Using .SD for Data Analysis

In data.table: Extension of `data.frame`

require(data.table)
knitr::opts_chunk$set(
  comment = "#",
  error = FALSE,
  tidy = FALSE,
  cache = FALSE,
  collapse = TRUE,
  out.width = '100%',
  dpi = 144
)
.old.th = setDTthreads(1)

This vignette will explain the most common ways to use the .SD variable in your data.table analyses. It is an adaptation of this answer given on StackOverflow.

What is .SD?

In the broadest sense, .SD is just shorthand for capturing a variable that comes up frequently in the context of data analysis. It can be understood to stand for Subset, Selfsame, or Self-reference of the Data. That is, .SD is in its most basic guise a reflexive reference to the data.table itself -- as we'll see in examples below, this is particularly helpful for chaining together "queries" (extractions/subsets/etc using [). In particular, this also means that .SD is itself a data.table (with the caveat that it does not allow assignment with :=).

The simpler usage of .SD is for column subsetting (i.e., when .SDcols is specified); as this version is much more straightforward to understand, we'll cover that first below. The interpretation of .SD in its second usage, grouping scenarios (i.e., when by = or keyby = is specified), is slightly different, conceptually (though at core it's the same, since, after all, a non-grouped operation is an edge case of grouping with just one group).

Loading and Previewing Lahman Data

To give this a more real-world feel, rather than making up data, let's load some data sets about baseball from the Lahman database. In typical R usage, we'd simply load these data sets from the Lahman R package; in this vignette, we've pre-downloaded them directly from the package's GitHub page instead.

load('Teams.RData')
setDT(Teams)
Teams

load('Pitching.RData')
setDT(Pitching)
Pitching

Readers up on baseball lingo should find the tables' contents familiar; Teams records some statistics for a given team in a given year, while Pitching records statistics for a given pitcher in a given year. Please do check out the documentation and explore the data yourself a bit before proceeding to familiarize yourself with their structure.

.SD on Ungrouped Data

To illustrate what I mean about the reflexive nature of .SD, consider its most banal usage:

Pitching[ , .SD]

That is, Pitching[ , .SD] has simply returned the whole table, i.e., this was an overly verbose way of writing Pitching or Pitching[]:

identical(Pitching, Pitching[ , .SD])

In terms of subsetting, .SD is still a subset of the data, it's just a trivial one (the set itself).

Column Subsetting: .SDcols

The first way to impact what .SD is is to limit the columns contained in .SD using the .SDcols argument to [:

# W: Wins; L: Losses; G: Games
Pitching[ , .SD, .SDcols = c('W', 'L', 'G')]

This is just for illustration and was pretty boring. In addition to accepting a character vector, .SDcols also accepts:

1. any function such as is.character to filter columns
2. the function^{*} patterns() to filter column names by regular expression
3. integer and logical vectors

*see ?patterns for more details

This simple usage lends itself to a wide variety of highly beneficial / ubiquitous data manipulation operations:

Column Type Conversion

Column type conversion is a fact of life for data munging. Though fwrite recently gained the ability to declare the class of each column up front, not all data sets come from fread (e.g. in this vignette) and conversions back and forth among character/factor/numeric types are common. We can use .SD and .SDcols to batch-convert groups of columns to a common type.

We notice that the following columns are stored as character in the Teams data set, but might more logically be stored as factors:

# teamIDBR: Team ID used by Baseball Reference website
# teamIDlahman45: Team ID used in Lahman database version 4.5
# teamIDretro: Team ID used by Retrosheet
fkt = c('teamIDBR', 'teamIDlahman45', 'teamIDretro')
# confirm that they're stored as `character`
str(Teams[ , ..fkt])

The syntax to now convert these columns to factor is simple:

Teams[ , names(.SD) := lapply(.SD, factor), .SDcols = patterns('teamID')]
# print out the first column to demonstrate success
head(unique(Teams[[fkt[1L]]]))

Note:

1. The := is an assignment operator to update the data.table in place without making a copy. See reference semantics for more.
2. The LHS, names(.SD), indicates which columns we are updating - in this case we update the entire .SD.
3. The RHS, lapply(), loops through each column of the .SD and converts the column to a factor.
4. We use the .SDcols to only select columns that have pattern of teamID.

