tests/Parametric.hs10
-rw-r--r--tests/Tests/Quantile.hs10
-rw-r--r--tests/Tests/Serialization.hs10
-rw-r--r--tests/Tests/Transform.hs10
-rw-r--r--tests/tests.hs25
18 files changed, 205 insertions, 140 deletions
diff --git a/Statistics/ConfidenceInt.hs b/Statistics/ConfidenceInt.hs
index 020f23f..e0a5351 100644
--- a/Statistics/ConfidenceInt.hs
+++ b/Statistics/ConfidenceInt.hs
@@ -30,7 +30,7 @@ poissonNormalCI n
poissonCI :: CL Double -> Int -> Estimate ConfInt Double
poissonCI cl@(significanceLevel -> p) n
| n < 0 = error "Statistics.ConfidenceInt.poissonCI: negative number of trials"
- | n == 0 = estimateFromInterval m (m1,m2) cl
+ | n == 0 = estimateFromInterval m (0 ,m2) cl
| otherwise = estimateFromInterval m (m1,m2) cl
where
m = fromIntegral n
diff --git a/Statistics/Distribution/Exponential.hs b/Statistics/Distribution/Exponential.hs
index 357e5ff..b1cb00e 100644
--- a/Statistics/Distribution/Exponential.hs
+++ b/Statistics/Distribution/Exponential.hs
@@ -30,7 +30,7 @@ import Data.Aeson (FromJSON(..),ToJSON,Value(..),(.:))
import Data.Binary (Binary, put, get)
import Data.Data (Data, Typeable)
import GHC.Generics (Generic)
-import Numeric.SpecFunctions (log1p)
+import Numeric.SpecFunctions (log1p,expm1)
import Numeric.MathFunctions.Constants (m_neg_inf)
import qualified System.Random.MWC.Distributions as MWC
import qualified Data.Vector.Generic as G
@@ -101,7 +101,7 @@ instance D.ContGen ExponentialDistribution where
cumulative :: ExponentialDistribution -> Double -> Double
cumulative (ED l) x | x <= 0 = 0
- | otherwise = 1 - exp (-l * x)
+ | otherwise = - expm1 (-l * x)
complCumulative :: ExponentialDistribution -> Double -> Double
complCumulative (ED l) x | x <= 0 = 1
diff --git a/Statistics/Distribution/Geometric.hs b/Statistics/Distribution/Geometric.hs
index 30f4c3f..6eaa502 100644
--- a/Statistics/Distribution/Geometric.hs
+++ b/Statistics/Distribution/Geometric.hs
@@ -40,6 +40,7 @@ import Data.Binary (Binary(..))
import Data.Data (Data, Typeable)
import GHC.Generics (Generic)
import Numeric.MathFunctions.Constants (m_pos_inf, m_neg_inf)
+import Numeric.SpecFunctions (log1p,expm1)
import qualified System.Random.MWC.Distributions as MWC
import qualified Statistics.Distribution as D
@@ -74,7 +75,8 @@ instance Binary GeometricDistribution where
instance D.Distribution GeometricDistribution where
- cumulative = cumulative
+ cumulative = cumulative
+ complCumulative = complCumulative
instance D.DiscreteDistr GeometricDistribution where
probability (GD s) n
@@ -118,7 +120,14 @@ cumulative (GD s) x
| x < 1 = 0
| isInfinite x = 1
| isNaN x = error "Statistics.Distribution.Geometric.cumulative: NaN input"
- | otherwise = 1 - (1-s) ^ (floor x :: Int)
+ | otherwise = negate $ expm1 $ fromIntegral (floor x :: Int) * log1p (-s)
+
+complCumulative :: GeometricDistribution -> Double -> Double
+complCumulative (GD s) x
+ | x < 1 = 1
+ | isInfinite x = 0
+ | isNaN x = error "Statistics.Distribution.Geometric.cumulative: NaN input"
+ | otherwise = exp $ fromIntegral (floor x :: Int) * log1p (-s)
-- | Create geometric distribution.
