Secondary indices and auto indexing

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This vignette assumes that the reader is familiar with data.table’s [i, j, by] syntax, and how to perform fast key based subsets. If you’re not familiar with these concepts, please read the following vignettes first:

Data

We will use the same flights data as in the vignette("datatable-intro", package="data.table") vignette.

flights <- fread("flights14.csv")
head(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
# 6:  2014     1     1         4         0      AA    EWR    LAX      339     2454    18
dim(flights)
# [1] 253316     11

Introduction

In this vignette, we will

discuss secondary indices and provide rationale as to why we need them by citing cases where setting keys is not necessarily ideal,
perform fast subsetting, once again, but using the new on argument, which computes secondary indices internally for the task (temporarily), and reuses if one already exists,
and finally look at auto indexing which goes a step further and creates secondary indices automatically, but does so on native R syntax for subsetting.

1. Secondary indices

a) What are secondary indices?

Secondary indices are similar to keys in data.table, except for two major differences:

It doesn’t physically reorder the entire data.table in RAM. Instead, it only computes the order for the set of columns provided and stores that order vector in an additional attribute called index.
There can be more than one secondary index for a data.table (as we will see below).

Keyed vs. Indexed Subsetting

While both keys and indices enable fast binary search subsetting, they differ significantly in usage:

Keyed subsetting (implicit column matching)

DT = data.table(a = c(TRUE, FALSE), b = 1:2)
setkey(DT, a)                # Set key, reordering DT
DT[.(TRUE)]                  # 'on' is optional; if omitted, the key is used
# Key: <a>
#         a     b
#    <lgcl> <int>
# 1:   TRUE     1

Indexed subsetting (explicit column specification)

DT = data.table(a = c(TRUE, FALSE), b = 1:2)
setindex(DT, a)              # Set index only (no reorder)
DT[.(TRUE), on = "a"]        # 'on' is required
#         a     b
#    <lgcl> <int>
# 1:   TRUE     1

b) Set and get secondary indices

– How can we set the column `origin` as a secondary index in the data.table `flights`?

setindex(flights, origin)
head(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
# 6:  2014     1     1         4         0      AA    EWR    LAX      339     2454    18

## alternatively we can provide character vectors to the function 'setindexv()'
# setindexv(flights, "origin") # useful to program with

# 'index' attribute added
names(attributes(flights))
# [1] "names"             "row.names"         "class"             ".internal.selfref"
# [5] "index"

setindex and setindexv() allows adding a secondary index to the data.table.
Note that flights is not physically reordered in increasing order of origin, as would have been the case with setkey().
Also note that the attribute index has been added to flights.
setindex(flights, NULL) would remove all secondary indices.

– How can we get all the secondary indices set so far in `flights`?

indices(flights)
# [1] "origin"

setindex(flights, origin, dest)
indices(flights)
# [1] "origin"       "origin__dest"

The function indices() returns all current secondary indices in the data.table. If none exists, NULL is returned.
Note that by creating another index on the columns origin, dest, we do not lose the first index created on the column origin, i.e., we can have multiple secondary indices.

c) Why do we need secondary indices?

– Reordering a data.table can be expensive and not always ideal

Consider the case where you would like to perform a fast key based subset on origin column for the value “JFK”. We’d do this as:

## not run
setkey(flights, origin)
flights["JFK"] # or flights[.("JFK")]

`setkey()` requires:

computing the order vector for the column(s) provided, here, origin, and
reordering the entire data.table, by reference, based on the order vector computed.

Computing the order isn’t the time consuming part, since data.table uses true radix sorting on integer, character and numeric vectors. However, reordering the data.table could be time consuming (depending on the number of rows and columns).

Unless our task involves repeated subsetting on the same column, fast key based subsetting could effectively be nullified by the time to reorder, depending on our data.table dimensions.

– There can be only one `key` at the most

Now if we would like to repeat the same operation but on dest column instead, for the value “LAX”, then we have to setkey(), again.

