Package 'duckplyr'

Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance. Also defines a set of generics that provide a low-level implementer's interface for the high-level user interface of 'dplyr'.
Authors: Hannes Mühleisen [aut] , Kirill Müller [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Kirill Müller <[email protected]>
License: MIT + file LICENSE
Version: 0.4.1.9003
Built: 2024-11-21 23:46:43 UTC
Source: https://github.com/tidyverse/duckplyr

Help Index


Convert to a duckplyr data frame

Description

These functions convert a data-frame-like input to an object of class "duckpylr_df". For such objects, dplyr verbs such as mutate(), select() or filter() will attempt to use DuckDB. If this is not possible, the original dplyr implementation is used.

as_duckplyr_df() requires the input to be a plain data frame or a tibble, and will fail for any other classes, including subclasses of "data.frame" or "tbl_df". This behavior is likely to change, do not rely on it.

as_duckplyr_tibble() converts the input to a tibble and then to a duckplyr data frame.

Usage

as_duckplyr_df(.data)

as_duckplyr_tibble(.data)

Arguments

.data

data frame or tibble to transform

Details

Set the DUCKPLYR_FALLBACK_INFO and DUCKPLYR_FORCE environment variables for more control over the behavior, see config for more details.

Value

For as_duckplyr_df(), an object of class "duckplyr_df", inheriting from the classes of the .data argument.

For as_duckplyr_tibble(), an object of class c("duckplyr_df", class(tibble())) .

Examples

tibble(a = 1:3) %>%
  mutate(b = a + 1)

tibble(a = 1:3) %>%
  as_duckplyr_df() %>%
  mutate(b = a + 1)

Configuration options

Description

The behavior of duckplyr can be fine-tuned with several environment variables, and one option.

Options

duckdb.materialize_message: Set to FALSE to turn off diagnostic output from duckdb on data frame materialization. Currenty set to TRUE when duckplyr is loaded.

Environment variables

DUCKPLYR_OUTPUT_ORDER: If TRUE, row output order is preserved. The default may change the row order where dplyr would keep it stable.

DUCKPLYR_FORCE: If TRUE, fail if duckdb cannot handle a request.

DUCKPLYR_FALLBACK_INFO: If TRUE, print a message when a fallback to dplyr occurs because duckdb cannot handle a request.

DUCKPLYR_CHECK_ROUNDTRIP: If TRUE, check if all columns are roundtripped perfectly when creating a relational object from a data frame, This is slow, and mostly useful for debugging. The default is to check roundtrip of attributes.

DUCKPLYR_EXPERIMENTAL: If TRUE, pass experimental = TRUE to certain duckdb functions. Currently unused.

DUCKPLYR_METHODS_OVERWRITE: If TRUE, call methods_overwrite() when the package is loaded.

See fallback for more options related to logging and uploading of fallback events.

Examples

# options(duckdb.materialize_message = FALSE)
data.frame(a = 3:1) %>%
  as_duckplyr_df() %>%
  inner_join(data.frame(a = 1:4), by = "a")

rlang::with_options(duckdb.materialize_message = FALSE, {
  data.frame(a = 3:1) %>%
    as_duckplyr_df() %>%
    inner_join(data.frame(a = 1:4), by = "a") %>%
    print()
})

# Sys.setenv(DUCKPLYR_OUTPUT_ORDER = TRUE)
data.frame(a = 3:1) %>%
  as_duckplyr_df() %>%
  inner_join(data.frame(a = 1:4), by = "a")

withr::with_envvar(c(DUCKPLYR_OUTPUT_ORDER = "TRUE"), {
  data.frame(a = 3:1) %>%
    as_duckplyr_df() %>%
    inner_join(data.frame(a = 1:4), by = "a")
})

# Sys.setenv(DUCKPLYR_FORCE = TRUE)
add_one <- function(x) {
  x + 1
}

data.frame(a = 3:1) %>%
  as_duckplyr_df() %>%
  mutate(b = add_one(a))

try(withr::with_envvar(c(DUCKPLYR_FORCE = "TRUE"), {
  data.frame(a = 3:1) %>%
    as_duckplyr_df() %>%
    mutate(b = add_one(a))
}))