@@ -164,7 +173,8 @@ instance Binary GeometricDistribution0 where
instance D.Distribution GeometricDistribution0 where
- cumulative (GD0 s) x = cumulative (GD s) (x + 1)
+ cumulative (GD0 s) x = cumulative (GD s) (x + 1)
+ complCumulative (GD0 s) x = complCumulative (GD s) (x + 1)
instance D.DiscreteDistr GeometricDistribution0 where
probability (GD0 s) n = D.probability (GD s) (n + 1)
diff --git a/Statistics/Sample/Histogram.hs b/Statistics/Sample/Histogram.hs
index 7579286..96e9efd 100644
--- a/Statistics/Sample/Histogram.hs
+++ b/Statistics/Sample/Histogram.hs
@@ -73,7 +73,7 @@ histogram_ numBins lo hi xs0 = G.create (GM.replicate numBins 0 >>= bin xs0)
b = truncate $ (x - lo) / d
write' bins b . (+1) =<< GM.read bins b
go (i+1)
- write' bins b !e = GM.write bins b e
+ write' bins' b !e = GM.write bins' b e
len = G.length xs
d = ((hi - lo) * (1 + realToFrac m_epsilon)) / fromIntegral numBins
{-# INLINE histogram_ #-}
diff --git a/changelog.md b/changelog.md
index 7ea5c2b..50bdd0a 100755
--- a/changelog.md
+++ b/changelog.md
@@ -1,3 +1,16 @@
+## Changes in 0.15.2.0
+
+ * Test suite is finally fixed (#42, #123). It took very-very-very long
+ time but finally happened.
+
+ * Avoid loss of precision when computing CDF for exponential districution.
+
+ * Avoid loss of precision when computing CDF for geometric districution. Add
+ complement of CDF.
+
+ * Correctly handle case of n=0 in poissonCI
+
+
## Changes in 0.15.1.1
* Fix build for GHC8.0 & 7.10
diff --git a/statistics.cabal b/statistics.cabal
index 04d25cd..d4954e9 100644
--- a/statistics.cabal
+++ b/statistics.cabal
@@ -1,5 +1,5 @@
name: statistics
-version: 0.15.1.1
+version: 0.15.2.0
synopsis: A library of statistical types, data, and functions
description:
This library provides a number of common functions and types useful
@@ -54,6 +54,7 @@ tested-with:
|| ==8.2.2
|| ==8.4.4
|| ==8.6.5
+ || ==8.8.1
, GHCJS ==8.4
@@ -158,7 +159,6 @@ test-suite tests
build-depends: base
, statistics
, dense-linear-algebra
- , HUnit
, QuickCheck >= 2.7.5
, binary
, erf
@@ -167,9 +167,10 @@ test-suite tests
, math-functions
, mwc-random
, primitive
- , test-framework
- , test-framework-hunit
- , test-framework-quickcheck2
+ , tasty
+ , tasty-hunit
+ , tasty-quickcheck
+ , tasty-expected-failure
, vector
, vector-algorithms
diff --git a/tests/Tests/Correlation.hs b/tests/Tests/Correlation.hs
index 0e50278..7563583 100644
--- a/tests/Tests/Correlation.hs
+++ b/tests/Tests/Correlation.hs
@@ -8,10 +8,9 @@ import qualified Data.Vector as V
import Statistics.Correlation
import Statistics.Correlation.Kendall
import Test.QuickCheck ((==>),Property,counterexample)
-import Test.Framework
-import Test.Framework.Providers.QuickCheck2
-import Test.Framework.Providers.HUnit
-import Test.HUnit (Assertion, (@=?))
+import Test.Tasty
+import Test.Tasty.QuickCheck
+import Test.Tasty.HUnit
import Tests.ApproxEq
@@ -19,7 +18,7 @@ import Tests.ApproxEq
-- Tests list
----------------------------------------------------------------
-tests :: Test
+tests :: TestTree
tests = testGroup "Correlation"
[ testProperty "Pearson correlation" testPearson
, testProperty "Spearman correlation is scale invariant" testSpearmanScale
diff --git a/tests/Tests/Distribution.hs b/tests/Tests/Distribution.hs
index 070485d..e07b5ba 100644
--- a/tests/Tests/Distribution.hs
+++ b/tests/Tests/Distribution.hs
@@ -1,4 +1,4 @@
-{-# LANGUAGE FlexibleInstances, OverlappingInstances, ScopedTypeVariables,
+{-# LANGUAGE FlexibleInstances, ScopedTypeVariables,
ViewPatterns #-}
module Tests.Distribution (tests) where
@@ -6,8 +6,7 @@ import Control.Applicative ((<$), (<$>), (<*>))
import qualified Control.Exception as E
import Data.List (find)
import Data.Typeable (Typeable)
-import qualified Numeric.IEEE as IEEE
-import Numeric.MathFunctions.Constants (m_tiny,m_epsilon)
+import Numeric.MathFunctions.Constants (m_tiny,m_huge,m_epsilon)
import Numeric.MathFunctions.Comparison
import Statistics.Distribution
import Statistics.Distribution.Beta (BetaDistribution)
@@ -23,11 +22,12 @@ import Statistics.Distribution.Laplace (LaplaceDistribution)
