markov-realization 0.3.3 → 0.4

raw patch · 6 files changed

+39/−29 lines, 6 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• README.md +4/−3
• markov-realization.cabal +4/−9
• src/Markov.hs +3/−1
• src/Markov/Example.hs +3/−0
• src/Markov/Extra.hs +9/−6
• test/Test.hs +16/−10

@@ -14,7 +14,7 @@ p(x,x+1) = s. Let p(x,y) = 0 in all other cases. Suppose we wanted to find-P\[Xₙ = j ∩ d = k],+P\[Xₙ = j and d = k], where d denotes the number of transitions from a positive integer to zero. There are three values we need to track — extinctions, probability, and state.@@ -52,7 +52,7 @@         where q = 0.1; r = 0.3; s = 0.6 ``` -We can now easily see a list of states, deaths, and the probabilities.+We can now see a list of states, extinctions, and the probabilities.  __`> chain [pure 0 :: Sum Int :* Product Rational :* Extinction] !! 3`__ ```@@ -66,4 +66,5 @@  This means that starting from a state of zero, after three time steps there is a 51/500 chance-that the state is zero and there has been one death.+that the state is zero and there has been one extinction.+

@@ -1,19 +1,13 @@ cabal-version: 1.12 --- This file has been generated from package.yaml by hpack version 0.31.1.------ see: https://github.com/sol/hpack------ hash: b164fe328e9edef0858d48e61b56997280bd4bb2ea6ffe923afb24084a14efe6- name:           markov-realization-version:        0.3.3+version:        0.4 description:    Please see the README on GitHub at <https://github.com/alexloomis/markov#markov-tutorial> homepage:       https://github.com/alexloomis/markov bug-reports:    https://github.com/alexloomis/markov/issues author:         Alex Loomis maintainer:     atloomis@math.arizona.edu-copyright:      2019 Alex Loomis+copyright:      2020 Alex Loomis license:        BSD3 license-file:   LICENSE build-type:     Simple@@ -55,6 +49,7 @@     -Wall -Wcompat -Wincomplete-uni-patterns -Wincomplete-record-updates -Wredundant-constraints   build-depends:       base >=4.7 && <5-    , HTF     , markov-realization+    , HTF+    , MonadRandom   default-language: Haskell2010

@@ -140,8 +140,10 @@ -- and combined additively for equal states. -- E.g., probabilities. newtype Product a = Product a-    deriving newtype (Num, Fractional, Enum, Show)+    deriving newtype (Enum, Fractional, Integral, Num, Real, Show) +-- Don't sort by probability.+-- |WARNING! Defined @compare _ _ = EQ@! instance Ord (Product a) where     compare _ _ = EQ 

@@ -115,6 +115,9 @@ -- |An urn contains balls of two colors. -- At each step, a ball is chosen uniformly at random from the urn -- and a ball of the same color is added.+--+-- >>> randomPath (mkStdGen 70) (Urn (2,5)) !! 8 :: (Product Double, Urn)+-- (0.1648351648351649, Urn (2,13)) newtype Urn = Urn (Int,Int)     deriving newtype (Eq, Ord, Show) 