Again, the .SDcols argument is quite flexible; above, we supplied patterns but we could have also supplied fkt or any character vector of column names. In other situations, it is more convenient to supply an integer vector of column positions or a logical vector dictating include/exclude for each column. Finally, the use of a function to filter columns is very helpful.

For example, we could do the following to convert all factor columns to character:

fct_idx = Teams[, which(sapply(.SD, is.factor))] # column numbers to show the class changing
str(Teams[[fct_idx[1L]]])
Teams[ , names(.SD) := lapply(.SD, as.character), .SDcols = is.factor]
str(Teams[[fct_idx[1L]]])

Lastly, we can do pattern-based matching of columns in .SDcols to select all columns which contain team back to factor:

Teams[ , .SD, .SDcols = patterns('team')]
Teams[ , names(.SD) := lapply(.SD, factor), .SDcols = patterns('team')]

** A proviso to the above: explicitly using column numbers (like DT[ , (1) := rnorm(.N)]) is bad practice and can lead to silently corrupted code over time if column positions change. Even implicitly using numbers can be dangerous if we don't keep smart/strict control over the ordering of when we create the numbered index and when we use it.

Controlling a Model's Right-Hand Side

Varying model specification is a core feature of robust statistical analysis. Let's try and predict a pitcher's ERA (Earned Runs Average, a measure of performance) using the small set of covariates available in the Pitching table. How does the (linear) relationship between W (wins) and ERA vary depending on which other covariates are included in the specification?

Here's a short script leveraging the power of .SD which explores this question:

# this generates a list of the 2^k possible extra variables
#   for models of the form ERA ~ G + (...)
extra_var = c('yearID', 'teamID', 'G', 'L')
models = unlist(
  lapply(0L:length(extra_var), combn, x = extra_var, simplify = FALSE),
  recursive = FALSE
)

# here are 16 visually distinct colors, taken from the list of 20 here:
#   https://sashat.me/2017/01/11/list-of-20-simple-distinct-colors/
col16 = c('#e6194b', '#3cb44b', '#ffe119', '#0082c8',
          '#f58231', '#911eb4', '#46f0f0', '#f032e6',
          '#d2f53c', '#fabebe', '#008080', '#e6beff',
          '#aa6e28', '#fffac8', '#800000', '#aaffc3')

par(oma = c(2, 0, 0, 0))
lm_coef = sapply(models, function(rhs) {
  # using ERA ~ . and data = .SD, then varying which
  #   columns are included in .SD allows us to perform this
  #   iteration over 16 models succinctly.
  #   coef(.)['W'] extracts the W coefficient from each model fit
  Pitching[ , coef(lm(ERA ~ ., data = .SD))['W'], .SDcols = c('W', rhs)]
})
barplot(lm_coef, names.arg = sapply(models, paste, collapse = '/'),
        main = 'Wins Coefficient\nWith Various Covariates',
        col = col16, las = 2L, cex.names = 0.8)

The coefficient always has the expected sign (better pitchers tend to have more wins and fewer runs allowed), but the magnitude can vary substantially depending on what else we control for.

Conditional Joins

data.table syntax is beautiful for its simplicity and robustness. The syntax x[i] flexibly handles three common approaches to subsetting -- when i is a logical vector, x[i] will return those rows of x corresponding to where i is TRUE; when i is another data.table (or a list), a (right) join is performed (in the plain form, using the keys of x and i, otherwise, when on = is specified, using matches of those columns); and when i is a character, it is interpreted as shorthand for x[list(i)], i.e., as a join.

This is great in general, but falls short when we wish to perform a conditional join, wherein the exact nature of the relationship among tables depends on some characteristics of the rows in one or more columns.

This example is admittedly a tad contrived, but illustrates the idea; see here (1, 2) for more.