## not run
setkey(flights, dest)
flights["LAX"]

And this reorders flights by dest, again. What we would really like is to be able to perform the fast subsetting by eliminating the reordering step.

And this is precisely what secondary indices allow for!

– Secondary indices can be reused

Since there can be multiple secondary indices, and creating an index is as simple as storing the order vector as an attribute, this allows us to even eliminate the time to recompute the order vector if an index already exists.

– The new `on` argument allows for cleaner syntax and automatic creation and reuse of secondary indices

As we will see in the next section, the on argument provides several advantages:

`on` argument

enables subsetting by computing secondary indices on the fly. This eliminates having to do setindex() every time.
allows easy reuse of existing indices by just checking the attributes.
allows for a cleaner syntax by having the columns on which the subset is performed as part of the syntax. This makes the code easier to follow when looking at it at a later point.

Note that on argument can also be used on keyed subsets as well. In fact, we encourage providing the on argument even when subsetting using keys for better readability.

2. Fast subsetting using `on` argument and secondary indices

a) Fast subsets in `i`

– Subset all rows where the origin airport matches “JFK” using `on`

flights["JFK", on = "origin"]
#         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         2         1      AA    JFK    LAX      350     2475    13
#     5:  2014     1     1        -2       -18      AA    JFK    LAX      338     2475    21
#    ---                                                                                    
# 81479:  2014    10    31        -4       -21      UA    JFK    SFO      337     2586    17
# 81480:  2014    10    31        -2       -37      UA    JFK    SFO      344     2586    18
# 81481:  2014    10    31         0       -33      UA    JFK    LAX      320     2475    17
# 81482:  2014    10    31        -6       -38      UA    JFK    SFO      343     2586     9
# 81483:  2014    10    31        -6       -38      UA    JFK    LAX      323     2475    11

## alternatively
# flights[.("JFK"), on = "origin"] (or)
# flights[list("JFK"), on = "origin"]

This statement performs a fast binary search based subset as well, by computing the index on the fly. However, note that it doesn’t save the index as an attribute automatically. This may change in the future.

If we had already created a secondary index, using setindex(), then on would reuse it instead of (re)computing it. We can see that by using verbose = TRUE:

setindex(flights, origin)
flights["JFK", on = "origin", verbose = TRUE][1:5]
# i.V1 has same type (character) as x.origin. No coercion needed.
# on= matches existing index, using index
# Starting bmerge ...
# forder.c received 1 rows and 1 columns
# forderReuseSorting: opt=-1, took 0.000s
# bmerge: looping bmerge_r took 0.000s
# bmerge: took 0.000s
# bmerge done in 0.000s elapsed (0.000s cpu)
# Constructing irows for '!byjoin || nqbyjoin' ... 0.000s elapsed (0.000s cpu)
#     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         2         1      AA    JFK    LAX      350     2475    13
# 5:  2014     1     1        -2       -18      AA    JFK    LAX      338     2475    21

– How can I subset based on `origin` and `dest` columns?

For example, if we want to subset "JFK", "LAX" combination, then:

flights[.("JFK", "LAX"), on = c("origin", "dest")][1:5]
#     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         2         1      AA    JFK    LAX      350     2475    13
# 5:  2014     1     1        -2       -18      AA    JFK    LAX      338     2475    21

on argument accepts a character vector of column names corresponding to the order provided to i-argument.
Since the time to compute the secondary index is quite small, we don’t have to use setindex(), unless, once again, the task involves repeated subsetting on the same column.
For clarity/readability, it might help to name the inputs in i, e.g.,

flights[.(origin = "JFK", dest = "LAX"), on = c("origin", "dest")]
#         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         2         1      AA    JFK    LAX      350     2475    13
#     5:  2014     1     1        -2       -18      AA    JFK    LAX      338     2475    21
#    ---                                                                                    
# 10204:  2014    10    31        -4        -9      VX    JFK    LAX      327     2475    20
# 10205:  2014    10    31         0       -38      UA    JFK    LAX      320     2475     6
# 10206:  2014    10    31        85        62      UA    JFK    LAX      323     2475     9
# 10207:  2014    10    31         0       -33      UA    JFK    LAX      320     2475    17
# 10208:  2014    10    31        -6       -38      UA    JFK    LAX      323     2475    11

This makes it clear which entries in j correspond to which element of on.

b) Select in `j`

All the operations we will discuss below are no different to the ones we already saw in the vignette("datatable-keys-fast-subset", package="data.table") vignette. Except we’ll be using the on argument instead of setting keys.