# Sys.setenv(DUCKPLYR_FALLBACK_INFO = TRUE)
withr::with_envvar(c(DUCKPLYR_FALLBACK_INFO = "TRUE"), {
  data.frame(a = 3:1) %>%
    as_duckplyr_df() %>%
    mutate(b = add_one(a))
})

Read Parquet, CSV, and other files using DuckDB

Description

df_from_file() uses arbitrary table functions to read data. See https://duckdb.org/docs/data/overview for a documentation of the available functions and their options. To read multiple files with the same schema, pass a wildcard or a character vector to the path argument,

duckplyr_df_from_file() is a thin wrapper around df_from_file() that calls as_duckplyr_df() on the output.

These functions ingest data from a file using a table function. The results are transparently converted to a data frame, but the data is only read when the resulting data frame is actually accessed.

df_from_csv() reads a CSV file using the read_csv_auto() table function.

duckplyr_df_from_csv() is a thin wrapper around df_from_csv() that calls as_duckplyr_df() on the output.

df_from_parquet() reads a Parquet file using the read_parquet() table function.

duckplyr_df_from_parquet() is a thin wrapper around df_from_parquet() that calls as_duckplyr_df() on the output.

df_to_parquet() writes a data frame to a Parquet file via DuckDB. If the data frame is a duckplyr_df, the materialization occurs outside of R. An existing file will be overwritten. This function requires duckdb >= 0.10.0.

Usage

df_from_file(path, table_function, ..., options = list(), class = NULL)

duckplyr_df_from_file(
  path,
  table_function,
  ...,
  options = list(),
  class = NULL
)

df_from_csv(path, ..., options = list(), class = NULL)

duckplyr_df_from_csv(path, ..., options = list(), class = NULL)

df_from_parquet(path, ..., options = list(), class = NULL)

duckplyr_df_from_parquet(path, ..., options = list(), class = NULL)

df_to_parquet(data, path)

Arguments

path

Path to files, glob patterns * and ⁠?⁠ are supported.

table_function

The name of a table-valued DuckDB function such as "read_parquet", "read_csv", "read_csv_auto" or "read_json".

...

These dots are for future extensions and must be empty.

options

Arguments to the DuckDB function indicated by table_function.

class

The class of the output. By default, a tibble is created. The returned object will always be a data frame. Use class = "data.frame" or class = character() to create a plain data frame.

data

A data frame to be written to disk.

Value

A data frame for df_from_file(), or a duckplyr_df for duckplyr_df_from_file(), extended by the provided class.

Examples

# Create simple CSV file
path <- tempfile("duckplyr_test_", fileext = ".csv")
write.csv(data.frame(a = 1:3, b = letters[4:6]), path, row.names = FALSE)

# Reading is immediate
df <- df_from_csv(path)

# Materialization only upon access
names(df)
df$a

# Return as tibble, specify column types:
df_from_file(
  path,
  "read_csv",
  options = list(delim = ",", types = list(c("DOUBLE", "VARCHAR"))),
  class = class(tibble())
)

# Read multiple file at once
path2 <- tempfile("duckplyr_test_", fileext = ".csv")
write.csv(data.frame(a = 4:6, b = letters[7:9]), path2, row.names = FALSE)

duckplyr_df_from_csv(file.path(tempdir(), "duckplyr_test_*.csv"))

unlink(c(path, path2))

# Write a Parquet file:
path_parquet <- tempfile(fileext = ".parquet")
df_to_parquet(df, path_parquet)

# With a duckplyr_df, the materialization occurs outside of R:
df %>%
  as_duckplyr_df() %>%
  mutate(b = a + 1) %>%
  df_to_parquet(path_parquet)

duckplyr_df_from_parquet(path_parquet)

unlink(path_parquet)

Execute a statement for the default connection

Description

The duckplyr package relies on a DBI connection to an in-memory database. The duckplyr_execute() function allows running SQL statements with this connection to, e.g., set up credentials or attach other databases.

Usage

duckplyr_execute(sql)

Arguments

sql

The statement to run.

