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This vignette introduces the data.table
syntax, its
general form, how to subset rows, select and compute
on columns, and perform aggregations by group. Familiarity with
the data.frame
data structure from base R is useful, but
not essential to follow this vignette.
data.table
Data manipulation operations such as subset, group, update, join, etc. are all inherently related. Keeping these related operations together allows for:
concise and consistent syntax irrespective of the set of operations you would like to perform to achieve your end goal.
performing analysis fluidly without the cognitive burden of having to map each operation to a particular function from a potentially huge set of functions available before performing the analysis.
automatically optimising operations internally and very effectively by knowing precisely the data required for each operation, leading to very fast and memory-efficient code.
Briefly, if you are interested in reducing programming and
compute time tremendously, then this package is for you. The
philosophy that data.table
adheres to makes this possible.
Our goal is to illustrate it through this series of vignettes.
In this vignette, we will use NYC-flights14 data obtained from the flights package (available on GitHub only). It contains On-Time flights data from the Bureau of Transportation Statistics for all the flights that departed from New York City airports in 2014 (inspired by nycflights13). The data is available only for Jan-Oct’14.
We can use data.table
’s fast-and-friendly file reader
fread
to load flights
directly as follows:
input <- if (file.exists("flights14.csv")) {
"flights14.csv"
} else {
"https://raw.githubusercontent.com/Rdatatable/data.table/master/vignettes/flights14.csv"
}
flights <- fread(input)
flights
# year month day dep_delay arr_delay carrier origin dest air_time distance hour
# <int> <int> <int> <int> <int> <char> <char> <char> <int> <int> <int>
# 1: 2014 1 1 14 13 AA JFK LAX 359 2475 9
# 2: 2014 1 1 -3 13 AA JFK LAX 363 2475 11
# 3: 2014 1 1 2 9 AA JFK LAX 351 2475 19
# 4: 2014 1 1 -8 -26 AA LGA PBI 157 1035 7
# 5: 2014 1 1 2 1 AA JFK LAX 350 2475 13
# ---
# 253312: 2014 10 31 1 -30 UA LGA IAH 201 1416 14
# 253313: 2014 10 31 -5 -14 UA EWR IAH 189 1400 8
# 253314: 2014 10 31 -8 16 MQ LGA RDU 83 431 11
# 253315: 2014 10 31 -4 15 MQ LGA DTW 75 502 11
# 253316: 2014 10 31 -5 1 MQ LGA SDF 110 659 8
dim(flights)
# [1] 253316 11
Aside: fread
accepts http
and
https
URLs directly, as well as operating system commands
such as sed
and awk
output. See
?fread
for examples.
In this vignette, we will
Start with the basics - what is a data.table
, its
general form, how to subset rows, how to select and
compute on columns;
Then we will look at performing data aggregations by group
data.table
?data.table
is an R package that provides an
enhanced version of a data.frame
, the standard
data structure for storing data in base
R. In the Data section above, we saw how to create a
data.table
using fread()
, but alternatively we
can also create one using the data.table()
function. Here
is an example:
DT = data.table(
ID = c("b","b","b","a","a","c"),
a = 1:6,
b = 7:12,
c = 13:18
)
DT
# ID a b c
# <char> <int> <int> <int>
# 1: b 1 7 13
# 2: b 2 8 14
# 3: b 3 9 15
# 4: a 4 10 16
# 5: a 5 11 17
# 6: c 6 12 18
class(DT$ID)
# [1] "character"
You can also convert existing objects to a data.table
using setDT()
(for data.frame
and
list
structures) or as.data.table()
(for other
structures). For more details pertaining to the difference (goes beyond
the scope of this vignette), please see ?setDT
and
?as.data.table
.
Row numbers are printed with a :
in order to
visually separate the row number from the first column.
