13 files changed, 87 insertions, 108 deletions

diff --git a/examples/error.hs b/examples/error.hs
index 5efae7c..77467df 100644
--- a/examples/error.hs
+++ b/examples/error.hs
@@ -8,6 +8,7 @@ test x = catch
        (print x)
        (\e -> putStrLn $ "captured ["++ show (e :: SomeException) ++"]")
 
+
 main = do
     setErrorHandlerOff
 
@@ -15,7 +16,8 @@ main = do
     test $ 5 + (fst.exp_e) 1000
     test $ bessel_zero_Jnu_e (-0.3) 2
 
-    test $ (linearSolve 0 4 :: Matrix Double)
-    test $ (linearSolve 5 (sqrt (-1)) :: Matrix Double)
+    test $ (inv 0 :: Matrix Double)
+    test $ (linearSolveLS 5 (sqrt (-1)) :: Matrix Double)
+
+    putStrLn "Bye"
 
-    putStrLn "Bye"
\ No newline at end of file
diff --git a/examples/inplace.hs b/examples/inplace.hs
index 574aa44..19f9bc9 100644
--- a/examples/inplace.hs
+++ b/examples/inplace.hs
@@ -1,7 +1,9 @@
 -- some tests of the interface for pure
 -- computations with inplace updates
 
-import Numeric.LinearAlgebra.HMatrix
+{-# LANGUAGE FlexibleContexts #-}
+
+import Numeric.LinearAlgebra
 import Numeric.LinearAlgebra.Devel
 
 import Data.Array.Unboxed
diff --git a/examples/kalman.hs b/examples/kalman.hs
index 7fbe3d2..9756aa0 100644
--- a/examples/kalman.hs
+++ b/examples/kalman.hs
@@ -1,17 +1,15 @@
 import Numeric.LinearAlgebra
 import Graphics.Plot
 
-vector l = fromList l :: Vector Double
-matrix ls = fromLists ls :: Matrix Double
-diagl = diag . vector
+f = fromLists
+    [[1,0,0,0],
+     [1,1,0,0],
+     [0,0,1,0],
+     [0,0,0,1]]
 
-f = matrix [[1,0,0,0],
-            [1,1,0,0],
-            [0,0,1,0],
-            [0,0,0,1]]
-
-h = matrix [[0,-1,1,0],
-            [0,-1,0,1]]
+h = fromLists
+    [[0,-1,1,0],
+     [0,-1,0,1]]
 
 q = diagl [1,1,0,0]
 
@@ -25,13 +23,13 @@ type Measurement = Vector Double
 
 kalman :: System -> State -> Measurement -> State
 kalman (System f h q r) (State x p) z = State x' p' where
-    px = f <> x                            -- prediction
-    pq = f <> p <> trans f + q             -- its covariance
-    y  = z - h <> px                       -- residue
-    cy = h <> pq <> trans h + r            -- its covariance
-    k  = pq <> trans h <> inv cy           -- kalman gain
-    x' = px + k <> y                       -- new state
-    p' = (ident (dim x) - k <> h) <> pq    -- its covariance
+    px = f #> x                            -- prediction
+    pq = f <> p <> tr f + q             -- its covariance
+    y  = z - h #> px                       -- residue
+    cy = h <> pq <> tr h + r            -- its covariance
+    k  = pq <> tr h <> inv cy           -- kalman gain
+    x' = px + k #> y                       -- new state
+    p' = (ident (size x) - k <> h) <> pq    -- its covariance
 
 sys = System f h q r
 
@@ -49,3 +47,4 @@ main = do
     print $ fromRows $ take 10 (map sX xs)
     mapM_ (print . sP) $ take 10 xs
     mplot (evolution 20 (xs,des))
+
diff --git a/examples/lie.hs b/examples/lie.hs
index db21ea8..4933df6 100644
--- a/examples/lie.hs
+++ b/examples/lie.hs
@@ -1,8 +1,8 @@
 -- The magic of Lie Algebra
 