Value

The return value of the DBI::dbExecute() call, invisibly.

Examples

duckplyr_execute("SET threads TO 2")

Fallback to dplyr

Description

The duckplyr package aims at providing a fully compatible drop-in replacement for dplyr. To achieve this, only a carefully selected subset of dplyr's operations, R functions, and R data types are implemented. Whenever duckplyr encounters an incompatibility, it falls back to dplyr.

To assist future development, the fallback situations can be logged to the console or to a local file and uploaded for analysis. By default, duckplyr will not log or upload anything. The functions and environment variables on this page control the process.

fallback_sitrep() prints the current settings for fallback logging and uploading, the number of reports ready for upload, and the location of the logs.

fallback_review() prints the available reports for review to the console.

fallback_upload() uploads the available reports to a central server for analysis. The server is hosted on AWS and the reports are stored in a private S3 bucket. Only authorized personnel have access to the reports.

fallback_purge() deletes some or all available reports.

Usage

fallback_sitrep()

fallback_review(oldest = NULL, newest = NULL, detail = TRUE)

fallback_upload(oldest = NULL, newest = NULL, strict = TRUE)

fallback_purge(oldest = NULL, newest = NULL)

Arguments

oldest, newest

The number of oldest or newest reports to review. If not specified, all reports are dispayed.

detail

Print the full content of the reports. Set to FALSE to only print the file names.

strict

If TRUE, the function aborts if any of the reports fail to upload. With FALSE, only a message is printed.

Details

Logging and uploading are both opt-in. By default, for logging, a message is printed to the console for the first time in a session and then once every 8 hours.

The following environment variables control the logging and uploading:

  • DUCKPLYR_FALLBACK_COLLECT controls logging, set it to 1 or greater to enable logging. If the value is 0, logging is disabled. Future versions of duckplyr may start logging additional data and thus require a higher value to enable logging. Set to 99 to enable logging for all future versions. Use usethis::edit_r_environ() to edit the environment file.

  • DUCKPLYR_FALLBACK_VERBOSE controls printing, set it to TRUE or FALSE to enable or disable printing. If the value is TRUE, a message is printed to the console for each fallback situation. This setting is only relevant if logging is enabled.

  • DUCKPLYR_FALLBACK_AUTOUPLOAD controls uploading, set it to 1 or greater to enable uploading. If the value is 0, uploading is disabled. Currently, uploading is active if the value is 1 or greater. Future versions of duckplyr may start logging additional data and thus require a higher value to enable uploading. Set to 99 to enable uploading for all future versions. Use usethis::edit_r_environ() to edit the environment file.

  • DUCKPLYR_FALLBACK_LOG_DIR controls the location of the logs. It must point to a directory (existing or not) where the logs will be written. By default, logs are written to a directory in the user's cache directory as returned by tools::R_user_dir("duckplyr", "cache").

All code related to fallback logging and uploading is in the fallback.R and telemetry.R files.

Examples

fallback_sitrep()

Class predicate for duckplyr data frames

Description

Tests if the input object is of class "duckplyr_df".

Usage

is_duckplyr_df(.data)

Arguments

.data

The object to test

Value

TRUE if the input object is of class "duckplyr_df", otherwise FALSE.

Examples

tibble(a = 1:3) %>%
  is_duckplyr_df()

tibble(a = 1:3) %>%
  as_duckplyr_df() %>%
  is_duckplyr_df()

Forward all dplyr methods to duckplyr

Description

After calling methods_overwrite(), all dplyr methods are redirected to duckplyr for the duraton of the session, or until a call to methods_restore(). The methods_overwrite() function is called automatically when the package is loaded if the environment variable DUCKPLYR_METHODS_OVERWRITE is set to TRUE.

Usage

methods_overwrite()

methods_restore()

Value

Called for their side effects.