– Return `arr_delay` column alone as a data.table corresponding to `origin = "LGA"` and `dest = "TPA"`

flights[.("LGA", "TPA"), .(arr_delay), on = c("origin", "dest")]
#       arr_delay
#           <int>
#    1:         1
#    2:        14
#    3:       -17
#    4:        -4
#    5:       -12
#   ---          
# 1848:        39
# 1849:       -24
# 1850:       -12
# 1851:        21
# 1852:       -11

c) Chaining

– On the result obtained above, use chaining to order the column in decreasing order.

flights[.("LGA", "TPA"), .(arr_delay), on = c("origin", "dest")][order(-arr_delay)]
#       arr_delay
#           <int>
#    1:       486
#    2:       380
#    3:       351
#    4:       318
#    5:       300
#   ---          
# 1848:       -40
# 1849:       -43
# 1850:       -46
# 1851:       -48
# 1852:       -49

d) Compute or do in `j`

– Find the maximum arrival delay corresponding to `origin = "LGA"` and `dest = "TPA"`.

flights[.("LGA", "TPA"), max(arr_delay), on = c("origin", "dest")]
# [1] 486

e) sub-assign by reference using `:=` in `j`

We have seen this example already in the vignettes vignette("datatable-reference-semantics", package="data.table") and vignette("datatable-keys-fast-subset", package="data.table"). Let’s take a look at all the hours available in the flights data.table:

# get all 'hours' in flights
flights[, sort(unique(hour))]
#  [1]  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

We see that there are totally 25 unique values in the data. Both 0 and 24 hours seem to be present. Let’s go ahead and replace 24 with 0, but this time using on instead of setting keys.

flights[.(24L), hour := 0L, on = "hour"]

Now, let’s check if 24 is replaced with 0 in the hour column.

flights[, sort(unique(hour))]
#  [1]  0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

This is particularly a huge advantage of secondary indices. Previously, just to update a few rows of hour, we had to setkey() on it, which inevitably reorders the entire data.table. With on, the order is preserved, and the operation is much faster! Looking at the code, the task we wanted to perform is also quite clear.

f) Aggregation using `by`

– Get the maximum departure delay for each `month` corresponding to `origin = "JFK"`. Order the result by `month`

ans <- flights["JFK", max(dep_delay), keyby = month, on = "origin"]
head(ans)
# Key: <month>
#    month    V1
#    <int> <int>
# 1:     1   881
# 2:     2  1014
# 3:     3   920
# 4:     4  1241
# 5:     5   853
# 6:     6   798

We would have had to set the key back to origin, dest again, if we did not use on which internally builds secondary indices on the fly.

g) The mult argument

The other arguments including mult work exactly the same way as we saw in the vignette("datatable-keys-fast-subset", package="data.table") vignette. The default value for mult is “all”. We can choose, instead only the “first” or “last” matching rows should be returned.

– Subset only the first matching row where `dest` matches “BOS” and “DAY”

flights[c("BOS", "DAY"), on = "dest", mult = "first"]
#     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         3         1      AA    JFK    BOS       39      187    12
# 2:  2014     1     1        25        35      EV    EWR    DAY      102      533    17

– Subset only the last matching row where `origin` matches “LGA”, “JFK”, “EWR” and `dest` matches “XNA”

flights[.(c("LGA", "JFK", "EWR"), "XNA"), on = c("origin", "dest"), mult = "last"]
#     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    10    31        -5       -11      MQ    LGA    XNA      165     1147     6
# 2:    NA    NA    NA        NA        NA    <NA>    JFK    XNA       NA       NA    NA
# 3:  2014    10    31        -2       -25      EV    EWR    XNA      160     1131     6

h) The nomatch argument

We can choose if queries that do not match should return NA or be skipped altogether using the nomatch argument.

