container and algorithms moved to base

6 files changed, 28 insertions, 40 deletions

diff --git a/packages/base/hmatrix-base.cabal b/packages/base/hmatrix-base.cabal
index 8eeb97e..9a84b7e 100644
--- a/packages/base/hmatrix-base.cabal
+++ b/packages/base/hmatrix-base.cabal
@@ -37,10 +37,12 @@ library
                         Data.Packed.Development,
                         Numeric.Conversion
                         Numeric.LinearAlgebra.LAPACK
+                        Numeric.LinearAlgebra.Algorithms
                         Data.Packed.Numeric
                         Numeric.Vectorized
                         Numeric.Vector
                         Numeric.Matrix
+                        Numeric.Container
                         
     other-modules:      Data.Packed.Internal,
                         Data.Packed.Internal.Common,
diff --git a/packages/hmatrix/src/Numeric/Container.hs b/packages/base/src/Numeric/Container.hs
index e7f23d4..b7d3b80 100644
--- a/packages/hmatrix/src/Numeric/Container.hs
+++ b/packages/base/src/Numeric/Container.hs
@@ -42,12 +42,6 @@ module Numeric.Container (
     optimiseMult,
     mXm,mXv,vXm,LSDiv(..),
     outer, kronecker,
-    -- * Random numbers
-    RandDist(..),
-    randomVector,
-    gaussianSample,
-    uniformSample,
-    meanCov,
     -- * Element conversion
     Convert(..),
     Complexable(),
@@ -56,20 +50,13 @@ module Numeric.Container (
     RealOf, ComplexOf, SingleOf, DoubleOf,
 
     IndexOf,
-    module Data.Complex,
-    -- * IO
-    dispf, disps, dispcf, vecdisp, latexFormat, format,
-    loadMatrix, saveMatrix, fromFile, fileDimensions,
-    readMatrix,
-    fscanfVector, fprintfVector, freadVector, fwriteVector,
+    module Data.Complex
 ) where
 
 import Data.Packed hiding (stepD, stepF, condD, condF, conjugateC, conjugateQ)
 import Data.Packed.Numeric
-import Numeric.IO
 import Data.Complex
 import Numeric.LinearAlgebra.Algorithms(Field,linearSolveSVD)
-import Numeric.Random
 import Data.Monoid(Monoid(mconcat))
 
 ------------------------------------------------------------------
@@ -235,26 +222,6 @@ instance Container Matrix e => Build (Int,Int) (e -> e -> e) Matrix e
 
 --------------------------------------------------------------------------------
 
-{- | Compute mean vector and covariance matrix of the rows of a matrix.
-
->>> meanCov $ gaussianSample 666 1000 (fromList[4,5]) (diagl[2,3])
-(fromList [4.010341078059521,5.0197204699640405],
-(2><2)
- [     1.9862461923890056, -1.0127225830525157e-2
- , -1.0127225830525157e-2,     3.0373954915729318 ])
-
--}
-meanCov :: Matrix Double -> (Vector Double, Matrix Double)
-meanCov x = (med,cov) where
-    r    = rows x
-    k    = 1 / fromIntegral r
-    med  = konst k r `vXm` x
-    meds = konst 1 r `outer` med
-    xc   = x `sub` meds
-    cov  = scale (recip (fromIntegral (r-1))) (trans xc `mXm` xc)
-
---------------------------------------------------------------------------------
-
 {- | alternative operator for '(\<.\>)'
 
 x25c7, white diamond
diff --git a/packages/hmatrix/src/Numeric/LinearAlgebra/Algorithms.hs b/packages/base/src/Numeric/LinearAlgebra/Algorithms.hs
index b4d0c5b..6f40683 100644
--- a/packages/hmatrix/src/Numeric/LinearAlgebra/Algorithms.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Algorithms.hs
@@ -21,8 +21,6 @@ imported from "Numeric.LinearAlgebra.LAPACK".
 
