Frames: Data frames For working with tabular data files

[ bsd3, data, library ] [ Propose Tags ]

User-friendly, type safe, runtime efficient tooling for working with tabular data deserialized from comma-separated values (CSV) files. The type of each row of data is inferred from data, which can then be streamed from disk, or worked with in memory.


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Versions 0.1.0.0, 0.1.1.0, 0.1.1.1, 0.1.2, 0.1.2.1, 0.1.3, 0.1.4, 0.1.6, 0.1.8, 0.1.9, 0.2.0, 0.2.1, 0.2.1.1, 0.3.0, 0.3.0.1, 0.3.0.2, 0.4.0, 0.5.0
Change log CHANGELOG.md
Dependencies base (>=4.8 && <4.12), bytestring, containers, contravariant, deepseq (>=1.4), discrimination, ghc-prim (>=0.3 && <0.6), hashable, pipes (>=4.1 && <5), pipes-bytestring (>=2.1.6 && <2.2), pipes-group (>=1.0.8 && <1.1), pipes-parse (==3.0.*), pipes-safe (>=2.2.6 && <2.3), primitive (==0.6.*), readable (>=0.3.1), template-haskell, text (>=1.1.1.0), transformers, vector, vector-th-unbox (>=0.2.1.6), vinyl (>=0.10.0 && <0.11) [details]
License BSD-3-Clause
Copyright Copyright (C) 2014-2015 Anthony Cowley
Author Anthony Cowley
Maintainer acowley@gmail.com
Category Data
Source repo head: git clone http://github.com/acowley/Frames.git
Uploaded by AnthonyCowley at Tue Aug 28 15:31:11 UTC 2018
Distributions NixOS:0.5.0
Executables kata04, missing, benchdemo, tutorial, demo, plot2, plot, getdata
Downloads 4832 total (100 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2018-08-28 [all 1 reports]
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Readme for Frames-0.5.0

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Frames

Data Frames for Haskell

User-friendly, type safe, runtime efficient tooling for working with tabular data deserialized from comma-separated values (CSV) files. The type of each row of data is inferred from data, which can then be streamed from disk, or worked with in memory.

We provide streaming and in-memory interfaces for efficiently working with datasets that can be safely indexed by column names found in the data files themselves. This type safety of column access and manipulation is checked at compile time.

Use Cases

For a running example, we will use variations of the prestige.csv data set. Each row includes 7 columns, but we just want to compute the average ratio of income to prestige.

Clean Data

If you have a CSV data where the values of each column may be classified by a single type, and ideally you have a header row giving each column a name, you may simply want to avoid writing out the Haskell type corresponding to each row. Frames provides TemplateHaskell machinery to infer a Haskell type for each row of your data set, thus preventing the situation where your code quietly diverges from your data.

We generate a collection of definitions generated by inspecting the data file at compile time (using tableTypes), then, at runtime, load that data into column-oriented storage in memory (an in-core array of structures (AoS)). We're going to compute the average ratio of two columns, so we'll use the foldl library. Our fold will project the columns we want, and apply a function that divides one by the other after appropriate numeric type conversions. Here is the entirety of that program.

{-# LANGUAGE DataKinds, FlexibleContexts, QuasiQuotes, TemplateHaskell #-}
module UncurryFold where
import qualified Control.Foldl as L
import Data.Vinyl (rcast)
import Data.Vinyl.Curry (runcurryX)
import Frames

-- Data set from http://vincentarelbundock.github.io/Rdatasets/datasets.html
tableTypes "Row" "test/data/prestige.csv"

loadRows :: IO (Frame Row)
loadRows = inCoreAoS (readTable "test/data/prestige.csv")

-- | Compute the ratio of income to prestige for a record containing
-- only those fields.
ratio :: Record '[Income, Prestige] -> Double
ratio = runcurryX (\i p -> fromIntegral i / p)

averageRatio :: IO Double
averageRatio = L.fold (L.premap (ratio . rcast) avg) <$> loadRows
  where avg = (/) <$> L.sum <*> L.genericLength

Missing Header Row

Now consider a case where our data file lacks a header row (I deleted the first row from `prestige.csv`). We will provide our own name for the generated row type, our own column names, and, for the sake of demonstration, we will also specify a prefix to be added to every column-based identifier (particularly useful if the column names do come from a header row, and you want to work with multiple CSV files some of whose column names coincide). We customize behavior by updating whichever fields of the record produced by rowGen we care to change, passing the result to tableTypes'. Link to code.