@@ -1,9 +1,10 @@-{-# LANGUAGE FlexibleContexts           #-}-{-# LANGUAGE TypeOperators              #-}+{-# LANGUAGE FlexibleContexts #-}+{-# LANGUAGE TypeOperators    #-}  {-| Module      : Markov.Extra Maintainer  : atloomis@math.arizona.edu+Description : Utilities for "Markov". Stability   : Experimental -} @@ -14,9 +15,9 @@      , (>*<)      ) where -import Markov import qualified Control.Monad.Random as MR-import qualified Data.List as DL+import qualified Data.List            as DL+import           Markov  --------------------------------------------------------------------------------------- -- Misc@@ -27,8 +28,9 @@ randomProduct = MR.fromList . fmap (\x -> (x, toRational $ fst x))  -- |Returns a single realization of a Markov chain.-randomPath :: (Markov ((,) a) b, Real a, MR.RandomGen g) => (a,b) -> g -> [(a,b)]-randomPath x g = fmap (`MR.evalRand` g) . iterate (>>= (randomProduct . step)) $ pure x+randomPath :: (Markov ((,) a) b, Real a, MR.RandomGen g) => g -> b -> [(a,b)]+randomPath g x = fmap (`MR.evalRand` g) . iterate (>>= (randomProduct . step))+  $ pure (1,x)  -- |Create a transition function from a transition matrix. -- Inputs should obey:@@ -52,3 +54,4 @@ (>*<) :: a -> b -> a :* b a >*< b = (a,b) infixl 5 >*<+

@@ -1,6 +1,7 @@ {-# OPTIONS_GHC -F -pgmF htfpp #-}-{-# LANGUAGE TypeOperators     #-}+{-# LANGUAGE TypeOperators #-} +import Control.Monad.Random (mkStdGen) import Data.Ratio import Test.Framework @@ -10,47 +11,46 @@  main = htfMain htf_thisModulesTests --- Examples in the documentation. test_fromLists =     assertEqual-    (chain [pure (FromLists 't') :: (Product Double, FromLists)] !! 100)     [ (0.5060975609756099, FromLists 'a')     , (0.29268292682926833, FromLists 'l')     , (0.201219512195122, FromLists 't') ]+    (chain [pure (FromLists 't') :: (Product Double, FromLists)] !! 100)  test_m0Simple =     assertEqual-    (take 3 $ chain0 [Simple 0])     [ [0]     , [-1,1]     , [-2,0,2] ]+    (take 3 $ chain0 [Simple 0])  test_pdSimple =     assertEqual-    (take 3 $ chain [pure 0 :: (Product Double, Simple)])     [ [(1.0,0)]     , [(0.5,-1),(0.5,1)]     , [(0.25,-2),(0.5,0),(0.25,2)] ]+    (take 3 $ chain [pure 0 :: (Product Double, Simple)])  test_piSimple =     assertEqual-    (take 3 $ chain [pure 0 :: (Product Int, Simple)])     [ [(1,0)]     , [(1,-1),(1,1)]     , [(1,-2),(2,0),(1,2)] ]+    (take 3 $ chain [pure 0 :: (Product Int, Simple)])  test_siSimple =     assertEqual-    (chain [pure 0 :: (Sum Int, Simple)] !! 2)     [ (0,0), (0,1), (0,2), (1,-1), (1,0), (2,-2) ]+    (chain [pure 0 :: (Sum Int, Simple)] !! 2)  test_HMM =     assertEqual-    (filter (\((_,Merge xs),_) -> xs == "aaa") $ chain-    [1 >*< Merge "" >*< 1 :: Product Rational :* Merge String :* Room] !! 3)     [ ((Product $ 3243 % 200000, Merge "aaa"),Room 1)     , ((Product $ 9729 % 500000, Merge "aaa"),Room 2)     , ((Product $ 4501 % 250000, Merge "aaa"),Room 3) ]+    (filter (\((_,Merge xs),_) -> xs == "aaa") $ chain+    [1 >*< Merge "" >*< 1 :: Product Rational :* Merge String :* Room] !! 3)  test_expLoss =     assertEqual@@ -59,5 +59,11 @@  test_expLossMore =     assertEqual-    (expectedLoss [pure $ initial [1,0,3,2,2,5] :: (Product Double, FillBin)])     9.764425505050506+    (expectedLoss [pure $ initial [1,0,3,2,2,5] :: (Product Double, FillBin)])++test_randomPath =+    assertEqual+    (0.1648351648351649, Urn (2,13))+    (randomPath (mkStdGen 70) (Urn (2,5)) !! 8 :: (Product Double, Urn))+