When the number of rows to print exceeds the global option
datatable.print.nrows
(default = 100), it automatically
prints only the top 5 and bottom 5 rows (as can be seen in the Data section). For a large data.frame
, you
may have found yourself waiting around while larger tables
print-and-page, sometimes seemingly endlessly. This restriction helps
with that, and you can query the default number like so:
data.table
doesn’t set or use row names,
ever. We will see why in the vignette("datatable-keys-fast-subset", package="data.table")
vignette.
data.table
enhanced?In contrast to a data.frame
, you can do a lot
more than just subsetting rows and selecting columns within the
frame of a data.table
, i.e., within [ ... ]
(NB: we might also refer to writing things inside DT[...]
as “querying DT
”, as an analogy or in relevance to SQL). To
understand it we will have to first look at the general form of
the data.table
syntax, as shown below:
Users with an SQL background might perhaps immediately relate to this syntax.
Take DT
, subset/reorder rows using i
, then
calculate j
, grouped by by
.
Let’s begin by looking at i
and j
first -
subsetting rows and operating on columns.
i
ans <- flights[origin == "JFK" & month == 6L]
head(ans)
# year month day dep_delay arr_delay carrier origin dest air_time distance hour
# <int> <int> <int> <int> <int> <char> <char> <char> <int> <int> <int>
# 1: 2014 6 1 -9 -5 AA JFK LAX 324 2475 8
# 2: 2014 6 1 -10 -13 AA JFK LAX 329 2475 12
# 3: 2014 6 1 18 -1 AA JFK LAX 326 2475 7
# 4: 2014 6 1 -6 -16 AA JFK LAX 320 2475 10
# 5: 2014 6 1 -4 -45 AA JFK LAX 326 2475 18
# 6: 2014 6 1 -6 -23 AA JFK LAX 329 2475 14
Within the frame of a data.table
, columns can be
referred to as if they are variables, much like in SQL or
Stata. Therefore, we simply refer to origin
and
month
as if they are variables. We do not need to add the
prefix flights$
each time. Nevertheless, using
flights$origin
and flights$month
would work
just fine.
The row indices that satisfy the condition
origin == "JFK" & month == 6L
are computed, and since
there is nothing else left to do, all columns from flights
at rows corresponding to those row indices are simply returned
as a data.table
.
A comma after the condition in i
is not required.
But flights[origin == "JFK" & month == 6L, ]
would work
just fine. In a data.frame
, however, the comma is
necessary.
flights
.ans <- flights[1:2]
ans
# year month day dep_delay arr_delay carrier origin dest air_time distance hour
# <int> <int> <int> <int> <int> <char> <char> <char> <int> <int> <int>
# 1: 2014 1 1 14 13 AA JFK LAX 359 2475 9
# 2: 2014 1 1 -3 13 AA JFK LAX 363 2475 11
i
. We therefore return a
data.table
with all columns from flights
at
rows for those row indices.flights
first by column origin
in
ascending order, and then by dest
in
descending order:We can use the R function order()
to accomplish
this.
ans <- flights[order(origin, -dest)]
head(ans)
# year month day dep_delay arr_delay carrier origin dest air_time distance hour
# <int> <int> <int> <int> <int> <char> <char> <char> <int> <int> <int>
# 1: 2014 1 5 6 49 EV EWR XNA 195 1131 8
# 2: 2014 1 6 7 13 EV EWR XNA 190 1131 8
# 3: 2014 1 7 -6 -13 EV EWR XNA 179 1131 8
# 4: 2014 1 8 -7 -12 EV EWR XNA 184 1131 8
# 5: 2014 1 9 16 7 EV EWR XNA 181 1131 8
# 6: 2014 1 13 66 66 EV EWR XNA 188 1131 9
order()
is internally optimisedWe can use “-” on character
columns within the frame
of a data.table
to sort in decreasing order.
In addition, order(...)
within the frame of a
data.table
uses data.table
’s internal fast
radix order forder()
. This sort provided such a compelling
improvement over R’s base::order
that the R project adopted
the data.table
algorithm as its default sort in 2016 for R
3.3.0 (for reference, check ?sort
and the R
Release NEWS).
We will discuss data.table
’s fast order in more detail
in the data.table
internals vignette.
j
arr_delay
column, but return it as a
vector.Since columns can be referred to as if they are variables within
the frame of a data.table
, we directly refer to the
variable we want to subset. Since we want all the
rows, we simply skip i
.