{-# LANGUAGE DataKinds, FlexibleContexts, QuasiQuotes, TemplateHaskell #-}
module UncurryFoldNoHeader where
import qualified Control.Foldl as L
import Data.Vinyl (rcast)
import Data.Vinyl.Curry (runcurryX)
import Frames
import Frames.TH (rowGen, RowGen(..))

-- Data set from http://vincentarelbundock.github.io/Rdatasets/datasets.html
tableTypes' (rowGen "test/data/prestigeNoHeader.csv")
            { rowTypeName = "NoH"
            , columnNames = [ "Job", "Schooling", "Money", "Females"
                            , "Respect", "Census", "Category" ]
            , tablePrefix = "NoHead"}

loadRows :: IO (Frame NoH)
loadRows = inCoreAoS (readTableOpt noHParser "test/data/prestigeNoHeader.csv")

-- | Compute the ratio of money to respect for a record containing
-- only those fields.
ratio :: Record '[NoHeadMoney, NoHeadRespect] -> Double
ratio = runcurryX (\m r -> fromIntegral m / r)

averageRatio :: IO Double
averageRatio = L.fold (L.premap (ratio . rcast) avg) <$> loadRows
  where avg = (/) <$> L.sum <*> L.genericLength

Missing Data

Sometimes not every row has a value for every column. I went ahead and blanked the prestige column of every row whose type column was NA in prestige.csv. For example, the first such row now reads,

"athletes",11.44,8206,8.13,,3373,NA

We can no longer parse a Double for that row, so we will work with row types parameterized by a Maybe type constructor. We are substantially filtering our data, so we will perform this operation in a streaming fashion without ever loading the entire table into memory. Our process will be to check if the prestige column was parsed, only keeping those rows for which it was not, then project the income column from those rows, and finally throw away Nothing elements. Link to code.

{-# LANGUAGE DataKinds, FlexibleContexts, QuasiQuotes, TemplateHaskell, TypeApplications, TypeOperators #-}
module UncurryFoldPartialData where
import qualified Control.Foldl as L
import Data.Maybe (isNothing)
import Data.Vinyl.XRec (toHKD)
import Frames
import Pipes (Producer, (>->))
import qualified Pipes.Prelude as P

-- Data set from http://vincentarelbundock.github.io/Rdatasets/datasets.html
-- The prestige column has been left blank for rows whose "type" is
-- listed as "NA".
tableTypes "Row" "test/data/prestigePartial.csv"

-- | A pipes 'Producer' of our 'Row' type with a column functor of
-- 'Maybe'. That is, each element of each row may have failed to parse
-- from the CSV file.
maybeRows :: MonadSafe m => Producer (Rec (Maybe :. ElField) (RecordColumns Row)) m ()
maybeRows = readTableMaybe "test/data/prestigePartial.csv"

-- | Return the number of rows with unknown prestige, and the average
-- income of those rows.
incomeOfUnknownPrestige :: IO (Int, Double)
incomeOfUnknownPrestige =
  runSafeEffect . L.purely P.fold avg $
    maybeRows >-> P.filter prestigeUnknown >-> P.map getIncome >-> P.concat
  where avg = (\s l -> (l, s / fromIntegral l)) <$> L.sum <*> L.length
        getIncome = fmap fromIntegral . toHKD . rget @Income
        prestigeUnknown :: Rec (Maybe :. ElField) (RecordColumns Row) -> Bool
        prestigeUnknown = isNothing . toHKD . rget @Prestige

Tutorial

For comparison to working with data frames in other languages, see the tutorial.

Demos

There are various demos in the repository. Be sure to run the getdata build target to download the data files used by the demos! You can also download the data files manually and put them in a data directory in the directory from which you will be running the executables.

Benchmarks

The benchmark shows several ways of dealing with data when you want to perform multiple traversals.

Another demo shows how to fuse multiple passes into one so that the full data set is never resident in memory. A Pandas version of a similar program is also provided for comparison.

This is a trivial program, but shows that performance is comparable to Pandas, and the memory savings of a compiled program are substantial.

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