The goal is to add a column team_performance to the Pitching table that records the team's performance (rank) of the best pitcher on each team (as measured by the lowest ERA, among pitchers with at least 6 recorded games).

# to exclude pitchers with exceptional performance in a few games,
#   subset first; then define rank of pitchers within their team each year
#   (in general, we should put more care into the 'ties.method' of frank)
Pitching[G > 5, rank_in_team := frank(ERA), by = .(teamID, yearID)]
Pitching[rank_in_team == 1, team_performance :=
           Teams[.SD, Rank, on = c('teamID', 'yearID')]]

Note that the x[y] syntax returns nrow(y) values (i.e., it's a right join), which is why .SD is on the right in Teams[.SD] (since the RHS of := in this case requires nrow(Pitching[rank_in_team == 1]) values).

Grouped .SD operations

Often, we'd like to perform some operation on our data at the group level. When we specify by = (or keyby =), the mental model for what happens when data.table processes j is to think of your data.table as being split into many component sub-data.tables, each of which corresponds to a single value of your by variable(s):

In the case of grouping, .SD is multiple in nature -- it refers to each of these sub-data.tables, one-at-a-time (slightly more accurately, the scope of .SD is a single sub-data.table). This allows us to concisely express an operation that we'd like to perform on each sub-data.table before the re-assembled result is returned to us.

This is useful in a variety of settings, the most common of which are presented here:

Group Subsetting

Let's get the most recent season of data for each team in the Lahman data. This can be done quite simply with:

# the data is already sorted by year; if it weren't
#   we could do Teams[order(yearID), .SD[.N], by = teamID]
Teams[ , .SD[.N], by = teamID]

Recall that .SD is itself a data.table, and that .N refers to the total number of rows in a group (it's equal to nrow(.SD) within each group), so .SD[.N] returns the entirety of .SD for the final row associated with each teamID.

Another common version of this is to use .SD[1L] instead to get the first observation for each group, or .SD[sample(.N, 1L)] to return a random row for each group.

Group Optima

Suppose we wanted to return the best year for each team, as measured by their total number of runs scored (R; we could easily adjust this to refer to other metrics, of course). Instead of taking a fixed element from each sub-data.table, we now define the desired index dynamically as follows:

Teams[ , .SD[which.max(R)], by = teamID]

Note that this approach can of course be combined with .SDcols to return only portions of the data.table for each .SD (with the caveat that .SDcols should be fixed across the various subsets)

NB: .SD[1L] is currently optimized by GForce (see also), data.table internals which massively speed up the most common grouped operations like sum or mean -- see ?GForce for more details and keep an eye on/voice support for feature improvement requests for updates on this front: 1, 2, 3, 4, 5, 6

Grouped Regression

Returning to the inquiry above regarding the relationship between ERA and W, suppose we expect this relationship to differ by team (i.e., there's a different slope for each team). We can easily re-run this regression to explore the heterogeneity in this relationship as follows (noting that the standard errors from this approach are generally incorrect -- the specification ERA ~ W*teamID will be better -- this approach is easier to read and the coefficients are OK):

# Overall coefficient for comparison
overall_coef = Pitching[ , coef(lm(ERA ~ W))['W']]
# use the .N > 20 filter to exclude teams with few observations
Pitching[ , if (.N > 20L) .(w_coef = coef(lm(ERA ~ W))['W']), by = teamID
          ][ , hist(w_coef, 20L, las = 1L,
                    xlab = 'Fitted Coefficient on W',
                    ylab = 'Number of Teams', col = 'darkgreen',
                    main = 'Team-Level Distribution\nWin Coefficients on ERA')]
abline(v = overall_coef, lty = 2L, col = 'red')

While there is indeed a fair amount of heterogeneity, there's a distinct concentration around the observed overall value.

The above is just a short introduction of the power of .SD in facilitating beautiful, efficient code in data.table!

setDTthreads(.old.th)

data.table documentation built on Oct. 10, 2024, 5:07 p.m.