-import Numeric.LinearAlgebra
+{-# LANGUAGE FlexibleContexts #-}
 
-disp = putStrLn . dispf 5
+import Numeric.LinearAlgebra
 
 rot1 :: Double -> Matrix Double
 rot1 a = (3><3)
@@ -58,8 +58,8 @@ main = do
        exact = rot3 a <> rot1 b <> rot2 c
        lie = scalar a * g3 |+| scalar b * g1 |+| scalar c * g2
    putStrLn "position in the tangent space:"
-   disp lie
+   disp 5 lie
    putStrLn "exponential map back to the group (2 terms):"
-   disp (expm lie)
+   disp 5 (expm lie)
    putStrLn "exact position:"
-   disp exact
+   disp 5 exact
diff --git a/examples/minimize.hs b/examples/minimize.hs
index 19b2cb3..c27afc2 100644
--- a/examples/minimize.hs
+++ b/examples/minimize.hs
@@ -20,7 +20,7 @@ partialDerivative n f v = fst (derivCentral 0.01 g (v!!n)) where
     g x = f (concat [a,x:b])
     (a,_:b) = splitAt n v
 
-disp = putStrLn . format "  " (printf "%.3f")
+disp' = putStrLn . format "  " (printf "%.3f")
 
 allMethods :: (Enum a, Bounded a) => [a]
 allMethods = [minBound .. maxBound]
@@ -29,22 +29,23 @@ test method = do
     print method
     let (s,p) = minimize method 1E-2 30 [1,1] f [5,7]
     print s
-    disp p
+    disp' p
 
 testD method = do
     print method
     let (s,p) = minimizeD method 1E-3 30 1E-2 1E-4 f df [5,7]
     print s
-    disp p
+    disp' p
 
 testD' method = do
     putStrLn $ show method ++ " with estimated gradient"
     let (s,p) = minimizeD method 1E-3 30 1E-2 1E-4 f (gradient f) [5,7]
     print s
-    disp p
+    disp' p
 
 main = do
     mapM_ test [NMSimplex, NMSimplex2]
     mapM_ testD allMethods
     testD' ConjugateFR
     mplot $ drop 3 . toColumns . snd $ minimizeS f [5,7]
+
diff --git a/examples/monadic.hs b/examples/monadic.hs
index 7c6e0f4..cf8aacc 100644
--- a/examples/monadic.hs
+++ b/examples/monadic.hs
@@ -1,35 +1,37 @@
 -- monadic computations
 -- (contributed by Vivian McPhail)
 
+{-# LANGUAGE FlexibleContexts #-}
+
 import Numeric.LinearAlgebra
+import Numeric.LinearAlgebra.Devel
 import Control.Monad.State.Strict
-import Control.Monad.Maybe
+import Control.Monad.Trans.Maybe
 import Foreign.Storable(Storable)
 import System.Random(randomIO)
 
 -------------------------------------------
 
 -- an instance of MonadIO, a monad transformer
-type VectorMonadT = StateT Int IO
+type VectorMonadT = StateT I IO
 
-test1 :: Vector Int -> IO (Vector Int)
+test1 :: Vector I -> IO (Vector I)
 test1 = mapVectorM $ \x -> do
     putStr $ (show x) ++ " "
     return (x + 1)
 
 -- we can have an arbitrary monad AND do IO
-addInitialM :: Vector Int -> VectorMonadT ()
+addInitialM :: Vector I -> VectorMonadT ()
 addInitialM = mapVectorM_ $ \x -> do
     i <- get
     liftIO $ putStr $ (show $ x + i) ++ " "
     put $ x + i
 
 -- sum the values of the even indiced elements
-sumEvens :: Vector Int -> Int
+sumEvens :: Vector I -> I
 sumEvens = foldVectorWithIndex (\x a b -> if x `mod` 2 == 0 then a + b else b) 0
 
 -- sum and print running total of evens
-sumEvensAndPrint :: Vector Int -> VectorMonadT ()
 sumEvensAndPrint = mapVectorWithIndexM_ $ \ i x -> do
     when (i `mod` 2 == 0) $ do
         v <- get
@@ -38,7 +40,7 @@ sumEvensAndPrint = mapVectorWithIndexM_ $ \ i x -> do
         liftIO $ putStr $ (show v') ++ " "
 