It returns all the rows for the column
arr_delay
.
arr_delay
column, but return as a
data.table
instead.ans <- flights[, list(arr_delay)]
head(ans)
# arr_delay
# <int>
# 1: 13
# 2: 13
# 3: 9
# 4: -26
# 5: 1
# 6: 0
We wrap the variables (column names) within
list()
, which ensures that a data.table
is
returned. In the case of a single column name, not wrapping with
list()
returns a vector instead, as seen in the previous example.
data.table
also allows wrapping columns with
.()
instead of list()
. It is an alias
to list()
; they both mean the same. Feel free to use
whichever you prefer; we have noticed most users seem to prefer
.()
for conciseness, so we will continue to use
.()
hereafter.
A data.table
(and a data.frame
too) is
internally a list
as well, with the stipulation that each
element has the same length and the list
has a
class
attribute. Allowing j
to return a
list
enables converting and returning
data.table
very efficiently.
As long as j-expression
returns a list
,
each element of the list will be converted to a column in the resulting
data.table
. This makes j
quite powerful, as we
will see shortly. It is also very important to understand this for when
you’d like to make more complicated queries!!
arr_delay
and dep_delay
columns.ans <- flights[, .(arr_delay, dep_delay)]
head(ans)
# arr_delay dep_delay
# <int> <int>
# 1: 13 14
# 2: 13 -3
# 3: 9 2
# 4: -26 -8
# 5: 1 2
# 6: 0 4
## alternatively
# ans <- flights[, list(arr_delay, dep_delay)]
.()
, or list()
.
That’s it.arr_delay
and dep_delay
columns and rename them to delay_arr
and
delay_dep
.Since .()
is just an alias for list()
, we
can name columns as we would while creating a list
.
j
data.table
’s j
can handle more than just
selecting columns - it can handle expressions, i.e.,
computing on columns. This shouldn’t be surprising, as columns
can be referred to as if they are variables. Then we should be able to
compute by calling functions on those variables. And that’s
what precisely happens here.i
and do in j
ans <- flights[origin == "JFK" & month == 6L,
.(m_arr = mean(arr_delay), m_dep = mean(dep_delay))]
ans
# m_arr m_dep
# <num> <num>
# 1: 5.839349 9.807884
We first subset in i
to find matching row
indices where origin
airport equals
"JFK"
, and month
equals 6L
. We
do not subset the entire data.table
corresponding to those rows yet.
Now, we look at j
and find that it uses only two
columns. And what we have to do is to compute their
mean()
. Therefore, we subset just those columns
corresponding to the matching rows, and compute their
mean()
.
Because the three main components of the query (i
,
j
and by
) are together inside
[...]
, data.table
can see all three and
optimise the query altogether before evaluation, rather than
optimizing each separately. We are able to therefore avoid the entire
subset (i.e., subsetting the columns besides
arr_delay
and dep_delay
), for both speed and
memory efficiency.
The function length()
requires an input argument. We
just need to compute the number of rows in the subset. We could have
used any other column as the input argument to length()
.
This approach is reminiscent of
SELECT COUNT(dest) FROM flights WHERE origin = 'JFK' AND month = 6
in SQL.
This type of operation occurs quite frequently, especially while
grouping (as we will see in the next section), to the point where
data.table
provides a special symbol
.N
for it.
i
When querying a data.table
for elements that do not
exist, the behavior differs based on the method used.
Key-based subsetting: dt["d"]
This performs a right join on the key column x
,
resulting in a row with d
and NA
for columns
not found. When using setkeyv
, the table is sorted by the
specified keys and an internal index is created, enabling binary search
for efficient subsetting.
Logical subsetting:
dt[x == "d"]
This performs a standard subset operation that does not find any
matching rows and thus returns an empty data.table
.
Exact match using nomatch=NULL
For exact matches without NA
for non-existing elements,
use nomatch=NULL
:
Understanding these behaviors can help prevent confusion when dealing with non-existing elements in your data.
.N
:.N
is a special built-in variable that holds the number
of observations in the current group. It is particularly useful
when combined with by
as we’ll see in the next section. In
the absence of group by operations, it simply returns the number of rows
in the subset.
Now that we now, we can now accomplish the same task by using
.N
as follows:
Once again, we subset in i
to get the row
indices where origin
airport equals “JFK”,
and month
equals 6.
