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Wicked Fast, Accurate Quantiles Using ‘t-Digests’ in R with the {tdigest} Package

by hrbrmstr on April 3, 2019

@ted_dunning recently updated the t-Digest algorithm he created back in 2013. What is this “t-digest”? Fundamentally, it is a probabilistic data structure for estimating any percentile of distributed/streaming data. Ted explains it quite elegantly in this short video:

Said video has a full transcript as well.

T-digests have been baked into many “big data” analytics ecosystems for a while but I hadn’t seen any R packages for them (ref any in a comment if you do know of some) so I wrapped one of the low-level implementation libraries by ajwerner into a diminutive R package boringly, but appropriately named tdigest:

SourceHut
GitLab
CINC (The CINC repo has R 3.5 package binaries for Windows and macOS.)
GitUgh

There are wrappers for the low-level accumulators and quantile/value extractors along with vectorised functions for creating t-digest objects and retrieving quantiles from them (including a tdigest S3 method for stats::quantile()).

This:

install.packages("tdigest", repos="https://cinc.rud.is/")

will install from source or binaries onto your system(s).

Basic Ops

The low-level interface is more useful in “streaming” operations (i.e. accumulating input over time):

set.seed(2019-04-03)td <- td_create()for (i in 1:100000) {  td_add(td, sample(100, 1), 1)}quantile(td)## [1]   1.00000  25.62222  53.09883  74.75522 100.00000

More R-like Ops

Vectorisation is the name of the game in R and we can use tdigest() to work in a vectorised manner:

set.seed(2019-04-03)x <- sample(100, 1000000, replace=TRUE)td <- tdigest(x)quantile(td)## [1]   1.00000  25.91914  50.79468  74.76439 100.00000

Need for Speed

The t-digest algorithm was designed for both streaming operations and speed. It’s pretty, darned fast:

microbenchmark::microbenchmark(  tdigest = tquantile(td, c(0, 0.01, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1)),  r_quantile = quantile(x, c(0, 0.01, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1)))## Unit: microseconds##        expr      min         lq        mean    median       uq       max neval##     tdigest    22.81    26.6525    48.70123    53.355    63.31    151.29   100##  r_quantile 57675.34 59118.4070 62992.56817 60488.932 64731.23 160130.50   100

Note that “accurate” is not the same thing as “precise”, so regular quantile ops in R will be close to what t-digest computes, but not always exactly the same.

FIN

This was a quick (but, complete) wrapper and could use some tyre kicking. I’ve a mind to add serialization to the C implementation so I can then enable [de]serialization on the R-side since that would (IMO) make t-digest ops more useful in an R-context, especially since you can merge two different t-digests.

As always, code/PR where you want to and file issues with any desired functionality/enhancements.

Also, whomever started the braces notation for package names (e.g. {ggplot2}): brilliant!