 
-indexPlusSum :: Vector Int -> VectorMonadT ()
+--indexPlusSum :: Vector I -> VectorMonadT ()
 indexPlusSum v' = do
     let f i x = do
             s <- get
@@ -63,7 +65,7 @@ monoStep d = do
 
 isMonotoneIncreasing :: Vector Double -> Bool
 isMonotoneIncreasing v =
-    let res = evalState (runMaybeT $ (mapVectorM_ monoStep v)) (v @> 0)
+    let res = evalState (runMaybeT $ (mapVectorM_ monoStep v)) (v ! 0)
      in case res of
         Nothing -> False
         Just _  -> True
@@ -72,8 +74,8 @@ isMonotoneIncreasing v =
 -------------------------------------------
 
 -- | apply a test to successive elements of a vector, evaluates to true iff test passes for all pairs
-successive_ :: Storable a => (a -> a -> Bool) -> Vector a -> Bool
-successive_ t v = maybe False (\_ -> True) $ evalState (runMaybeT (mapVectorM_ step (subVector 1 (dim v - 1) v))) (v @> 0)
+successive_ :: (Container Vector a, Indexable (Vector a) a) => (a -> a -> Bool) -> Vector a -> Bool
+successive_ t v = maybe False (\_ -> True) $ evalState (runMaybeT (mapVectorM_ step (subVector 1 (size v - 1) v))) (v ! 0)
    where step e = do
                   ep <- lift $ get
                   if t e ep
@@ -81,8 +83,10 @@ successive_ t v = maybe False (\_ -> True) $ evalState (runMaybeT (mapVectorM_ s
                      else (fail "successive_ test failed")
 
 -- | operate on successive elements of a vector and return the resulting vector, whose length 1 less than that of the input
-successive :: (Storable a, Storable b) => (a -> a -> b) -> Vector a -> Vector b
-successive f v = evalState (mapVectorM step (subVector 1 (dim v - 1) v)) (v @> 0)
+successive
+  :: (Storable b, Container Vector s, Indexable (Vector s) s)
+  => (s -> s -> b) -> Vector s -> Vector b
+successive f v = evalState (mapVectorM step (subVector 1 (size v - 1) v)) (v ! 0)
    where step e = do
                   ep <- get
                   put e
@@ -90,7 +94,7 @@ successive f v = evalState (mapVectorM step (subVector 1 (dim v - 1) v)) (v @> 0
 
 -------------------------------------------
 
-v :: Vector Int
+v :: Vector I
 v = 10 |> [0..]
 
 w = fromList ([1..10]++[10,9..1]) :: Vector Double
@@ -116,3 +120,4 @@ main = do
     print $ successive_ (>) v
     print $ successive_ (>) w
     print $ successive (+) v
+
diff --git a/examples/multiply.hs b/examples/multiply.hs
index 572961c..be8fa73 100644
--- a/examples/multiply.hs
+++ b/examples/multiply.hs
@@ -22,10 +22,10 @@ instance Container Vector t => Scaling t (Vector t) (Vector t) where
 instance Container Vector t => Scaling (Vector t) t (Vector t) where
     (⋅) = flip scale
 
-instance Container Vector t => Scaling t (Matrix t) (Matrix t) where
+instance (Num t, Container Vector t) => Scaling t (Matrix t) (Matrix t) where
     (⋅) = scale
 
-instance Container Vector t => Scaling (Matrix t) t (Matrix t) where
+instance (Num t, Container Vector t) => Scaling (Matrix t) t (Matrix t) where
     (⋅) = flip scale
 
 
@@ -42,14 +42,14 @@ class Mul a b c | a b -> c, a c -> b, b c -> a where
 instance Product t => Mul (Vector t) (Vector t) t where
     (×) = udot
 
-instance Product t => Mul (Matrix t) (Vector t) (Vector t) where
-    (×) = mXv
+instance (Numeric t, Product t) => Mul (Matrix t) (Vector t) (Vector t) where
+    (×) = (#>)
 
-instance Product t => Mul (Vector t) (Matrix t) (Vector t) where
-    (×) = vXm
+instance (Numeric t, Product t) => Mul (Vector t) (Matrix t) (Vector t) where
+    (×) = (<#)
 
-instance Product t => Mul (Matrix t) (Matrix t) (Matrix t) where
-    (×) = mXm
+instance (Numeric t, Product t) => Mul (Matrix t) (Matrix t) (Matrix t) where
+    (×) = (<>)
 