We see that j
uses only .N
and no other
columns. Therefore, the entire subset is not materialised. We simply
return the number of rows in the subset (which is just the length of row
indices).
Note that we did not wrap .N
with
list()
or .()
. Therefore, a vector is
returned.
We could have accomplished the same operation by doing
nrow(flights[origin == "JFK" & month == 6L])
. However,
it would have to subset the entire data.table
first
corresponding to the row indices in i
and
then return the rows using nrow()
, which is
unnecessary and inefficient. We will cover this and other optimisation
aspects in detail under the data.table
design
vignette.
j
(like in a data.frame
)?If you’re writing out the column names explicitly, there’s no
difference compared to a data.frame
(since v1.9.8).
arr_delay
and dep_delay
columns the data.frame
way.ans <- flights[, c("arr_delay", "dep_delay")]
head(ans)
# arr_delay dep_delay
# <int> <int>
# 1: 13 14
# 2: 13 -3
# 3: 9 2
# 4: -26 -8
# 5: 1 2
# 6: 0 4
If you’ve stored the desired columns in a character vector, there are
two options: Using the ..
prefix, or using the
with
argument.
..
prefixselect_cols = c("arr_delay", "dep_delay")
flights[ , ..select_cols]
# arr_delay dep_delay
# <int> <int>
# 1: 13 14
# 2: 13 -3
# 3: 9 2
# 4: -26 -8
# 5: 1 2
# ---
# 253312: -30 1
# 253313: -14 -5
# 253314: 16 -8
# 253315: 15 -4
# 253316: 1 -5
For those familiar with the Unix terminal, the ..
prefix
should be reminiscent of the “up-one-level” command, which is analogous
to what’s happening here – the ..
signals to
data.table
to look for the select_cols
variable “up-one-level”, i.e., within the global environment in this
case.
with = FALSE
flights[ , select_cols, with = FALSE]
# arr_delay dep_delay
# <int> <int>
# 1: 13 14
# 2: 13 -3
# 3: 9 2
# 4: -26 -8
# 5: 1 2
# ---
# 253312: -30 1
# 253313: -14 -5
# 253314: 16 -8
# 253315: 15 -4
# 253316: 1 -5
The argument is named with
after the R function
with()
because of similar functionality. Suppose you have a
data.frame
DF
and you’d like to subset all
rows where x > 1
. In base
R you can do the
following:
DF = data.frame(x = c(1,1,1,2,2,3,3,3), y = 1:8)
## (1) normal way
DF[DF$x > 1, ] # data.frame needs that ',' as well
# x y
# 4 2 4
# 5 2 5
# 6 3 6
# 7 3 7
# 8 3 8
## (2) using with
DF[with(DF, x > 1), ]
# x y
# 4 2 4
# 5 2 5
# 6 3 6
# 7 3 7
# 8 3 8
Using with()
in (2) allows using DF
’s
column x
as if it were a variable.
Hence, the argument name with
in
data.table
. Setting with = FALSE
disables the
ability to refer to columns as if they are variables, thereby restoring
the “data.frame
mode”.
We can also deselect columns using -
or
!
. For example:
From v1.9.5+
, we can also select by specifying start
and end column names, e.g., year:day
to select the first
three columns.
## not run
# returns year,month and day
ans <- flights[, year:day]
# returns day, month and year
ans <- flights[, day:year]
# returns all columns except year, month and day
ans <- flights[, -(year:day)]
ans <- flights[, !(year:day)]
This is particularly handy while working interactively.
with = TRUE
is the default in data.table
because we can do much more by allowing j
to handle
expressions - especially when combined with by
, as we’ll
see in a moment.
We’ve already seen i
and j
from
data.table
’s general form in the previous section. In this
section, we’ll see how they can be combined together with
by
to perform operations by group. Let’s look at
some examples.
by
ans <- flights[, .(.N), by = .(origin)]
ans
# origin N
# <char> <int>
# 1: JFK 81483
# 2: LGA 84433
# 3: EWR 87400
## or equivalently using a character vector in 'by'
# ans <- flights[, .(.N), by = "origin"]
We know .N
is a special
variable that holds the number of rows in the current group.
