first

Author: ocramz

statistics-dense-linear-algebra/README.md

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+# statistics-dense-linear-algebra
+
+[![Build Status](https://travis-ci.org/githubuser/statistics-dense-linear-algebra.png)](https://travis-ci.org/githubuser/statistics-dense-linear-algebra)
+
+TODO Description.

statistics-dense-linear-algebra/Setup.hs

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+import Distribution.Simple
+main = defaultMain

statistics-dense-linear-algebra/src/Statistics/Function.hs

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+{-# LANGUAGE BangPatterns, CPP, FlexibleContexts, Rank2Types #-}
+{-# OPTIONS_GHC -fsimpl-tick-factor=200 #-}
+-- |
+-- Module    : Statistics.Function
+-- Copyright : (c) 2009, 2010, 2011 Bryan O'Sullivan
+-- License   : BSD3
+--
+-- Maintainer  : [email protected]
+-- Stability   : experimental
+-- Portability : portable
+--
+-- Useful functions.
+
+module Statistics.Function
+    (
+    -- * Scanning
+      minMax
+    -- * Sorting
+    , sort
+    , gsort
+    , sortBy
+    , partialSort
+    -- * Indexing
+    , indexed
+    , indices
+    -- * Bit twiddling
+    , nextHighestPowerOfTwo
+    -- * Comparison
+    , within
+    -- * Arithmetic
+    , square
+    -- * Vectors
+    , unsafeModify
+    -- * Combinators
+    , for
+    , rfor
+    ) where
+
+#include "MachDeps.h"
+
+import Control.Monad.ST (ST)
+import Data.Bits ((.|.), shiftR)
+import qualified Data.Vector.Algorithms.Intro as I
+import qualified Data.Vector.Generic as G
+import qualified Data.Vector.Unboxed as U
+import qualified Data.Vector.Unboxed.Mutable as M
+import Numeric.MathFunctions.Comparison (within)
+
+-- | Sort a vector.
+sort :: U.Vector Double -> U.Vector Double
+sort = G.modify I.sort
+{-# NOINLINE sort #-}
+
+-- | Sort a vector.
+gsort :: (Ord e, G.Vector v e) => v e -> v e
+gsort = G.modify I.sort
+{-# INLINE gsort #-}
+
+-- | Sort a vector using a custom ordering.
+sortBy :: (G.Vector v e) => I.Comparison e -> v e -> v e
+sortBy f = G.modify $ I.sortBy f
+{-# INLINE sortBy #-}
+
+-- | Partially sort a vector, such that the least /k/ elements will be
+-- at the front.
+partialSort :: (G.Vector v e, Ord e) =>
+               Int -- ^ The number /k/ of least elements.
+            -> v e
+            -> v e
+partialSort k = G.modify (`I.partialSort` k)
+{-# SPECIALIZE partialSort :: Int -> U.Vector Double -> U.Vector Double #-}
+
+-- | Return the indices of a vector.
+indices :: (G.Vector v a, G.Vector v Int) => v a -> v Int
+indices a = G.enumFromTo 0 (G.length a - 1)
+{-# INLINE indices #-}
+
+-- | Zip a vector with its indices.
+indexed :: (G.Vector v e, G.Vector v Int, G.Vector v (Int,e)) => v e -> v (Int,e)
+indexed a = G.zip (indices a) a
+{-# INLINE indexed #-}
+
+data MM = MM {-# UNPACK #-} !Double {-# UNPACK #-} !Double
+
+-- | Compute the minimum and maximum of a vector in one pass.
+minMax :: (G.Vector v Double) => v Double -> (Double, Double)
+minMax = fini . G.foldl' go (MM (1/0) (-1/0))
+  where
+    go (MM lo hi) k = MM (min lo k) (max hi k)
+    fini (MM lo hi) = (lo, hi)
+{-# INLINE minMax #-}
+
+-- | Efficiently compute the next highest power of two for a
+-- non-negative integer.  If the given value is already a power of
+-- two, it is returned unchanged.  If negative, zero is returned.
+nextHighestPowerOfTwo :: Int -> Int
+nextHighestPowerOfTwo n
+#if WORD_SIZE_IN_BITS == 64
+  = 1 + _i32
+#else
+  = 1 + i16
+#endif
+  where
+    i0   = n - 1
+    i1   = i0  .|. i0  `shiftR` 1
+    i2   = i1  .|. i1  `shiftR` 2
+    i4   = i2  .|. i2  `shiftR` 4
+    i8   = i4  .|. i4  `shiftR` 8
+    i16  = i8  .|. i8  `shiftR` 16
+    _i32 = i16 .|. i16 `shiftR` 32
+-- It could be implemented as
+--
+-- > nextHighestPowerOfTwo n = 1 + foldl' go (n-1) [1, 2, 4, 8, 16, 32]
+--     where go m i = m .|. m `shiftR` i
+--
+-- But GHC do not inline foldl (probably because it's recursive) and
+-- as result function walks list of boxed ints. Hand rolled version
+-- uses unboxed arithmetic.
+
+-- | Multiply a number by itself.
+square :: Double -> Double
+square x = x * x
+
+-- | Simple for loop.  Counts from /start/ to /end/-1.
+for :: Monad m => Int -> Int -> (Int -> m ()) -> m ()
+for n0 !n f = loop n0
+  where
+    loop i | i == n    = return ()
+           | otherwise = f i >> loop (i+1)
+{-# INLINE for #-}
+
+-- | Simple reverse-for loop.  Counts from /start/-1 to /end/ (which
+-- must be less than /start/).
+rfor :: Monad m => Int -> Int -> (Int -> m ()) -> m ()
+rfor n0 !n f = loop n0
+  where
+    loop i | i == n    = return ()
+           | otherwise = let i' = i-1 in f i' >> loop i'
+{-# INLINE rfor #-}
+
+unsafeModify :: M.MVector s Double -> Int -> (Double -> Double) -> ST s ()
+unsafeModify v i f = do
+  k <- M.unsafeRead v i
+  M.unsafeWrite v i (f k)
+{-# INLINE unsafeModify #-}