import Statistics.Distribution.Normal (NormalDistribution)
import Statistics.Distribution.Poisson (PoissonDistribution)
import Statistics.Distribution.StudentT
-import Statistics.Distribution.Transform (LinearTransform, linTransDistr)
+import Statistics.Distribution.Transform (LinearTransform)
import Statistics.Distribution.Uniform (UniformDistribution)
-import Statistics.Distribution.DiscreteUniform (DiscreteUniform, discreteUniformAB)
-import Test.Framework (Test, testGroup)
-import Test.Framework.Providers.QuickCheck2 (testProperty)
+import Statistics.Distribution.DiscreteUniform (DiscreteUniform)
+import Test.Tasty (TestTree, testGroup)
+import Test.Tasty.QuickCheck (testProperty)
+import Test.Tasty.ExpectedFailure (ignoreTest)
import Test.QuickCheck as QC
import Test.QuickCheck.Monadic as QC
import Text.Printf (printf)
@@ -38,7 +38,7 @@ import Tests.Helpers (monotonicallyIncreasesIEEE,isDenorm)
import Tests.Orphanage ()
-- | Tests for all distributions
-tests :: Test
+tests :: TestTree
tests = testGroup "Tests for all distributions"
[ contDistrTests (T :: T BetaDistribution )
, contDistrTests (T :: T CauchyDistribution )
@@ -67,18 +67,20 @@ tests = testGroup "Tests for all distributions"
----------------------------------------------------------------
-- Tests for continuous distribution
-contDistrTests :: (Param d, ContDistr d, QC.Arbitrary d, Typeable d, Show d) => T d -> Test
+contDistrTests :: (Param d, ContDistr d, QC.Arbitrary d, Typeable d, Show d) => T d -> TestTree
contDistrTests t = testGroup ("Tests for: " ++ typeName t) $
cdfTests t ++
[ testProperty "PDF sanity" $ pdfSanityCheck t
- , testProperty "Quantile is CDF inverse" $ quantileIsInvCDF t
+ ] ++
+ [ (if quantileIsInvCDF_enabled t then id else ignoreTest)
+ $ testProperty "Quantile is CDF inverse" $ quantileIsInvCDF t
, testProperty "quantile fails p<0||p>1" $ quantileShouldFail t
, testProperty "log density check" $ logDensityCheck t
, testProperty "complQuantile" $ complQuantileCheck t
]
-- Tests for discrete distribution
-discreteDistrTests :: (Param d, DiscreteDistr d, QC.Arbitrary d, Typeable d, Show d) => T d -> Test
+discreteDistrTests :: (Param d, DiscreteDistr d, QC.Arbitrary d, Typeable d, Show d) => T d -> TestTree
discreteDistrTests t = testGroup ("Tests for: " ++ typeName t) $
cdfTests t ++
[ testProperty "Prob. sanity" $ probSanityCheck t
@@ -88,7 +90,7 @@ discreteDistrTests t = testGroup ("Tests for: " ++ typeName t) $
]
-- Tests for distributions which have CDF
-cdfTests :: (Param d, Distribution d, QC.Arbitrary d, Show d) => T d -> [Test]
+cdfTests :: (Param d, Distribution d, QC.Arbitrary d, Show d) => T d -> [TestTree]
cdfTests t =
[ testProperty "C.D.F. sanity" $ cdfSanityCheck t
, testProperty "CDF limit at +inf" $ cdfLimitAtPosInfinity t
@@ -122,29 +124,33 @@ cdfAtNegInfinity _ d
= cumulative d (-1/0) == 0
-- CDF limit at +∞ is 1
-cdfLimitAtPosInfinity :: (Param d, Distribution d) => T d -> d -> Property
-cdfLimitAtPosInfinity _ d =
- okForInfLimit d ==> counterexample ("Last elements: " ++ show (drop 990 probs))
- $ Just 1.0 == (find (>=1) probs)
+cdfLimitAtPosInfinity :: (Param d, Distribution d) => T d -> d -> Bool
+cdfLimitAtPosInfinity _ d
+ = Just 1.0 == find (>=1) probs
where
- probs = take 1000 $ map (cumulative d) $ iterate (*1.4) 1000
+ probs = map (cumulative d)
+ $ takeWhile (< (m_huge/2))
+ $ iterate (*1.4) 1
-- CDF limit at -∞ is 0
-cdfLimitAtNegInfinity :: (Param d, Distribution d) => T d -> d -> Property
-cdfLimitAtNegInfinity _ d =
- okForInfLimit d ==> counterexample ("Last elements: " ++ show (drop 990 probs))
- $ case find (< IEEE.epsilon) probs of
- Nothing -> False
- Just p -> p >= 0
+cdfLimitAtNegInfinity :: (Param d, Distribution d) => T d -> d -> Bool
+cdfLimitAtNegInfinity _ d
+ = Just 0 == find (<=0) probs
where
- probs = take 1000 $ map (cumulative d) $ iterate (*1.4) (-1)
+ probs = map (cumulative d)
+ $ takeWhile (> (-m_huge/2))
+ $ iterate (*1.4) (-1)
+
-- CDF's complement is implemented correctly
-cdfComplementIsCorrect :: (Distribution d) => T d -> d -> Double -> Bool
-cdfComplementIsCorrect _ d x = (eq 1e-14) 1 (cumulative d x + complCumulative d x)
