rank-product 0.2.1.1 → 0.2.2.0

raw patch · 4 files changed

+33/−11 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• app/Main.hs +6/−2
• rank-product.cabal +1/−1
• src/Statistics/Load.hs +25/−8
• src/Statistics/Types.hs +1/−0

@@ -31,13 +31,16 @@                                      <?> "([,] | CHAR) The delimiter of the CSV file. Format is name,replicate,value."                        , sortType         :: Maybe Sort                                      <?> "([Ascending] | Descending) Ascending ranks 1 as the lowest value while Descending ranks the highest value as 1."+                       , defaultValue     :: Maybe Double+                                     <?> "([Nothing] | DOUBLE) Default value of missing replicate rather than removing entity."                        }                deriving (Generic)  modifiers :: Modifiers modifiers = lispCaseModifiers { shortNameModifier = short }   where-    short x         = firstLetter x+    short "defaultValue" = Just 'v'+    short x              = firstLetter x  instance ParseField Sort @@ -55,6 +58,7 @@         delim'        =             Delimiter . fromMaybe ',' . unHelpful . delimiter $ opts         sortType'     = fromMaybe Ascending . unHelpful . sortType $ opts+        defaultValue' = fmap DefaultValue . unHelpful . defaultValue $ opts         decodeOpt       = CSV.defaultDecodeOptions                             { CSV.decDelimiter =                                 fromIntegral (ord . unDelimiter $ delim')@@ -64,7 +68,7 @@                                 fromIntegral (ord . unDelimiter $ delim')                             } -    entities <- loadNamedEntities+    entities <- loadNamedEntities defaultValue'               . either error snd               . CSV.decodeByNameWith decodeOpt             <$> B.getContents

@@ -1,5 +1,5 @@ name:                rank-product-version:             0.2.1.1+version:             0.2.2.0 synopsis:            Find the rank product of a data set. description:         Find the rank product of a data set and get the p-value from a permutation test. homepage:            http://github.com/GregorySchwartz/rank-product#readme

@@ -12,10 +12,11 @@     ) where  -- Standard-import Data.List (sort)+import Data.List (sort, find) import qualified Data.Foldable as F import qualified Data.Map.Strict as Map import qualified Data.Sequence as Seq+import qualified Data.Set as Set import qualified Data.Text as T import qualified Data.Text.Read as T import qualified Data.Vector as V@@ -26,14 +27,18 @@ import Statistics.Types  -- | Load entities from a list of rows.-loadNamedEntities :: V.Vector (Map.Map T.Text T.Text) -> [NamedEntity]-loadNamedEntities = fmap (uncurry NamedEntity)-                  . Map.toAscList-                  . Map.map (fmap snd . sort . F.toList)-                  . Map.fromListWith (Seq.><)-                  . fmap lookupInfo-                  . V.toList+loadNamedEntities ::+  Maybe DefaultValue -> V.Vector (Map.Map T.Text T.Text) -> [NamedEntity]+loadNamedEntities defVal rows =+  fmap (uncurry NamedEntity)+    . Map.toAscList+    . Map.map (fmap snd . supplyReplicates defVal allReplicates . F.toList)+    . Map.fromListWith (Seq.><)+    . fmap lookupInfo+    . V.toList+    $ rows   where+    allReplicates = Set.fromList . fmap (lookupErr "replicate") . V.toList $ rows     lookupErr x = Map.findWithDefault (error $ "Missing column: " <> show x) x     lookupInfo m =       ( Name $ lookupErr "name" m@@ -41,3 +46,15 @@                       , either error fst . T.double $ lookupErr "value" m                       )       )++-- | Give a default value to missing replicates.+supplyReplicates :: Maybe DefaultValue+                 -> Set.Set T.Text+                 -> [(T.Text, Double)]+                 -> [(T.Text, Double)]+supplyReplicates Nothing _ xs = sort xs+supplyReplicates (Just (DefaultValue defVal)) allReplicates xs =+    Map.toAscList . F.foldl' supply repMap . Set.toList $ allReplicates+  where+    supply m x = if Map.member x m then m else Map.insert x defVal m+    repMap = Map.fromList xs

@@ -20,6 +20,7 @@ newtype Delimiter         = Delimiter { unDelimiter :: Char } deriving (Read, Show) newtype Name              = Name { unName :: T.Text } deriving (Eq, Ord, Show) newtype Permutations      = Permutations Int deriving (Show)+newtype DefaultValue      = DefaultValue Double newtype Entity            = Entity { unEntity :: [Double] } deriving (Show) newtype RankEntity        = RankEntity { unRankEntity :: [Double] } deriving (Show) newtype RankProductEntity = RankProductEntity