statistics-dense-linear-algebra/src/Statistics/Function/Comparison.hs

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+-- |
+-- Module    : Statistics.Function.Comparison
+-- Copyright : (c) 2011 Bryan O'Sullivan
+-- License   : BSD3
+--
+-- Maintainer  : [email protected]
+-- Stability   : experimental
+-- Portability : portable
+--
+-- Approximate floating point comparison, based on Bruce Dawson's
+-- \"Comparing floating point numbers\":
+-- <http://www.cygnus-software.com/papers/comparingfloats/comparingfloats.htm>
+module Statistics.Function.Comparison
+    {-# DEPRECATED "Use Numeric.MathFunctions.Comparison from math-functions" #-}
+    (
+      within
+    ) where
+import Numeric.MathFunctions.Comparison (within)

Statistics/Matrix.hs renamed to statistics-dense-linear-algebra/src/Statistics/Matrix.hs

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+{-# LANGUAGE FlexibleContexts #-}
+
+-- |
+-- Module    : Statistics.Sample.Internal
+-- Copyright : (c) 2013 Bryan O'Sullivan
+-- License   : BSD3
+--
+-- Maintainer  : [email protected]
+-- Stability   : experimental
+-- Portability : portable
+--
+-- Internal functions for computing over samples.
+module Statistics.Sample.Internal
+    (
+      robustSumVar
+    , sum
+    ) where
+
+import Numeric.Sum (kbn, sumVector)
+import Prelude hiding (sum)
+import Statistics.Function (square)
+import qualified Data.Vector.Generic as G
+
+robustSumVar :: (G.Vector v Double) => Double -> v Double -> Double
+robustSumVar m = sum . G.map (square . subtract m)
+{-# INLINE robustSumVar #-}
+
+sum :: (G.Vector v Double) => v Double -> Double
+sum = sumVector kbn
+{-# INLINE sum #-}

Statistics/Matrix/Algorithms.hs renamed to statistics-dense-linear-algebra/src/Statistics/Matrix/Algorithms.hs