+cdfComplementIsCorrect :: (Distribution d, Param d) => T d -> d -> Double -> Bool
+cdfComplementIsCorrect _ d x
+ = 1 - (cumulative d x + complCumulative d x) <= tol
+ where
+ tol = prec_complementCDF d
-- CDF for discrete distribution uses <= for comparison
-cdfDiscreteIsCorrect :: (DiscreteDistr d) => T d -> d -> Property
+cdfDiscreteIsCorrect :: (Param d, DiscreteDistr d) => T d -> d -> Property
cdfDiscreteIsCorrect _ d
= counterexample (unlines badN)
$ null badN
@@ -163,8 +169,9 @@ cdfDiscreteIsCorrect _ d
dp = probability d i
relerr = ((p1 - p) - dp) / max p1 dp
, not (p == 0 && p1 == 0 && dp == 0)
- && relerr > 1e-14
+ && relerr > tol
]
+ tol = prec_discreteCDF d
logDensityCheck :: (ContDistr d) => T d -> d -> Double -> Property
logDensityCheck _ d x
@@ -175,7 +182,11 @@ logDensityCheck _ d x
$ counterexample (printf "eps = %g" (abs (logP - log p) / max (abs (log p)) (abs logP)))
$ or [ p == 0 && logP == (-1/0)
, p <= m_tiny && logP < log m_tiny
- , eq 1e-14 (log p) logP
+ -- To avoid problems with roundtripping error in case
+ -- when density is computed as exponent of logDensity we
+ -- accept either inequality
+ , (ulpDistance (log p) logP <= 32)
+ || (ulpDistance p (exp logP) <= 32)
])
where
p = density d x
@@ -187,19 +198,25 @@ pdfSanityCheck _ d x = p >= 0
where p = density d x
complQuantileCheck :: (ContDistr d) => T d -> d -> Double01 -> Property
-complQuantileCheck _ d (Double01 p) =
+complQuantileCheck _ d (Double01 p)
+ = counterexample (printf "x0 = %g" x0)
+ $ counterexample (printf "x1 = %g" x1)
-- We avoid extreme tails of distributions
--
-- FIXME: all parameters are arbitrary at the moment
- p > 0.01 && p < 0.99 ==> (abs (x1 - x0) < 1e-6)
+ $ and [ p > 0.01
+ , p < 0.99
+ , not $ isInfinite x0
+ , not $ isInfinite x1
+ ] ==> (abs (x1 - x0) < 1e-6)
where
x0 = quantile d (1 - p)
x1 = complQuantile d p
-- Quantile is inverse of CDF
-quantileIsInvCDF :: (ContDistr d) => T d -> d -> Double01 -> Property
+quantileIsInvCDF :: (Param d, ContDistr d) => T d -> d -> Double01 -> Property
quantileIsInvCDF _ d (Double01 p) =
- and [ p > 1e-250
+ and [ p > m_tiny
, p < 1
, x > m_tiny
, dens > 0
@@ -207,20 +224,23 @@ quantileIsInvCDF _ d (Double01 p) =
( counterexample (printf "Quantile = %g" x )
$ counterexample (printf "Probability = %g" p )
$ counterexample (printf "Probability' = %g" p')
- $ counterexample (printf "Expected err. = %g" err)
$ counterexample (printf "Rel. error = %g" (relativeError p p'))
$ counterexample (printf "Abs. error = %e" (abs $ p - p'))
- $ eqRelErr err p p'
+ $ counterexample (printf "Expected err. = %g" err)
+ $ counterexample (printf "Distance = %i" (ulpDistance p p'))
+ $ counterexample (printf "Err/est = %g" (fromIntegral (ulpDistance p p') / err))
+ $ ulpDistance p p' <= round err
)
where
-- Algorithm for error estimation is taken from here
--
-- http://sepulcarium.org/posts/2012-07-19-rounding_effect_on_inverse.html
dens = density d x
- err = 64 * m_epsilon * (1 + abs (x / p) * dens)
+ err = eps + eps' * abs (x / p) * dens
--
x = quantile d p
p' = cumulative d x
+ (eps,eps') = prec_quantile_CDF d
-- Test that quantile fails if p<0 or p>1
quantileShouldFail :: (ContDistr d) => T d -> d -> Double -> Property
@@ -261,36 +281,60 @@ logProbabilityCheck _ d x
$ counterexample (printf "eps = %g" (abs (logP - log p) / max (abs (log p)) (abs logP)))
$ or [ p == 0 && logP == (-1/0)
, p < 1e-308 && logP < 609
- , eq 1e-14 (log p) logP
+ -- To avoid problems with roundtripping error in case
+ -- when density is computed as exponent of logDensity we
+ -- accept either inequality
+ , (ulpDistance (log p) logP <= 32)
+ || (ulpDistance p (exp logP) <= 32)
]
where
p = probability d x
logP = logProbability d x
--- Parameters for distribution testing. Some distribution require
--- relaxing parameters a bit
+-- | Parameters for distribution testing. Some distribution require
+-- relaxing parameters a bit
class Param a where
- -- Precision for quantileIsInvCDF
- invQuantilePrec :: a -> Double
- invQuantilePrec _ = 1e-14
- -- Distribution is OK for testing limits