Grouping by origin
obtains the number of rows,
.N
, for each group.
By doing head(flights)
you can see that the origin
airports occur in the order “JFK”, “LGA”, and
“EWR”. The original order of grouping variables is preserved in
the result. This is important to keep in mind!
Since we did not provide a name for the column returned in
j
, it was named N
automatically by recognising
the special symbol .N
.
by
also accepts a character vector of column names.
This is particularly useful for coding programmatically, e.g., designing
a function with the grouping columns (in the form of a
character
vector) as a function argument.
When there’s only one column or expression to refer to in
j
and by
, we can drop the .()
notation. This is purely for convenience. We could instead do:
ans <- flights[, .N, by = origin]
ans
# origin N
# <char> <int>
# 1: JFK 81483
# 2: LGA 84433
# 3: EWR 87400
We’ll use this convenient form wherever applicable hereafter.
"AA"
?The unique carrier code "AA"
corresponds to American
Airlines Inc.
ans <- flights[carrier == "AA", .N, by = origin]
ans
# origin N
# <char> <int>
# 1: JFK 11923
# 2: LGA 11730
# 3: EWR 2649
We first obtain the row indices for the expression
carrier == "AA"
from i
.
Using those row indices, we obtain the number of rows
while grouped by origin
. Once again no columns are actually
materialised here, because the j-expression
does not
require any columns to be actually subsetted and is therefore fast and
memory efficient.
origin, dest
pair for carrier code "AA"
?ans <- flights[carrier == "AA", .N, by = .(origin, dest)]
head(ans)
# origin dest N
# <char> <char> <int>
# 1: JFK LAX 3387
# 2: LGA PBI 245
# 3: EWR LAX 62
# 4: JFK MIA 1876
# 5: JFK SEA 298
# 6: EWR MIA 848
## or equivalently using a character vector in 'by'
# ans <- flights[carrier == "AA", .N, by = c("origin", "dest")]
by
accepts multiple columns. We just provide all the
columns by which to group by. Note the use of .()
again in
by
– again, this is just shorthand for list()
,
and list()
can be used here as well. Again, we’ll stick
with .()
in this vignette.orig,dest
pair for each month for carrier code
"AA"
?ans <- flights[carrier == "AA",
.(mean(arr_delay), mean(dep_delay)),
by = .(origin, dest, month)]
ans
# origin dest month V1 V2
# <char> <char> <int> <num> <num>
# 1: JFK LAX 1 6.590361 14.2289157
# 2: LGA PBI 1 -7.758621 0.3103448
# 3: EWR LAX 1 1.366667 7.5000000
# 4: JFK MIA 1 15.720670 18.7430168
# 5: JFK SEA 1 14.357143 30.7500000
# ---
# 196: LGA MIA 10 -6.251799 -1.4208633
# 197: JFK MIA 10 -1.880184 6.6774194
# 198: EWR PHX 10 -3.032258 -4.2903226
# 199: JFK MCO 10 -10.048387 -1.6129032
# 200: JFK DCA 10 16.483871 15.5161290
Since we did not provide column names for the expressions in
j
, they were automatically generated as V1
and
V2
.
Once again, note that the input order of grouping columns is preserved in the result.
Now what if we would like to order the result by those grouping
columns origin
, dest
and
month
?
by
: keyby
data.table
retaining the original order of groups is
intentional and by design. There are cases when preserving the original
order is essential. But at times we would like to automatically sort by
the variables in our grouping.
ans <- flights[carrier == "AA",
.(mean(arr_delay), mean(dep_delay)),
keyby = .(origin, dest, month)]
ans
# Key: <origin, dest, month>
# origin dest month V1 V2
# <char> <char> <int> <num> <num>
# 1: EWR DFW 1 6.427673 10.0125786
# 2: EWR DFW 2 10.536765 11.3455882
# 3: EWR DFW 3 12.865031 8.0797546
# 4: EWR DFW 4 17.792683 12.9207317
# 5: EWR DFW 5 18.487805 18.6829268
# ---
# 196: LGA PBI 1 -7.758621 0.3103448
# 197: LGA PBI 2 -7.865385 2.4038462
# 198: LGA PBI 3 -5.754098 3.0327869
# 199: LGA PBI 4 -13.966667 -4.7333333
# 200: LGA PBI 5 -10.357143 -6.8571429
by
to keyby
. This
automatically orders the result by the grouping variables in increasing
order. In fact, due to the internal implementation of by
first requiring a sort before recovering the original table’s order,
keyby
is typically faster than by
because it
doesn’t require this second step.Keys: Actually keyby
does a little more
than just ordering. It also sets a key after ordering
by setting an attribute
called sorted
.