Examples

tibble(a = 1:3) %>%
  mutate(b = a + 1)

methods_overwrite()

tibble(a = 1:3) %>%
  mutate(b = a + 1)

methods_restore()

tibble(a = 1:3) %>%
  mutate(b = a + 1)

Relational implementer's interface

Description

The constructor and generics described here define a class that helps separating dplyr's user interface from the actual underlying operations. In the longer term, this will help packages that implement the dplyr interface (such as dbplyr, dtplyr, arrow and similar) to focus on the core details of their functionality, rather than on the intricacies of dplyr's user interface.

new_relational() constructs an object of class "relational". Users are encouraged to provide the class argument. The typical use case will be to create a wrapper function.

rel_to_df() extracts a data frame representation from a relational object, to be used by dplyr::collect().

rel_filter() keeps rows that match a predicate, to be used by dplyr::filter().

rel_project() selects columns or creates new columns, to be used by dplyr::select(), dplyr::rename(), dplyr::mutate(), dplyr::relocate(), and others.

rel_aggregate() combines several rows into one, to be used by dplyr::summarize().

rel_order() reorders rows by columns or expressions, to be used by dplyr::arrange().

rel_join() joins or merges two tables, to be used by dplyr::left_join(), dplyr::right_join(), dplyr::inner_join(), dplyr::full_join(), dplyr::cross_join(), dplyr::semi_join(), and dplyr::anti_join().

rel_limit() limits the number of rows in a table, to be used by utils::head().

rel_distinct() only keeps the distinct rows in a table, to be used by dplyr::distinct().

rel_set_intersect() returns rows present in both tables, to be used by intersect().

rel_set_diff() returns rows present in any of both tables, to be used by setdiff().

rel_set_symdiff() returns rows present in any of both tables, to be used by dplyr::symdiff().

rel_union_all() returns rows present in any of both tables, to be used by dplyr::union_all().

rel_explain() prints an explanation of the plan executed by the relational object.

rel_alias() returns the alias name for a relational object.

rel_set_alias() sets the alias name for a relational object.

rel_names() returns the column names as character vector, to be used by colnames().

Usage

new_relational(..., class = NULL)

rel_to_df(rel, ...)

rel_filter(rel, exprs, ...)

rel_project(rel, exprs, ...)

rel_aggregate(rel, groups, aggregates, ...)

rel_order(rel, orders, ascending, ...)

rel_join(
  left,
  right,
  conds,
  join = c("inner", "left", "right", "outer", "cross", "semi", "anti"),
  join_ref_type = c("regular", "natural", "cross", "positional", "asof"),
  ...
)

rel_limit(rel, n, ...)

rel_distinct(rel, ...)

rel_set_intersect(rel_a, rel_b, ...)

rel_set_diff(rel_a, rel_b, ...)

rel_set_symdiff(rel_a, rel_b, ...)

rel_union_all(rel_a, rel_b, ...)

rel_explain(rel, ...)

rel_alias(rel, ...)

rel_set_alias(rel, alias, ...)

rel_names(rel, ...)

Arguments

...

Reserved for future extensions, must be empty.

class

Classes added in front of the "relational" base class.

rel, rel_a, rel_b, left, right

A relational object.

exprs

A list of "relational_relexpr" objects to filter by, created by new_relexpr().

groups

A list of expressions to group by.

aggregates

A list of expressions with aggregates to compute.

orders

A list of expressions to order by.

ascending

A logical vector describing the sort order.

conds

A list of expressions to use for the join.

join

The type of join.

join_ref_type

The ref type of join.

n

The number of rows.

alias

the new alias

Value

  • new_relational() returns a new relational object.

  • rel_to_df() returns a data frame.

  • rel_names() returns a character vector.

  • All other generics return a modified relational object.

Examples

new_dfrel <- function(x) {
  stopifnot(is.data.frame(x))
  new_relational(list(x), class = "dfrel")
}
mtcars_rel <- new_dfrel(mtcars[1:5, 1:4])

rel_to_df.dfrel <- function(rel, ...) {
  unclass(rel)[[1]]
}
rel_to_df(mtcars_rel)

rel_filter.dfrel <- function(rel, exprs, ...) {
  df <- unclass(rel)[[1]]

