5.3 Database Backends

In mlr3, Tasks store their data in an abstract data format, the DataBackend. The default backend uses data.table via the DataBackendDataTable as an in-memory data base.

For larger data, or when working with many tasks in parallel, it can be advantageous to interface an out-of-memory data. We use the excellent R package dbplyr which extends dplyr to work on many popular data bases like MariaDB, PostgreSQL or SQLite.

5.3.1 Use Case: NYC Flights

To generate a halfway realistic scenario, we use the NYC flights data set from package nycflights13:

# load data
requireNamespace("DBI")
## Loading required namespace: DBI
requireNamespace("RSQLite")
## Loading required namespace: RSQLite
requireNamespace("nycflights13")
## Loading required namespace: nycflights13
data("flights", package = "nycflights13")
str(flights)
## Classes 'tbl_df', 'tbl' and 'data.frame':    336776 obs. of  19 variables:
##  $ year          : int  2013 2013 2013 2013 2013 2013 2013 2013 2013 2013 ...
##  $ month         : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ day           : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ dep_time      : int  517 533 542 544 554 554 555 557 557 558 ...
##  $ sched_dep_time: int  515 529 540 545 600 558 600 600 600 600 ...
##  $ dep_delay     : num  2 4 2 -1 -6 -4 -5 -3 -3 -2 ...
##  $ arr_time      : int  830 850 923 1004 812 740 913 709 838 753 ...
##  $ sched_arr_time: int  819 830 850 1022 837 728 854 723 846 745 ...
##  $ arr_delay     : num  11 20 33 -18 -25 12 19 -14 -8 8 ...
##  $ carrier       : chr  "UA" "UA" "AA" "B6" ...
##  $ flight        : int  1545 1714 1141 725 461 1696 507 5708 79 301 ...
##  $ tailnum       : chr  "N14228" "N24211" "N619AA" "N804JB" ...
##  $ origin        : chr  "EWR" "LGA" "JFK" "JFK" ...
##  $ dest          : chr  "IAH" "IAH" "MIA" "BQN" ...
##  $ air_time      : num  227 227 160 183 116 150 158 53 140 138 ...
##  $ distance      : num  1400 1416 1089 1576 762 ...
##  $ hour          : num  5 5 5 5 6 5 6 6 6 6 ...
##  $ minute        : num  15 29 40 45 0 58 0 0 0 0 ...
##  $ time_hour     : POSIXct, format: "2013-01-01 05:00:00" "2013-01-01 05:00:00" ...

# add column of unique row ids
flights$row_id = 1:nrow(flights)

# create sqlite database in temporary file
path = tempfile("flights", fileext = ".sqlite")
con = DBI::dbConnect(RSQLite::SQLite(), path)
tbl = DBI::dbWriteTable(con, "flights", as.data.frame(flights))
DBI::dbDisconnect(con)

# remove in-memory data
rm(flights)

5.3.2 Preprocessing with `dplyr`

With the SQLite database in path, we now re-establish a connection and switch to dplyr/dbplyr for some essential preprocessing.

# establish connection
con = DBI::dbConnect(RSQLite::SQLite(), path)

# select the "flights" table, enter dplyr
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:data.table':
## 
##     between, first, last
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(dbplyr)
## 
## Attaching package: 'dbplyr'
## The following objects are masked from 'package:dplyr':
## 
##     ident, sql
tbl = tbl(con, "flights")

First, we select a subset of columns to work on:

keep = c("row_id", "year", "month", "day", "hour", "minute", "dep_time",
  "arr_time", "carrier", "flight", "air_time", "distance", "arr_delay")
tbl = select(tbl, keep)

Additionally, we remove those observations where the arrival delay (arr_delay) has a missing value:

tbl = filter(tbl, !is.na(arr_delay))

To keep runtime reasonable for this toy example, we filter the data to only use every second row:

tbl = filter(tbl, row_id %% 2 == 0)

The factor levels of the feature carrier are merged so that infrequent carriers are replaced by level “other”:

tbl = mutate(tbl, carrier = case_when(
    carrier %in% c("OO", "HA", "YV", "F9", "AS", "FL", "VX", "WN") ~ "other",
    TRUE ~ carrier)
)

5.3.3 DataBackendDplyr

The processed table is now used to create a mlr3db::DataBackendDplyr from mlr3db:

library("mlr3db")
b = as_data_backend(tbl, primary_key = "row_id")

We can now use the interface of DataBackend to query some basic information of the data:

b$nrow
## [1] 163707
b$ncol
## [1] 13
b$head()
##    row_id year month day hour minute dep_time arr_time carrier flight air_time
## 1:      2 2013     1   1    5     29      533      850      UA   1714      227
## 2:      4 2013     1   1    5     45      544     1004      B6    725      183
## 3:      6 2013     1   1    5     58      554      740      UA   1696      150
## 4:      8 2013     1   1    6      0      557      709      EV   5708       53
## 5:     10 2013     1   1    6      0      558      753      AA    301      138
## 6:     12 2013     1   1    6      0      558      853      B6     71      158
##    distance arr_delay
## 1:     1416        20
## 2:     1576       -18
## 3:      719        12
## 4:      229       -14
## 5:      733         8
## 6:     1005        -3

Note that the DataBackendDplyr does not know about any rows or columns we have filtered out with dplyr before, it just operates on the view we provided.

5.3.4 Model fitting

We create the following mlr3 objects:

A regression task, based on the previously created mlr3db::DataBackendDplyr.
A regression learner (regr.rpart).
A resampling strategy: 3 times repeated subsampling using 2% of the observations for training (“subsampling”)
Measures “mse”, “time_predict” and “time_predict”

task = TaskRegr$new("flights_sqlite", b, target = "arr_delay")
learner = lrn("regr.rpart")
measures = mlr_measures$mget(c("regr.mse", "time_train", "time_predict"))
resampling = rsmp("subsampling")
resampling$param_set$values = list(repeats = 3, ratio = 0.02)

We pass all these objects to resample() to perform a simple resampling with three iterations. In each iteration, only the required subset of the data is queried from the SQLite data base and passed to rpart::rpart():

rr = resample(task, learner, resampling)
print(rr)
## <ResampleResult> of 3 iterations
## * Task: flights_sqlite
## * Learner: regr.rpart
## * Warnings: 0 in 0 iterations
## * Errors: 0 in 0 iterations
rr$aggregate(measures)
##     regr.mse   time_train time_predict 
##    1203.1042       0.1653       1.8210

5.3.5 Cleanup

Finally, we remove the tbl object and close the connection.

rm(tbl)
DBI::dbDisconnect(con)