- okForInfLimit :: a -> Bool
- okForInfLimit _ = True
-
-
-instance Param a
+ -- | Whether quantileIsInvCDF is enabled
+ quantileIsInvCDF_enabled :: T a -> Bool
+ quantileIsInvCDF_enabled _ = True
+ -- | Precision for 'quantileIsInvCDF' test
+ prec_quantile_CDF :: a -> (Double,Double)
+ prec_quantile_CDF _ = (16,16)
+ -- |
+ prec_discreteCDF :: a -> Double
+ prec_discreteCDF _ = 32 * m_epsilon
+ -- | Precision of CDF's complement
+ prec_complementCDF :: a -> Double
+ prec_complementCDF _ = 1e-14
instance Param StudentT where
- invQuantilePrec _ = 1e-13
- okForInfLimit d = studentTndf d > 0.75
+ -- FIXME: disabled unless incompleteBeta troubles are sorted out
+ quantileIsInvCDF_enabled _ = False
+instance Param BetaDistribution where
+ -- FIXME: See https://github.com/bos/statistics/issues/161 for details
+ quantileIsInvCDF_enabled _ = False
+instance Param FDistribution where
+ -- FIXME: disabled unless incompleteBeta troubles are sorted out
+ quantileIsInvCDF_enabled _ = False
-instance Param (LinearTransform StudentT) where
- invQuantilePrec _ = 1e-13
- okForInfLimit d = (studentTndf . linTransDistr) d > 0.75
+instance Param ChiSquared where
+ prec_quantile_CDF _ = (32,32)
-instance Param FDistribution where
- invQuantilePrec _ = 1e-12
+instance Param BinomialDistribution where
+ prec_discreteCDF _ = 1e-13
+instance Param CauchyDistribution
+instance Param DiscreteUniform
+instance Param ExponentialDistribution
+instance Param GammaDistribution
+instance Param GeometricDistribution
+instance Param GeometricDistribution0
+instance Param HypergeometricDistribution
+instance Param LaplaceDistribution
+instance Param NormalDistribution
+instance Param PoissonDistribution
+instance Param UniformDistribution
+instance Param a => Param (LinearTransform a)
@@ -298,7 +342,7 @@ instance Param FDistribution where
-- Unit tests
----------------------------------------------------------------
-unitTests :: Test
+unitTests :: TestTree
unitTests = testGroup "Unit tests"
[ testAssertion "density (gammaDistr 150 1/150) 1 == 4.883311" $
4.883311418525483 =~ density (gammaDistr 150 (1/150)) 1
diff --git a/tests/Tests/Function.hs b/tests/Tests/Function.hs
index 42b54cc..256c3b6 100644
--- a/tests/Tests/Function.hs
+++ b/tests/Tests/Function.hs
@@ -1,14 +1,14 @@
module Tests.Function ( tests ) where
import Statistics.Function
-import Test.Framework
-import Test.Framework.Providers.QuickCheck2
+import Test.Tasty
+import Test.Tasty.QuickCheck
import Test.QuickCheck
import Tests.Helpers
import qualified Data.Vector.Unboxed as U
-tests :: Test
+tests :: TestTree
tests = testGroup "S.Function"
[ testProperty "Sort is sort" p_sort
, testAssertion "nextHighestPowerOfTwo is OK" p_nextHighestPowerOfTwo
diff --git a/tests/Tests/Helpers.hs b/tests/Tests/Helpers.hs
index eb35115..5818ede 100644
--- a/tests/Tests/Helpers.hs
+++ b/tests/Tests/Helpers.hs
@@ -21,11 +21,11 @@ module Tests.Helpers (
import Data.Typeable
import Numeric.MathFunctions.Constants (m_tiny)
-import Test.Framework
-import Test.Framework.Providers.HUnit
+import Test.Tasty
+import Test.Tasty.HUnit
import Test.QuickCheck
-import qualified Numeric.IEEE as IEEE
-import qualified Test.HUnit as HU
+import qualified Numeric.IEEE as IEEE
+import qualified Test.Tasty.HUnit as HU
-- | Phantom typed value used to select right instance in QC tests
data T a = T
@@ -75,10 +75,10 @@ monotonicallyIncreasesIEEE f x1 x2 =
-- HUnit helpers
----------------------------------------------------------------
-testAssertion :: String -> Bool -> Test
+testAssertion :: String -> Bool -> TestTree
testAssertion str cont = testCase str $ HU.assertBool str cont
-testEquality :: (Show a, Eq a) => String -> a -> a -> Test
+testEquality :: (Show a, Eq a) => String -> a -> a -> TestTree
testEquality msg a b = testCase msg $ HU.assertEqual msg a b
unsquare :: (Arbitrary a, Show a, Testable b) => (a -> b) -> Property
diff --git a/tests/Tests/KDE.hs b/tests/Tests/KDE.hs
index c77fb13..10c8711 100644
--- a/tests/Tests/KDE.hs
+++ b/tests/Tests/KDE.hs
@@ -3,17 +3,17 @@ module Tests.KDE (
tests
)where
-import Data.Vector.Unboxed ((!))