 -}
 -----------------------------------------------------------------------------
-{-# OPTIONS_HADDOCK hide #-}
-
 
 module Numeric.LinearAlgebra.Algorithms (
 -- * Supported types
diff --git a/packages/hmatrix/hmatrix.cabal b/packages/hmatrix/hmatrix.cabal
index 369c412..9719c96 100644
--- a/packages/hmatrix/hmatrix.cabal
+++ b/packages/hmatrix/hmatrix.cabal
@@ -18,7 +18,7 @@ cabal-version:      >=1.8
 
 build-type:         Simple
 
-extra-source-files: Config.hs THANKS.md INSTALL.md CHANGELOG
+extra-source-files: THANKS.md INSTALL.md CHANGELOG
 
 extra-source-files: examples/deriv.hs
                     examples/integrate.hs
@@ -90,9 +90,7 @@ library
                         Numeric.GSL.Fitting,
                         Numeric.GSL.ODE,
                         Numeric.GSL,
-                        Numeric.Container,
                         Numeric.LinearAlgebra,
-                        Numeric.LinearAlgebra.Algorithms,
                         Numeric.LinearAlgebra.Util,
                         Graphics.Plot,
                         Numeric.HMatrix,
diff --git a/packages/hmatrix/src/Numeric/HMatrix/Data.hs b/packages/hmatrix/src/Numeric/HMatrix/Data.hs
index 568dc05..5d7ce4f 100644
--- a/packages/hmatrix/src/Numeric/HMatrix/Data.hs
+++ b/packages/hmatrix/src/Numeric/HMatrix/Data.hs
@@ -64,6 +64,7 @@ module Numeric.HMatrix.Data(
 import Data.Packed.Vector
 import Data.Packed.Matrix
 import Numeric.Container
+import Numeric.IO
 import Numeric.LinearAlgebra.Util
 import Data.Complex
 
diff --git a/packages/hmatrix/src/Numeric/LinearAlgebra/Util.hs b/packages/hmatrix/src/Numeric/LinearAlgebra/Util.hs
index fb2d54c..e4f21b0 100644
--- a/packages/hmatrix/src/Numeric/LinearAlgebra/Util.hs
+++ b/packages/hmatrix/src/Numeric/LinearAlgebra/Util.hs
@@ -27,6 +27,7 @@ module Numeric.LinearAlgebra.Util(
     unitary,
     mt,
     pairwiseD2,
+    meanCov,
     rowOuters,
     null1,
     null1sym,
@@ -55,6 +56,7 @@ module Numeric.LinearAlgebra.Util(
 ) where
 
 import Numeric.Container
+import Numeric.IO
 import Numeric.LinearAlgebra.Algorithms hiding (i)
 import Numeric.Matrix()
 import Numeric.Vector()
@@ -196,7 +198,27 @@ size m = (rows m, cols m)
 mt :: Matrix Double -> Matrix Double
 mt = trans . inv
 
-----------------------------------------------------------------------
+--------------------------------------------------------------------------------
+
+{- | Compute mean vector and covariance matrix of the rows of a matrix.
+
+>>> meanCov $ gaussianSample 666 1000 (fromList[4,5]) (diagl[2,3])
+(fromList [4.010341078059521,5.0197204699640405],
+(2><2)
+ [     1.9862461923890056, -1.0127225830525157e-2
+ , -1.0127225830525157e-2,     3.0373954915729318 ])
+
+-}
+meanCov :: Matrix Double -> (Vector Double, Matrix Double)
+meanCov x = (med,cov) where
+    r    = rows x
+    k    = 1 / fromIntegral r
+    med  = konst k r `vXm` x
+    meds = konst 1 r `outer` med
+    xc   = x `sub` meds
+    cov  = scale (recip (fromIntegral (r-1))) (trans xc `mXm` xc)
+
+--------------------------------------------------------------------------------
 
 -- | Matrix of pairwise squared distances of row vectors
 -- (using the matrix product trick in blog.smola.org)