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+# This file was automatically generated by 'stack init'
+#
+# Some commonly used options have been documented as comments in this file.
+# For advanced use and comprehensive documentation of the format, please see:
+# https://docs.haskellstack.org/en/stable/yaml_configuration/
+
+# Resolver to choose a 'specific' stackage snapshot or a compiler version.
+# A snapshot resolver dictates the compiler version and the set of packages
+# to be used for project dependencies. For example:
+#
+# resolver: lts-3.5
+# resolver: nightly-2015-09-21
+# resolver: ghc-7.10.2
+# resolver: ghcjs-0.1.0_ghc-7.10.2
+# resolver:
+#  name: custom-snapshot
+#  location: "./custom-snapshot.yaml"
+resolver: lts-11.2
+
+# User packages to be built.
+# Various formats can be used as shown in the example below.
+#
+# packages:
+# - some-directory
+# - https://example.com/foo/bar/baz-0.0.2.tar.gz
+# - location:
+#    git: https://github.com/commercialhaskell/stack.git
+#    commit: e7b331f14bcffb8367cd58fbfc8b40ec7642100a
+# - location: https://github.com/commercialhaskell/stack/commit/e7b331f14bcffb8367cd58fbfc8b40ec7642100a
+#   extra-dep: true
+#  subdirs:
+#  - auto-update
+#  - wai
+#
+# A package marked 'extra-dep: true' will only be built if demanded by a
+# non-dependency (i.e. a user package), and its test suites and benchmarks
+# will not be run. This is useful for tweaking upstream packages.
+packages:
+- .
+# Dependency packages to be pulled from upstream that are not in the resolver
+# (e.g., acme-missiles-0.3)
+# extra-deps: []
+
+# Override default flag values for local packages and extra-deps
+# flags: {}
+
+# Extra package databases containing global packages
+# extra-package-dbs: []
+
+# Control whether we use the GHC we find on the path
+# system-ghc: true
+#
+# Require a specific version of stack, using version ranges
+# require-stack-version: -any # Default
+# require-stack-version: ">=1.6"
+#
+# Override the architecture used by stack, especially useful on Windows
+# arch: i386
+# arch: x86_64
+#
+# Extra directories used by stack for building
+# extra-include-dirs: [/path/to/dir]
+# extra-lib-dirs: [/path/to/dir]
+#
+# Allow a newer minor version of GHC than the snapshot specifies
+# compiler-check: newer-minor

Statistics/Matrix/Mutable.hs renamed to statistics-dense-linear-algebra/src/Statistics/Matrix/Mutable.hs

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+name:                statistics-dense-linear-algebra
+version:             0.1.0.0
+-- synopsis:
+-- description:
+homepage:            https://github.com/githubuser/statistics-dense-linear-algebra
+license:             BSD3
+license-file:        LICENSE
+author:              Author name here
+maintainer:          [email protected]
+copyright:           2018 Author name here
+category:            Math, Statistics, Numeric
+build-type:          Simple
+extra-source-files:  README.md
+cabal-version:       >=1.10
+tested-with: GHC==7.6.3, GHC==7.8.3, GHC==7.10.3, GHC==8.0.1
+
+library
+  default-language:    Haskell2010
+  ghc-options:         -Wall
+  hs-source-dirs:      src
+  exposed-modules:     Statistics.Function
+                       Statistics.Function.Comparison
+                       Statistics.Matrix
+                       Statistics.Matrix.Algorithms
+                       Statistics.Matrix.Mutable
+                       Statistics.Matrix.Types
+                       Statistics.Sample.Internal                       
+  build-depends:       base                    >= 4.5 && < 5
+                     , deepseq                 >= 1.1.0.2
+                     , math-functions          >= 0.1.7                     
+                     , primitive               >= 0.3
+                     , vector                  >= 0.10
+                     , vector-algorithms       >= 0.4
+                     , vector-th-unbox
+                     , vector-binary-instances >= 0.2.1
+
+test-suite spec
+  default-language:    Haskell2010
+  ghc-options:         -Wall
+  type:                exitcode-stdio-1.0
+  hs-source-dirs:      test
+  main-is:             Spec.hs
+  build-depends:       base
+                     , statistics-dense-linear-algebra
+                     , hspec
+                     , QuickCheck
+
+source-repository head
+  type:     git
+  location: https://github.com/githubuser/statistics-dense-linear-algebra