-import Numeric.Sum (kbn, sumVector)
+import Data.Vector.Unboxed ((!))
+import Numeric.Sum (kbn, sumVector)
import Statistics.Sample.KernelDensity
-import Test.Framework (Test, testGroup)
-import Test.Framework.Providers.QuickCheck2 (testProperty)
-import Test.QuickCheck (Property, (==>), counterexample)
-import Text.Printf (printf)
+import Test.Tasty (TestTree, testGroup)
+import Test.Tasty.QuickCheck (testProperty)
+import Test.QuickCheck (Property, (==>), counterexample)
+import Text.Printf (printf)
import qualified Data.Vector.Unboxed as U
-tests :: Test
+tests :: TestTree
tests = testGroup "KDE"
[ testProperty "integral(PDF) == 1" t_densityIsPDF
]
diff --git a/tests/Tests/Matrix.hs b/tests/Tests/Matrix.hs
index cce9e2d..a8dc9ee 100644
--- a/tests/Tests/Matrix.hs
+++ b/tests/Tests/Matrix.hs
@@ -2,8 +2,8 @@ module Tests.Matrix (tests) where
import Statistics.Matrix hiding (map)
import Statistics.Matrix.Algorithms
-import Test.Framework (Test, testGroup)
-import Test.Framework.Providers.QuickCheck2 (testProperty)
+import Test.Tasty (TestTree, testGroup)
+import Test.Tasty.QuickCheck (testProperty)
import Test.QuickCheck
import Tests.ApproxEq (ApproxEq(..))
import Tests.Matrix.Types
@@ -31,9 +31,9 @@ t_qr :: Matrix -> Property
t_qr a = hasNaN p .||. eql 1e-10 a p
where p = uncurry multiply (qr a)
-tests :: Test
-tests = testGroup "Matrix" [
- testProperty "t_row" t_row
+tests :: TestTree
+tests = testGroup "Matrix"
+ [ testProperty "t_row" t_row
, testProperty "t_column" t_column
, testProperty "t_center" t_center
, testProperty "t_transpose" t_transpose
diff --git a/tests/Tests/NonParametric.hs b/tests/Tests/NonParametric.hs
index e7086f5..a37add1 100644
--- a/tests/Tests/NonParametric.hs
+++ b/tests/Tests/NonParametric.hs
@@ -10,17 +10,16 @@ import Statistics.Test.KruskalWallis
import Statistics.Test.WilcoxonT
import Statistics.Types (PValue,pValue,mkPValue)
-import Test.Framework (testGroup)
-import Test.Framework.Providers.HUnit
-import qualified Test.Framework as Tst
-import Test.HUnit (assertEqual)
-import Tests.ApproxEq (eq)
-import Tests.Helpers (testAssertion, testEquality)
+import Test.Tasty (testGroup)
+import Test.Tasty.HUnit
+import Tests.ApproxEq (eq)
+import Tests.Helpers (testAssertion, testEquality)
import Tests.NonParametric.Table (tableKSD, tableKS2D)
+import qualified Test.Tasty as Tst
import qualified Data.Vector.Unboxed as U
-tests :: Tst.Test
+tests :: Tst.TestTree
tests = testGroup "Nonparametric tests"
$ concat [ mannWhitneyTests
, wilcoxonSumTests
@@ -32,7 +31,7 @@ tests = testGroup "Nonparametric tests"
----------------------------------------------------------------
-mannWhitneyTests :: [Tst.Test]
+mannWhitneyTests :: [Tst.TestTree]
mannWhitneyTests = zipWith test [(0::Int)..] testData ++
[ testEquality "Mann-Whitney U Critical Values, m=1"
(replicate (20*3) Nothing)
@@ -89,7 +88,7 @@ mannWhitneyTests = zipWith test [(0::Int)..] testData ++
)
]
-wilcoxonSumTests :: [Tst.Test]
+wilcoxonSumTests :: [Tst.TestTree]
wilcoxonSumTests = zipWith test [(0::Int)..] testData
where
test n (a, b, c) = testCase "Wilcoxon Sum"
@@ -106,7 +105,7 @@ wilcoxonSumTests = zipWith test [(0::Int)..] testData
)
]
-wilcoxonPairTests :: [Tst.Test]
+wilcoxonPairTests :: [Tst.TestTree]
wilcoxonPairTests = zipWith test [(0::Int)..] testData ++
-- Taken from the Mitic paper:
[ testAssertion "Sig 16, 35" (to4dp 0.0467 $ wilcoxonMatchedPairSignificance 16 35)