  # A real implementation would evaluate the predicates defined
  # by the exprs argument
  new_dfrel(df[seq_len(min(3, nrow(df))), ])
}

rel_filter(
  mtcars_rel,
  list(
    relexpr_function(
      "gt",
      list(relexpr_reference("cyl"), relexpr_constant("6"))
    )
  )
)

rel_project.dfrel <- function(rel, exprs, ...) {
  df <- unclass(rel)[[1]]

  # A real implementation would evaluate the expressions defined
  # by the exprs argument
  new_dfrel(df[seq_len(min(3, ncol(df)))])
}

rel_project(
  mtcars_rel,
  list(relexpr_reference("cyl"), relexpr_reference("disp"))
)

rel_order.dfrel <- function(rel, exprs, ...) {
  df <- unclass(rel)[[1]]

  # A real implementation would evaluate the expressions defined
  # by the exprs argument
  new_dfrel(df[order(df[[1]]), ])
}

rel_order(
  mtcars_rel,
  list(relexpr_reference("mpg"))
)

rel_join.dfrel <- function(left, right, conds, join, ...) {
  left_df <- unclass(left)[[1]]
  right_df <- unclass(right)[[1]]

  # A real implementation would evaluate the expressions
  # defined by the conds argument,
  # use different join types based on the join argument,
  # and implement the join itself instead of relaying to left_join().
  new_dfrel(dplyr::left_join(left_df, right_df))
}

rel_join(new_dfrel(data.frame(mpg = 21)), mtcars_rel)


rel_limit.dfrel <- function(rel, n, ...) {
  df <- unclass(rel)[[1]]

  new_dfrel(df[seq_len(n), ])
}

rel_limit(mtcars_rel, 3)

rel_distinct.dfrel <- function(rel, ...) {
  df <- unclass(rel)[[1]]

  new_dfrel(df[!duplicated(df), ])
}

rel_distinct(new_dfrel(mtcars[1:3, 1:4]))

rel_names.dfrel <- function(rel, ...) {
  df <- unclass(rel)[[1]]

  names(df)
}

rel_names(mtcars_rel)

Relational expressions

Description

These functions provide a backend-agnostic way to construct expression trees built of column references, constants, and functions. All subexpressions in an expression tree can have an alias.

new_relexpr() constructs an object of class "relational_relexpr". It is used by the higher-level constructors, users should rarely need to call it directly.

relexpr_reference() constructs a reference to a column.

relexpr_constant() wraps a constant value.

relexpr_function() applies a function. The arguments to this function are a list of other expression objects.

relexpr_window() applies a function over a window, similarly to the SQL OVER clause.

relexpr_set_alias() assigns an alias to an expression.

Usage

new_relexpr(x, class = NULL)

relexpr_reference(name, rel = NULL, alias = NULL)

relexpr_constant(val, alias = NULL)

relexpr_function(name, args, alias = NULL)

relexpr_window(
  expr,
  partitions,
  order_bys = list(),
  offset_expr = NULL,
  default_expr = NULL,
  alias = NULL
)

relexpr_set_alias(expr, alias = NULL)

Arguments

x

An object.

class

Classes added in front of the "relational_relexpr" base class.

name

The name of the column or function to reference.

rel

The name of the relation to reference.

alias

An alias for the new expression.

val

The value to use in the constant expression.

args

Function arguments, a list of expr objects.

expr

An expr object.

partitions

Partitions, a list of expr objects.

order_bys

which variables to order results by (list).

offset_expr

offset relational expression.

default_expr

default relational expression.

Value

an object of class "relational_relexpr"

an object of class "relational_relexpr"

an object of class "relational_relexpr"

an object of class "relational_relexpr"

an object of class "relational_relexpr"

Examples

relexpr_set_alias(
  alias = "my_predicate",
  relexpr_function(
    "<",
    list(
      relexpr_reference("my_number"),
      relexpr_constant(42)
    )
  )
)

Show stats

Description

Prints statistics on how many calls were handled by DuckDB. The output shows the total number of requests in the current session, split by fallbacks to dplyr and requests handled by duckdb.

Usage

stats_show()

Value

Called for its side effect.

Examples

stats_show()

tibble(a = 1:3) %>%
  as_duckplyr_df() %>%
  mutate(b = a + 1)

stats_show()