andrewla / dplyr

Plyr specialised for data frames: faster & with remote datastores

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dplyr

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dplyr is the next iteration of plyr, focussed on tools for working with data frames (hence the d in the name). It has three main goals:

  • Identify the most important data manipulation tools needed for data analysis and make them easy to use from R.

  • Provide blazing fast performance for in-memory data by writing key pieces in C++.

  • Use the same interface to work with data no matter where it's stored, whether in a data frame, a data table or database.

You can install:

  • the latest released version from CRAN with

    install.packages("dplyr")
  • the latest development version from github with

    devtools::install_github("hadley/dplyr")

To get started, read the notes below, then read the intro vignette: vignette("introduction", package = "dplyr"). To make the most of dplyr, I also recommend that you familiarise yourself with the principles of tidy data: this will help you get your data into a form that works well with dplyr, ggplot2 and R's many modelling functions.

If you encounter a clear bug, please file a minimal reproducible example on github. For questions and other discussion, please use the manipulatr mailing list.

tbls

The key object in dplyr is a tbl, a representation of a tabular data structure. Currently dplyr supports:

You can create them as follows:

library(dplyr) # for functions
library(hflights) # for data
head(hflights)

# Coerce to data table
hflights_dt <- tbl_dt(hflights)

# Caches data in local SQLite db
hflights_db1 <- tbl(hflights_sqlite(), "hflights")

# Caches data in local postgres db
hflights_db2 <- tbl(hflights_postgres(), "hflights")

Each tbl also comes in a grouped variant which allows you to easily perform operations "by group":

carriers_df  <- group_by(hflights, UniqueCarrier)
carriers_dt  <- group_by(hflights_dt, UniqueCarrier)
carriers_db1 <- group_by(hflights_db1, UniqueCarrier)
carriers_db2 <- group_by(hflights_db2, UniqueCarrier)

Single table verbs

dplyr implements the following verbs useful for data manipulation:

  • select(): focus on a subset of variables
  • filter(): focus on a subset of rows
  • mutate(): add new columns
  • summarise(): reduce each group to a smaller number of summary statistics
  • arrange(): re-order the rows

See ?manip for more details.

They all work as similarly as possible across the range of data sources. The main difference is performance:

system.time(summarise(carriers_df, delay = mean(ArrDelay, na.rm = TRUE)))
#   user  system elapsed
#  0.010   0.002   0.012
system.time(summarise(carriers_dt, delay = mean(ArrDelay, na.rm = TRUE)))
#   user  system elapsed
#  0.007   0.000   0.008
system.time(summarise(collect(carriers_db1, delay = mean(ArrDelay))))
#   user  system elapsed
#  0.402   0.058   0.465
system.time(summarise(collect(carriers_db2, delay = mean(ArrDelay))))
#   user  system elapsed
#  0.386   0.097   0.718

The data frame and data table methods are order of magnitude faster than plyr. The database methods are slower, but can work with data that don't fit in memory.

library(plyr)
system.time(ddply(hflights, "UniqueCarrier", summarise,
  delay = mean(ArrDelay, na.rm = TRUE)))
#   user  system elapsed
#  0.527   0.078   0.604

do()

As well as the specialised operations described above, dplyr also provides the generic do() function which applies any R function to each group of the data.

Let's take the batting database from the built-in Lahman database. We'll group it by year, and then fit a model to explore the relationship between their number of at bats and runs:

batting_db <- tbl(lahman_sqlite(), "Batting")
batting_df <- collect(batting_db)
batting_dt <- tbl_dt(batting_df)

years_db <- group_by(batting_db, yearID)
years_df <- group_by(batting_df, yearID)
years_dt <- group_by(batting_dt, yearID)

system.time(do(years_db, failwith(NULL, lm), formula = R ~ AB))
system.time(do(years_df, failwith(NULL, lm), formula = R ~ AB))
system.time(do(years_dt, failwith(NULL, lm), formula = R ~ AB))

Note that if you are fitting lots of linear models, it's a good idea to use biglm because it creates model objects that are considerably smaller:

library(biglm)
mod1 <- do(years_df, lm, formula = R ~ AB)
mod2 <- do(years_df, biglm, formula = R ~ AB)
print(object.size(mod1), unit = "MB")
print(object.size(mod2), unit = "MB")

Binary verbs

As well as verbs that work on a single tbl, there are also a set of useful verbs that work with two tbls are a time: joins. dplyr implements the four most useful joins from SQL:

  • inner_join(x, y): matching x + y
  • left_join(x, y): all x + matching y
  • semi_join(x, y): all x with match in y
  • anti_join(x, y): all x without match in y

Currently join variables must be the same in both the left-hand and right-hand sides.

Other operations

All tbls also provide head() and print() methods. The default print method gives information about the data source and shows the first 10 rows and all the columns that will fit on one screen.

Plyr compatibility

You'll need to be a little careful if you load both plyr and dplyr at the same time. I'd recommend loading plyr first, then dplyr, so that the faster dplyr functions come first in the search path. By and large, any function provided by both dplyr and plyr works in a similar way, although dplyr functions tend to be faster and more general.

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Plyr specialised for data frames: faster & with remote datastores

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