 
 --instance Scaling a b c => Contraction a b c where
@@ -92,9 +92,9 @@ u = fromList [3,0,5]
 w = konst 1 (2,3) :: Matrix Double
 
 main = do
-    print $ (scale s v <> m) `udot` v
-    print $ scale s v `udot` (m <> v)
-    print $ s * ((v <> m) `udot` v)
+    print $ (scale s v <# m) `udot` v
+    print $ scale s v `udot` (m #> v)
+    print $ s * ((v <# m) `udot` v)
     print $ s ⋅ v × m × v
     print a
 --    print (b == c)
diff --git a/examples/ode.hs b/examples/ode.hs
index dc6e0ec..4cf1673 100644
--- a/examples/ode.hs
+++ b/examples/ode.hs
@@ -43,7 +43,7 @@ vanderpol' mu = do
         jac t (toList->[x,v]) = (2><2) [ 0          ,          1
                                        , -1-2*x*v*mu, mu*(1-x**2) ]
         ts = linspace 1000 (0,50)
-        hi = (ts@>1 - ts@>0)/100
+        hi = (ts!1 - ts!0)/100
         sol = toColumns $ odeSolveV (MSBDF jac) hi 1E-8 1E-8 (xdot mu) (fromList [1,0]) ts
     mplot sol
 
diff --git a/examples/pca1.hs b/examples/pca1.hs
index a11eba9..ad2214d 100644
--- a/examples/pca1.hs
+++ b/examples/pca1.hs
@@ -8,27 +8,25 @@ import Control.Monad(when)
 type Vec = Vector Double
 type Mat = Matrix Double
 
-
+{-
 -- Vector with the mean value of the columns of a matrix
 mean a = constant (recip . fromIntegral . rows $ a) (rows a) <> a
 
 -- covariance matrix of a list of observations stored as rows
 cov x = (trans xc <> xc) / fromIntegral (rows x - 1)
     where xc = x - asRow (mean x)
+-}
 
 
 -- creates the compression and decompression functions from the desired number of components
 pca :: Int -> Mat -> (Vec -> Vec , Vec -> Vec)
 pca n dataSet = (encode,decode)
   where
-    encode x = vp <> (x - m)
-    decode x = x <> vp + m
-    m = mean dataSet
-    c = cov dataSet
-    (_,v) = eigSH' c
-    vp = takeRows n (trans v)
-
-norm = pnorm PNorm2
+    encode x = vp #> (x - m)
+    decode x = x <# vp + m
+    (m,c) = meanCov dataSet
+    (_,v) = eigSH (trustSym c)
+    vp = tr $ takeColumns n v
 
 main = do
     ok <- doesFileExist ("mnist.txt")
@@ -43,4 +41,4 @@ main = do
     let (pe,pd) = pca 10 xs
     let y = pe x
     print y  -- compressed version
-    print $ norm (x - pd y) / norm x --reconstruction quality
+    print $ norm_2 (x - pd y) / norm_2 x --reconstruction quality
diff --git a/examples/pca2.hs b/examples/pca2.hs
index e7ea95f..892d382 100644
--- a/examples/pca2.hs
+++ b/examples/pca2.hs
@@ -1,5 +1,7 @@
 -- Improved PCA, including illustrative graphics
 
+{-# LANGUAGE FlexibleContexts #-}
+
 import Numeric.LinearAlgebra
 import Graphics.Plot
 import System.Directory(doesFileExist)
@@ -10,27 +12,27 @@ type Vec = Vector Double
 type Mat = Matrix Double
 
 -- Vector with the mean value of the columns of a matrix
-mean a = constant (recip . fromIntegral . rows $ a) (rows a) <> a
+mean a = konst (recip . fromIntegral . rows $ a) (rows a) <# a
 
 -- covariance matrix of a list of observations stored as rows
-cov x = (trans xc <> xc) / fromIntegral (rows x - 1)
+cov x = (mTm xc) -- / fromIntegral (rows x - 1)
     where xc = x - asRow (mean x)
 
 
 type Stat = (Vec, [Double], Mat)
 -- 1st and 2nd order statistics of a dataset (mean, eigenvalues and eigenvectors of cov)
 stat :: Mat -> Stat
-stat x = (m, toList s, trans v) where
+stat x = (m, toList s, tr v) where
     m = mean x
-    (s,v) = eigSH' (cov x)
+    (s,v) = eigSH (cov x)
 
