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DataBackend for dplyr/dbplyr

Source: R/DataBackendDplyr.R
DataBackendDplyr.Rd

A mlr3::DataBackend using dplyr::tbl() from packages dplyr/dbplyr. This includes tibbles and abstract database connections interfaced by dbplyr. The latter allows mlr3::Tasks to interface an out-of-memory database.

Super class

mlr3::DataBackend -> DataBackendDplyr

Public fields

levels

(named list())
List (named with column names) of factor levels as character(). Used to auto-convert character columns to factor variables.

connector

(function())
Function which is called to re-connect in case the connection became invalid.

Active bindings

rownames

(integer())
Returns vector of all distinct row identifiers, i.e. the contents of the primary key column.

colnames

(character())
Returns vector of all column names, including the primary key column.

nrow

(integer(1))
Number of rows (observations).

ncol

(integer(1))
Number of columns (variables), including the primary key column.

valid

(logical(1))
Returns NA if the data does not inherits from "tbl_sql" (i.e., it is not a real SQL data base). Returns the result of DBI::dbIsValid() otherwise.

Methods

Public methods

Inherited methods

Method new()

Creates a backend for a dplyr::tbl() object.

Usage

DataBackendDplyr$new(
  data,
  primary_key,
  strings_as_factors = TRUE,
  connector = NULL
)

Arguments

data

(dplyr::tbl())
The data object.

Instead of calling the constructor yourself, you can call mlr3::as_data_backend() on a dplyr::tbl(). Note that only objects of class "tbl_lazy" will be converted to a DataBackendDplyr (this includes all connectors from dbplyr). Local "tbl" objects such as tibbles will converted to a DataBackendDataTable.

primary_key

(character(1))
Name of the primary key column.

strings_as_factors

(logical(1) || character())
Either a character vector of column names to convert to factors, or a single logical flag: if FALSE, no column will be converted, if TRUE all string columns (except the primary key). For conversion, the backend is queried for distinct values of the respective columns on construction and their levels are stored in $levels.

connector

(function())\cr If not NULL`, a function which re-connects to the database in case the connection has become invalid. Database connections can become invalid due to timeouts or if the backend is serialized to the file system and then de-serialized again. This round trip is often performed for parallelization, e.g. to send the objects to remote workers. DBI::dbIsValid() is called to validate the connection. The function must return just the connection, not a dplyr::tbl() object! Note that this this function is serialized together with the backend, including possible sensitive information such as login credentials. These can be retrieved from the stored mlr3::DataBackend/mlr3::Task. To protect your credentials, it is recommended to use the secret package.

Method finalize()

Finalizer which disconnects from the database. This is called during garbage collection of the instance.

Usage

DataBackendDplyr$finalize()

Returns

logical(1), the return value of DBI::dbDisconnect().

Method data()

Returns a slice of the data. Calls dplyr::filter() and dplyr::select() on the table and converts it to a data.table::data.table().

The rows must be addressed as vector of primary key values, columns must be referred to via column names. Queries for rows with no matching row id and queries for columns with no matching column name are silently ignored. Rows are guaranteed to be returned in the same order as rows, columns may be returned in an arbitrary order. Duplicated row ids result in duplicated rows, duplicated column names lead to an exception.

Usage

DataBackendDplyr$data(rows, cols, data_format = "data.table")

Arguments

rows

integer()
Row indices.

cols

character()
Column names.

data_format

(character(1))
Desired data format, e.g. "data.table" or "Matrix".

Method head()

Retrieve the first n rows.

Usage

DataBackendDplyr$head(n = 6L)

Arguments

n

(integer(1))
Number of rows.

Returns

data.table::data.table() of the first n rows.

Method distinct()

Returns a named list of vectors of distinct values for each column specified. If na_rm is TRUE, missing values are removed from the returned vectors of distinct values. Non-existing rows and columns are silently ignored.

Usage

DataBackendDplyr$distinct(rows, cols, na_rm = TRUE)

Arguments

rows

integer()
Row indices.

cols

character()
Column names.

na_rm

logical(1)
Whether to remove NAs or not.

Returns

Named list() of distinct values.

Method missings()

Returns the number of missing values per column in the specified slice of data. Non-existing rows and columns are silently ignored.

Usage

DataBackendDplyr$missings(rows, cols)

Arguments

rows

integer()
Row indices.

cols

character()
Column names.

Returns

Total of missing values per column (named numeric()).

Examples

if (mlr3misc::require_namespaces(c("tibble", "RSQLite", "dbplyr"), quietly = TRUE)) {
  # Backend using a in-memory tibble
  data = tibble::as_tibble(iris)
  data$Sepal.Length[1:30] = NA
  data$row_id = 1:150
  b = DataBackendDplyr$new(data, primary_key = "row_id")

  # Object supports all accessors of DataBackend
  print(b)
  b$nrow
  b$ncol
  b$colnames
  b$data(rows = 100:101, cols = "Species")
  b$distinct(b$rownames, "Species")

  # Classification task using this backend
  task = mlr3::TaskClassif$new(id = "iris_tibble", backend = b, target = "Species")
  print(task)
  head(task)

  # Create a temporary SQLite database
  con = DBI::dbConnect(RSQLite::SQLite(), ":memory:")
  dplyr::copy_to(con, data)
  tbl = dplyr::tbl(con, "data")

  # Define a backend on a subset of the database: do not use column "Sepal.Width"
  tbl = dplyr::select_at(tbl, setdiff(colnames(tbl), "Sepal.Width"))
  tbl = dplyr::filter(tbl, row_id %in% 1:120) # Use only first 120 rows
  b = DataBackendDplyr$new(tbl, primary_key = "row_id")
  print(b)

  # Query disinct values
  b$distinct(b$rownames, "Species")

  # Query number of missing values
  b$missings(b$rownames, b$colnames)

  # Note that SQLite does not support factors, column Species has been converted to character
  lapply(b$head(), class)

  # Cleanup
  rm(tbl)
  DBI::dbDisconnect(con)
}
#> <DataBackendDplyr> (150x6)
#>  Sepal.Length Sepal.Width Petal.Length Petal.Width Species row_id
#>            NA         3.5          1.4         0.2  setosa      1
#>            NA         3.0          1.4         0.2  setosa      2
#>            NA         3.2          1.3         0.2  setosa      3
#>            NA         3.1          1.5         0.2  setosa      4
#>            NA         3.6          1.4         0.2  setosa      5
#>            NA         3.9          1.7         0.4  setosa      6
#> [...] (144 rows omitted)
#> <TaskClassif:iris_tibble> (150 x 5)
#> * Target: Species
#> * Properties: multiclass
#> * Features (4):
#>   - dbl (4): Petal.Length, Petal.Width, Sepal.Length, Sepal.Width
#> <DataBackendDplyr> (120x5)
#>  Sepal.Length Petal.Length Petal.Width Species row_id
#>            NA          1.4         0.2  setosa      1
#>            NA          1.4         0.2  setosa      2
#>            NA          1.3         0.2  setosa      3
#>            NA          1.5         0.2  setosa      4
#>            NA          1.4         0.2  setosa      5
#>            NA          1.7         0.4  setosa      6
#> [...] (114 rows omitted)