@@ -158,7 +157,7 @@ wilcoxonPairTests = zipWith test [(0::Int)..] testData ++
----------------------------------------------------------------
-kruskalWallisRankTests :: [Tst.Test]
+kruskalWallisRankTests :: [Tst.TestTree]
kruskalWallisRankTests = zipWith test [(0::Int)..] testData
where
test n (a, b) = testCase "Kruskal-Wallis Ranking"
@@ -177,7 +176,7 @@ kruskalWallisRankTests = zipWith test [(0::Int)..] testData
)
]
-kruskalWallisTests :: [Tst.Test]
+kruskalWallisTests :: [Tst.TestTree]
kruskalWallisTests = zipWith test [(0::Int)..] testData
where
test n (a, b, c) = testCase "Kruskal-Wallis" $ do
@@ -228,7 +227,7 @@ kruskalWallisTests = zipWith test [(0::Int)..] testData
----------------------------------------------------------------
-kolmogorovSmirnovDTest :: [Tst.Test]
+kolmogorovSmirnovDTest :: [Tst.TestTree]
kolmogorovSmirnovDTest =
[ testAssertion "K-S D statistics" $
and [ eq 1e-6 (kolmogorovSmirnovD standard (toU sample)) reference
diff --git a/tests/Tests/Parametric.hs b/tests/Tests/Parametric.hs
index 11fb2e4..e2ffd9b 100644
--- a/tests/Tests/Parametric.hs
+++ b/tests/Tests/Parametric.hs
@@ -4,11 +4,11 @@ import Data.Maybe (fromJust)
import Statistics.Test.StudentT
import Statistics.Types
import qualified Data.Vector.Unboxed as U
-import Test.Framework (testGroup)
+import Test.Tasty (testGroup)
import Tests.Helpers (testEquality)
-import qualified Test.Framework as Tst
+import qualified Test.Tasty as Tst
-tests :: Tst.Test
+tests :: Tst.TestTree
tests = testGroup "Parametric tests" studentTTests
-- 2 samples x 20 obs data
@@ -71,14 +71,14 @@ sample2 = U.fromList [
testTTest :: String
-> PValue Double
-> Test d
- -> [Tst.Test]
+ -> [Tst.TestTree]
testTTest name pVal test =
[ testEquality name (isSignificant pVal test) NotSignificant
, testEquality name (isSignificant (mkPValue $ pValue pVal + 1e-5) test)
Significant
]
-studentTTests :: [Tst.Test]
+studentTTests :: [Tst.TestTree]
studentTTests = concat
[ -- R: t.test(sample1, sample2, alt="two.sided", var.equal=T)
testTTest "two-sample t-test SamplesDiffer Student"
diff --git a/tests/Tests/Quantile.hs b/tests/Tests/Quantile.hs
index 12a310f..256ae66 100644
--- a/tests/Tests/Quantile.hs
+++ b/tests/Tests/Quantile.hs
@@ -5,15 +5,13 @@ module Tests.Quantile (tests) where
import Control.Exception
import qualified Data.Vector.Unboxed as U
-import Test.Framework
-import Test.Framework.Providers.HUnit
-import Test.Framework.Providers.QuickCheck2
-import Test.HUnit (Assertion,assertEqual,assertFailure)
-import Test.QuickCheck hiding (sample)
+import Test.Tasty
+import Test.Tasty.HUnit
+import Test.Tasty.QuickCheck hiding (sample)
import Numeric.MathFunctions.Comparison (ulpDelta,ulpDistance)
import Statistics.Quantile
-tests :: Test
+tests :: TestTree
tests = testGroup "Quantiles"
[ testCase "R alg. 4" $ compareWithR cadpw (0.00, 0.50, 2.50, 8.25, 10.00)
, testCase "R alg. 5" $ compareWithR hazen (0.00, 1.00, 5.00, 9.00, 10.00)
diff --git a/tests/Tests/Serialization.hs b/tests/Tests/Serialization.hs
index c2a02ff..410b9cd 100644
--- a/tests/Tests/Serialization.hs
+++ b/tests/Tests/Serialization.hs
@@ -23,15 +23,15 @@ import Statistics.Distribution.Transform (LinearTransform)
import Statistics.Distribution.Uniform (UniformDistribution)
import Statistics.Types
-import Test.Framework (Test, testGroup)
-import Test.Framework.Providers.QuickCheck2 (testProperty)