We’ll learn more about keys
in the vignette("datatable-keys-fast-subset", package="data.table")
vignette; for now, all you have to know is that you can use
keyby
to automatically order the result by the columns
specified in by
.
Let’s reconsider the task of getting the
total number of trips for each origin, dest
pair for
carrier “AA”.
ans
using the columns
origin
in ascending order, and dest
in
descending order?We can store the intermediate result in a variable, and then use
order(origin, -dest)
on that variable. It seems fairly
straightforward.
ans <- ans[order(origin, -dest)]
head(ans)
# origin dest N
# <char> <char> <int>
# 1: EWR PHX 121
# 2: EWR MIA 848
# 3: EWR LAX 62
# 4: EWR DFW 1618
# 5: JFK STT 229
# 6: JFK SJU 690
Recall that we can use -
on a character
column in order()
within the frame of a
data.table
. This is possible due to
data.table
’s internal query optimisation.
Also recall that order(...)
with the frame of a
data.table
is automatically optimised to use
data.table
’s internal fast radix order
forder()
for speed.
But this requires having to assign the intermediate result and then overwriting that result. We can do one better and avoid this intermediate assignment to a temporary variable altogether by chaining expressions.
ans <- flights[carrier == "AA", .N, by = .(origin, dest)][order(origin, -dest)]
head(ans, 10)
# origin dest N
# <char> <char> <int>
# 1: EWR PHX 121
# 2: EWR MIA 848
# 3: EWR LAX 62
# 4: EWR DFW 1618
# 5: JFK STT 229
# 6: JFK SJU 690
# 7: JFK SFO 1312
# 8: JFK SEA 298
# 9: JFK SAN 299
# 10: JFK ORD 432
We can tack expressions one after another, forming a
chain of operations, i.e.,
DT[ ... ][ ... ][ ... ]
.
Or you can also chain them vertically:
by
by
accept expressions as well or does it
just take columns?Yes it does. As an example, if we would like to find out how many flights started late but arrived early (or on time), started and arrived late etc…
ans <- flights[, .N, .(dep_delay>0, arr_delay>0)]
ans
# dep_delay arr_delay N
# <lgcl> <lgcl> <int>
# 1: TRUE TRUE 72836
# 2: FALSE TRUE 34583
# 3: FALSE FALSE 119304
# 4: TRUE FALSE 26593
The last row corresponds to dep_delay > 0 = TRUE
and arr_delay > 0 = FALSE
. We can see that 26593 flights
started late but arrived early (or on time).
Note that we did not provide any names to
by-expression
. Therefore, names have been automatically
assigned in the result. As with j
, you can name these
expressions as you would for elements of any list
, like for
e.g. DT[, .N, .(dep_delayed = dep_delay>0, arr_delayed = arr_delay>0)]
.
You can provide other columns along with expressions, for
example: DT[, .N, by = .(a, b>0)]
.
j
- .SD
mean()
for each column
individually?It is of course not practical to have to type
mean(myCol)
for every column one by one. What if you had
100 columns to average mean()
?
How can we do this efficiently and concisely? To get there, refresh
on this tip - “As long as the
j
-expression returns a list
, each element of
the list
will be converted to a column in the resulting
data.table
”. If we can refer to the data subset
for each group as a variable while grouping, we can then
loop through all the columns of that variable using the already- or
soon-to-be-familiar base function lapply()
. No new names to
learn specific to data.table
.
.SD
:data.table
provides a special symbol called
.SD
. It stands for Subset of
Data. It by itself is a data.table
that
holds the data for the current group defined using
by
.
Recall that a data.table
is internally a
list
as well with all its columns of equal length.