 -- creates the compression and decompression functions from the desired reconstruction
 -- quality and the statistics of a data set
 pca :: Double -> Stat -> (Vec -> Vec , Vec -> Vec)
 pca prec (m,s,v) = (encode,decode)    
   where    
-    encode x = vp <> (x - m)
-    decode x = x <> vp + m
+    encode x = vp #> (x - m)
+    decode x = x <# vp + m
     vp = takeRows n v
     n = 1 + (length $ fst $ span (< (prec'*sum s)) $ cumSum s)
     cumSum = tail . scanl (+) 0.0
@@ -46,7 +48,7 @@ test :: Stat -> Double -> Vec -> IO ()
 test st prec x = do
     let (pe,pd) = pca prec st
     let y = pe x
-    print $ dim y
+    print $ size y
     shdigit (pd y)
 
 main = do
@@ -63,3 +65,4 @@ main = do
     let st = stat xs
     test st 0.90 x
     test st 0.50 x
+
diff --git a/examples/plot.hs b/examples/plot.hs
index f950aa5..90643ed 100644
--- a/examples/plot.hs
+++ b/examples/plot.hs
@@ -16,5 +16,5 @@ cumdist x = 0.5 * (1+ erf (x/sqrt 2))
 main = do
     let x = linspace 1000 (-4,4)
     mplot [f x]
-    mplot [x, mapVector cumdist x, mapVector gaussianPDF x]
-    mesh (sombrero 40)
\ No newline at end of file
+    mplot [x, cmap cumdist x, cmap gaussianPDF x]
+    mesh (sombrero 40)
diff --git a/examples/root.hs b/examples/root.hs
index 8546ff5..fa6e77a 100644
--- a/examples/root.hs
+++ b/examples/root.hs
@@ -9,7 +9,7 @@ test method = do
     print method
     let (s,p) = root method 1E-7 30 (rosenbrock 1 10) [-10,-5]
     print s -- solution
-    disp p -- evolution of the algorithm
+    disp' p -- evolution of the algorithm
 
 jacobian a b [x,y] = [ [-a    , 0]
                      , [-2*b*x, b] ]
@@ -18,9 +18,9 @@ testJ method = do
     print method
     let (s,p) = rootJ method 1E-7 30 (rosenbrock 1 10) (jacobian 1 10) [-10,-5]
     print s
-    disp p
+    disp' p
 
-disp = putStrLn . format "  " (printf "%.3f")
+disp' = putStrLn . format "  " (printf "%.3f")
 
 main = do
     test Hybrids
diff --git a/examples/vector.hs b/examples/vector.hs
deleted file mode 100644
index f531cbd..0000000
--- a/examples/vector.hs
+++ /dev/null
@@ -1,31 +0,0 @@
--- conversion to/from Data.Vector.Storable
--- from Roman Leshchinskiy "vector" package
---
--- In the future Data.Packed.Vector will be replaced by Data.Vector.Storable
-
--------------------------------------------
-
-import Numeric.LinearAlgebra as H
-import Data.Packed.Development(unsafeFromForeignPtr, unsafeToForeignPtr)
-import Foreign.Storable
-import qualified Data.Vector.Storable as V
-
-fromVector :: Storable t => V.Vector t -> H.Vector t
-fromVector v = unsafeFromForeignPtr p i n where
-    (p,i,n) = V.unsafeToForeignPtr v
-
-toVector :: Storable t => H.Vector t -> V.Vector t
-toVector v = V.unsafeFromForeignPtr p i n where
-    (p,i,n) = unsafeToForeignPtr v
-
--------------------------------------------
-
-v = V.slice 5 10 (V.fromList [1 .. 10::Double] V.++ V.replicate 10 7)
-
-w = subVector 2 3 (linspace 5 (0,1)) :: Vector Double
-
-main = do
-    print v
-    print $ fromVector v
-    print w
-    print $ toVector w