– From the previous example, subset all rows only if there’s a match

flights[.(c("LGA", "JFK", "EWR"), "XNA"), mult = "last", on = c("origin", "dest"), nomatch = NULL]
#     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    10    31        -5       -11      MQ    LGA    XNA      165     1147     6
# 2:  2014    10    31        -2       -25      EV    EWR    XNA      160     1131     6

There are no flights connecting “JFK” and “XNA”. Therefore, that row is skipped in the result.

3. Auto indexing

First we looked at how to fast subset using binary search using keys. Then we figured out that we could improve performance even further and have cleaner syntax by using secondary indices.

That is what auto indexing does. At the moment, it is only implemented for binary operators == and %in%. An index is automatically created and saved as an attribute. That is, unlike the on argument which computes the index on the fly each time (unless one already exists), a secondary index is created here.

Let’s start by creating a data.table big enough to highlight the advantage.

set.seed(1L)
dt = data.table(x = sample(1e5L, 1e7L, TRUE), y = runif(100L))
print(object.size(dt), units = "Mb")
# 114.4 Mb

When we use == or %in% on a single column for the first time, a secondary index is created automatically, and it is used to perform the subset.

## have a look at all the attribute names
names(attributes(dt))
# [1] "names"             "row.names"         "class"             ".internal.selfref"

## run thefirst time
(t1 <- system.time(ans <- dt[x == 989L]))
#    user  system elapsed 
#   0.579   0.062   0.641
head(ans)
#        x         y
#    <int>     <num>
# 1:   989 0.7757157
# 2:   989 0.6813302
# 3:   989 0.2815894
# 4:   989 0.4954259
# 5:   989 0.7885886
# 6:   989 0.5547504

## secondary index is created
names(attributes(dt))
# [1] "names"             "row.names"         "class"             ".internal.selfref"
# [5] "index"

indices(dt)
# [1] "x"

The time to subset the first time is the time to create the index + the time to subset. Since creating a secondary index involves only creating the order vector, this combined operation is faster than vector scans in many cases. But the real advantage comes in successive subsets. They are extremely fast.

## successive subsets
(t2 <- system.time(dt[x == 989L]))
#    user  system elapsed 
#   0.012   0.013   0.025
system.time(dt[x %in% 1989:2012])
#    user  system elapsed 
#   0.020   0.006   0.025

Running the first time took 0.641 seconds where as the second time took 0.025 seconds.
Auto indexing can be disabled by setting the global argument options(datatable.auto.index = FALSE).
Disabling auto indexing still allows to use indices created explicitly with setindex or setindexv. You can disable indices fully by setting global argument options(datatable.use.index = FALSE).

In recent version we extended auto indexing to expressions involving more than one column (combined with & operator). In the future, we plan to extend binary search to work with more binary operators like <, <=, > and >=.

We will discuss fast subsets using keys and secondary indices to joins in the next vignette (vignette("datatable-joins", package="data.table")).

2025-10-28

Data

Introduction

1. Secondary indices

a) What are secondary indices?

Keyed vs. Indexed Subsetting

b) Set and get secondary indices

– How can we set the column origin as a secondary index in the data.table flights?

– How can we get all the secondary indices set so far in flights?

c) Why do we need secondary indices?

– Reordering a data.table can be expensive and not always ideal

setkey() requires:

– There can be only one key at the most

– Secondary indices can be reused

– The new on argument allows for cleaner syntax and automatic creation and reuse of secondary indices

on argument

2. Fast subsetting using on argument and secondary indices

a) Fast subsets in i

– Subset all rows where the origin airport matches “JFK” using on

– How can I subset based on origin and dest columns?

b) Select in j

– Return arr_delay column alone as a data.table corresponding to origin = "LGA" and dest = "TPA"