Let’s use the data.table
DT
from before to get a glimpse of what
.SD
looks like.
DT
# ID a b c
# <char> <int> <int> <int>
# 1: b 1 7 13
# 2: b 2 8 14
# 3: b 3 9 15
# 4: a 4 10 16
# 5: a 5 11 17
# 6: c 6 12 18
DT[, print(.SD), by = ID]
# a b c
# <int> <int> <int>
# 1: 1 7 13
# 2: 2 8 14
# 3: 3 9 15
# a b c
# <int> <int> <int>
# 1: 4 10 16
# 2: 5 11 17
# a b c
# <int> <int> <int>
# 1: 6 12 18
# Empty data.table (0 rows and 1 cols): ID
.SD
contains all the columns except the grouping
columns by default.
It is also generated by preserving the original order - data
corresponding to ID = "b"
, then ID = "a"
, and
then ID = "c"
.
To compute on (multiple) columns, we can then simply use the base R
function lapply()
.
DT[, lapply(.SD, mean), by = ID]
# ID a b c
# <char> <num> <num> <num>
# 1: b 2.0 8.0 14.0
# 2: a 4.5 10.5 16.5
# 3: c 6.0 12.0 18.0
.SD
holds the rows corresponding to columns
a
, b
and c
for that group. We
compute the mean()
on each of these columns using the
already-familiar base function lapply()
.
Each group returns a list of three elements containing the mean
value which will become the columns of the resulting
data.table
.
Since lapply()
returns a list
, so there
is no need to wrap it with an additional .()
(if necessary,
refer to this tip).
We are almost there. There is one little thing left to address. In
our flights
data.table
, we only wanted to
calculate the mean()
of the two columns
arr_delay
and dep_delay
. But .SD
would contain all the columns other than the grouping variables by
default.
mean()
on?Using the argument .SDcols
. It accepts either column
names or column indices. For example,
.SDcols = c("arr_delay", "dep_delay")
ensures that
.SD
contains only these two columns for each group.
Similar to part g), you can also specify the
columns to remove instead of columns to keep using -
or
!
. Additionally, you can select consecutive columns as
colA:colB
and deselect them as !(colA:colB)
or
-(colA:colB)
.
Now let us try to use .SD
along with
.SDcols
to get the mean()
of
arr_delay
and dep_delay
columns grouped by
origin
, dest
and month
.
flights[carrier == "AA", ## Only on trips with carrier "AA"
lapply(.SD, mean), ## compute the mean
by = .(origin, dest, month), ## for every 'origin,dest,month'
.SDcols = c("arr_delay", "dep_delay")] ## for just those specified in .SDcols
# origin dest month arr_delay dep_delay
# <char> <char> <int> <num> <num>
# 1: JFK LAX 1 6.590361 14.2289157
# 2: LGA PBI 1 -7.758621 0.3103448
# 3: EWR LAX 1 1.366667 7.5000000
# 4: JFK MIA 1 15.720670 18.7430168
# 5: JFK SEA 1 14.357143 30.7500000
# ---
# 196: LGA MIA 10 -6.251799 -1.4208633
# 197: JFK MIA 10 -1.880184 6.6774194
# 198: EWR PHX 10 -3.032258 -4.2903226
# 199: JFK MCO 10 -10.048387 -1.6129032
# 200: JFK DCA 10 16.483871 15.5161290
.SD
for each group:month
?ans <- flights[, head(.SD, 2), by = month]
head(ans)
# month year day dep_delay arr_delay carrier origin dest air_time distance hour
# <int> <int> <int> <int> <int> <char> <char> <char> <int> <int> <int>
# 1: 1 2014 1 14 13 AA JFK LAX 359 2475 9
# 2: 1 2014 1 -3 13 AA JFK LAX 363 2475 11
# 3: 2 2014 1 -1 1 AA JFK LAX 358 2475 8
# 4: 2 2014 1 -5 3 AA JFK LAX 358 2475 11
# 5: 3 2014 1 -11 36 AA JFK LAX 375 2475 8
# 6: 3 2014 1 -3 14 AA JFK LAX 368 2475 11
.SD
is a data.table
that holds all the
rows for that group. We simply subset the first two rows as we
have seen here already.