+import Test.Tasty (TestTree, testGroup)
+import Test.Tasty.QuickCheck (testProperty)
import Test.QuickCheck as QC
import Tests.Helpers
import Tests.Orphanage ()
-tests :: Test
+tests :: TestTree
tests = testGroup "Test for data serialization"
[ serializationTests (T :: T (CL Float))
, serializationTests (T :: T (CL Double))
@@ -65,13 +65,13 @@ tests = testGroup "Test for data serialization"
serializationTests
:: (Eq a, Typeable a, Binary a, Show a, Read a, ToJSON a, FromJSON a, Arbitrary a)
- => T a -> Test
+ => T a -> TestTree
serializationTests t = serializationTests' (typeName t) t
-- Not all types are Typeable, unfortunately
serializationTests'
:: (Eq a, Binary a, Show a, Read a, ToJSON a, FromJSON a, Arbitrary a)
- => String -> T a -> Test
+ => String -> T a -> TestTree
serializationTests' name t = testGroup ("Tests for: " ++ name)
[ testProperty "show/read" (p_showRead t)
, testProperty "binary" (p_binary t)
diff --git a/tests/Tests/Transform.hs b/tests/Tests/Transform.hs
index 64a6b1d..1552b0c 100644
--- a/tests/Tests/Transform.hs
+++ b/tests/Tests/Transform.hs
@@ -12,8 +12,8 @@ import Data.Functor ((<$>))
import Numeric.Sum (kbn, sumVector)
import Statistics.Function (within)
import Statistics.Transform (CD, dct, fft, idct, ifft)
-import Test.Framework (Test, testGroup)
-import Test.Framework.Providers.QuickCheck2 (testProperty)
+import Test.Tasty (TestTree, testGroup)
+import Test.Tasty.QuickCheck (testProperty)
import Test.QuickCheck ( Positive(..), Arbitrary(..), Blind(..), (==>), Gen
, choose, vectorOf, counterexample, forAll)
import Test.QuickCheck.Property (Property(..))
@@ -23,7 +23,7 @@ import qualified Data.Vector.Generic as G
import qualified Data.Vector.Unboxed as U
-tests :: Test
+tests :: TestTree
tests = testGroup "fft" [
testProperty "t_impulse" t_impulse
, testProperty "t_impulse_offset" t_impulse_offset
@@ -103,13 +103,13 @@ t_fftInverse roundtrip =
$ nd <= 3e-14 * nx
-- Test discrete cosine transform
-testDCT :: [Double] -> [Double] -> Test
+testDCT :: [Double] -> [Double] -> TestTree
testDCT (U.fromList -> vec) (U.fromList -> res)
= testAssertion ("DCT test for " ++ show vec)
$ vecEqual 3e-14 (dct vec) res
-- Test inverse discrete cosine transform
-testIDCT :: [Double] -> [Double] -> Test
+testIDCT :: [Double] -> [Double] -> TestTree
testIDCT (U.fromList -> vec) (U.fromList -> res)
= testAssertion ("IDCT test for " ++ show vec)
$ vecEqual 3e-14 (idct vec) res
diff --git a/tests/tests.hs b/tests/tests.hs
index 7c8e395..a0059e8 100644
--- a/tests/tests.hs
+++ b/tests/tests.hs
@@ -1,4 +1,4 @@
-import Test.Framework (defaultMain)
+import Test.Tasty (defaultMain,testGroup)
import qualified Tests.Distribution
import qualified Tests.Function
@@ -12,14 +12,15 @@ import qualified Tests.Serialization
import qualified Tests.Quantile
main :: IO ()
-main = defaultMain [ Tests.Distribution.tests
- , Tests.Function.tests
- , Tests.KDE.tests
- , Tests.Matrix.tests
- , Tests.NonParametric.tests
- , Tests.Parametric.tests
- , Tests.Transform.tests
- , Tests.Correlation.tests
- , Tests.Serialization.tests
- , Tests.Quantile.tests
- ]
+main = defaultMain $ testGroup "statistics"
+ [ Tests.Distribution.tests
+ , Tests.Function.tests
+ , Tests.KDE.tests
+ , Tests.Matrix.tests
+ , Tests.NonParametric.tests
+ , Tests.Parametric.tests
+ , Tests.Transform.tests
+ , Tests.Correlation.tests
+ , Tests.Serialization.tests
+ , Tests.Quantile.tests
+ ]