For each group, head(.SD, 2)
returns the first two
rows as a data.table
, which is also a list
, so
we do not have to wrap it with .()
.
j
so flexible?So that we have a consistent syntax and keep using already existing
(and familiar) base functions instead of learning new functions. To
illustrate, let us use the data.table
DT
that
we created at the very beginning under the section What is a data.table?.
a
and b
for each group in ID
?DT[, .(val = c(a,b)), by = ID]
# ID val
# <char> <int>
# 1: b 1
# 2: b 2
# 3: b 3
# 4: b 7
# 5: b 8
# 6: b 9
# 7: a 4
# 8: a 5
# 9: a 10
# 10: a 11
# 11: c 6
# 12: c 12
c()
which concatenates vectors and the tip from before.a
and b
concatenated, but returned as a list
column?DT[, .(val = list(c(a,b))), by = ID]
# ID val
# <char> <list>
# 1: b 1,2,3,7,8,9
# 2: a 4, 5,10,11
# 3: c 6,12
Here, we first concatenate the values with c(a,b)
for each group, and wrap that with list()
. So for each
group, we return a list of all concatenated values.
Note that those commas are for display only. A list column can contain any object in each cell, and in this example, each cell is itself a vector and some cells contain longer vectors than others.
Once you start internalising usage in j
, you will
realise how powerful the syntax can be. A very useful way to understand
it is by playing around, with the help of print()
.
For example:
## look at the difference between
DT[, print(c(a,b)), by = ID] # (1)
# [1] 1 2 3 7 8 9
# [1] 4 5 10 11
# [1] 6 12
# Empty data.table (0 rows and 1 cols): ID
## and
DT[, print(list(c(a,b))), by = ID] # (2)
# [[1]]
# [1] 1 2 3 7 8 9
#
# [[1]]
# [1] 4 5 10 11
#
# [[1]]
# [1] 6 12
# Empty data.table (0 rows and 1 cols): ID
In (1), for each group, a vector is returned, with length = 6,4,2
here. However, (2) returns a list of length 1 for each group, with its
first element holding vectors of length 6,4,2. Therefore, (1) results in
a length of 6+4+2 = 12
, whereas (2) returns
1+1+1=3
.
The general form of data.table
syntax is:
We have seen so far that,
i
:We can subset rows similar to a data.frame
- except
you don’t have to use DT$
repetitively since columns within
the frame of a data.table
are seen as if they are
variables.
We can also sort a data.table
using
order()
, which internally uses data.table’s fast order for
better performance.
We can do much more in i
by keying a
data.table
, which allows for blazing fast subsets and
joins. We will see this in the vignettes vignette("datatable-keys-fast-subset", package="data.table")
and vignette("datatable-joins", package="data.table")
.
j
:Select columns the data.table
way:
DT[, .(colA, colB)]
.
Select columns the data.frame
way:
DT[, c("colA", "colB")]
.
Compute on columns:
DT[, .(sum(colA), mean(colB))]
.
Provide names if necessary:
DT[, .(sA = sum(colA), mB = mean(colB))]
.
Combine with i
:
DT[colA > value, sum(colB)]
.
by
:Using by
, we can group by columns by specifying a
list of columns or a character vector of column names
or even expressions. The flexibility of j
,
combined with by
and i
, makes for a very
powerful syntax.
by
can handle multiple columns and also
expressions.
We can keyby
grouping columns to automatically sort
the grouped result.
We can use .SD
and .SDcols
in
j
to operate on multiple columns using already familiar
base functions. Here are some examples:
DT[, lapply(.SD, fun), by = ..., .SDcols = ...]
-
applies fun
to all columns specified in
.SDcols
while grouping by the columns specified in
by
.
DT[, head(.SD, 2), by = ...]
- return the first two
rows for each group.
DT[col > val, head(.SD, 1), by = ...]
- combine
i
along with j
and by
.
As long as j
returns a list
, each element
of the list will become a column in the resulting
data.table
.
We will see how to add/update/delete columns by
reference and how to combine them with i
and
by
in the next
vignette
(vignette("datatable-reference-semantics", package="data.table")
).