Tidyverse and data.table, sitting side by side… and then base R walks in

Of course, I’m paraphrasing Dirk’s fifteenth post in the rarely rational R rambling series: #15: Tidyverse and data.table, sitting side by side … (Part 1). I very much liked it, because, although I’m a happy tidyverse user, I’m always trying not to be tied into that verse too much by replicating certain tasks with other tools (and languages) as an exercise. In this article, I’m going to repeat Dirk’s exercise in base R.

First of all, I would like to clean up the tidyverse version a little, because the original was distributed in chunks and was a little bit too verbose. We can also avoid using lubridate, because readr already parses the end_date column as a date (and that’s why it is significantly slower, among other reasons). This is how I would do it:

## Getting the polls

library(tidyverse)
library(zoo)

polls_2016 <- read_tsv(url("http://elections.huffingtonpost.com/pollster/api/v2/questions/16-US-Pres-GE%20TrumpvClinton/poll-responses-clean.tsv"))

## Wrangling the polls

polls_2016 <- polls_2016 %>%
  filter(sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters")) %>%
  right_join(data.frame(end_date = seq.Date(min(.$end_date), max(.$end_date), by="days")), by="end_date")

## Average the polls

rolling_average <- polls_2016 %>%
  group_by(end_date) %>%
  summarise(Clinton = mean(Clinton), Trump = mean(Trump)) %>%
  mutate(Clinton.Margin = Clinton-Trump,
         Clinton.Avg =  rollapply(Clinton.Margin,width=14,
                                  FUN=function(x){mean(x, na.rm=TRUE)},
                                  by=1, partial=TRUE, fill=NA, align="right"))

ggplot(rolling_average) +
  geom_line(aes(x=end_date, y=Clinton.Avg), col="blue") +
  geom_point(aes(x=end_date, y=Clinton.Margin))

which, by the way, has exactly the very same number of lines of code than the data.table version:

## Getting the polls

library(data.table)
library(zoo)
library(ggplot2)

pollsDT <- fread("http://elections.huffingtonpost.com/pollster/api/v2/questions/16-US-Pres-GE%20TrumpvClinton/poll-responses-clean.tsv")

## Wrangling the polls

pollsDT <- pollsDT[sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters"), ]
pollsDT[, end_date := as.IDate(end_date)]
pollsDT <- pollsDT[ data.table(end_date = seq(min(pollsDT[,end_date]),
                                              max(pollsDT[,end_date]), by="days")), on="end_date"]

## Average the polls

pollsDT <- pollsDT[, .(Clinton=mean(Clinton), Trump=mean(Trump)), by=end_date]
pollsDT[, Clinton.Margin := Clinton-Trump]
pollsDT[, Clinton.Avg := rollapply(Clinton.Margin, width=14,
                                   FUN=function(x){mean(x, na.rm=TRUE)},
                                   by=1, partial=TRUE, fill=NA, align="right")]

ggplot(pollsDT) +
  geom_line(aes(x=end_date, y=Clinton.Avg), col="blue") +
  geom_point(aes(x=end_date, y=Clinton.Margin))

Let’s translate this into base R. It is easier to start from the data.table version, mainly because filtering and assigning have a similar look and feel. Unsurprisingly, we have base::merge for the merge operation and stats::aggregate for the aggregation phase. base::as.Date works just fine for these dates and utils::read.csv has the only drawback that you have to specify the separatorutils::read.delim recognises the right separator by default. Without further ado, this is my version in base R:

## Getting the polls

library(zoo)

pollsB <- read.delim(url("http://elections.huffingtonpost.com/pollster/api/v2/questions/16-US-Pres-GE%20TrumpvClinton/poll-responses-clean.tsv"))

## Wrangling the polls

pollsB <- pollsB[pollsB$sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters"), ]
pollsB$end_date <- base::as.Date(pollsB$end_date)
endDate <- data.frame(end_date = seq.Date(min(pollsB$end_date), max(pollsB$end_date), by="days"))
pollsB <- merge(pollsB, endDate, by="end_date", all=TRUE)

## Average the polls

pollsB <- aggregate(cbind(Clinton, Trump) ~ end_date, data=pollsB, mean, na.action=na.pass)
pollsB$Clinton.Margin <- pollsB$Clinton - pollsB$Trump
pollsB$Clinton.Avg <- rollapply(pollsB$Clinton.Margin, width=14,
                                FUN=function(x){mean(x, na.rm=TRUE)},
                                by=1, partial=TRUE, fill=NA, align="right")

plot(pollsB$end_date, pollsB$Clinton.Margin, pch=16)
lines(pollsB$end_date, pollsB$Clinton.Avg, col="blue", lwd=2)

which is the shortest one! Finally, let’s repeat the benchmark too:

library(microbenchmark)

url <- "http://elections.huffingtonpost.com/pollster/api/v2/questions/16-US-Pres-GE%20TrumpvClinton/poll-responses-clean.tsv"
file <- "/tmp/poll-responses-clean.tsv"
download.file(url, destfile=file, quiet=TRUE)
res <- microbenchmark(tidy=suppressMessages(readr::read_tsv(file)),
                      dt=data.table::fread(file, showProgress=FALSE),
                      base=read.delim(file))
res
## Unit: milliseconds
##  expr       min        lq      mean    median        uq        max neval
##  tidy 13.877036 15.127885 18.549393 15.861311 17.813541 202.389391   100
##    dt  4.084022  4.505943  5.152799  4.845193  5.652579   7.736563   100
##  base 29.029366 30.437742 32.518009 31.449916 33.600937  45.104599   100

Base R is clearly the slowest option for the reading phase. Or, one might say, both readr and data.table have done a great job in improving things! Let’s take a look at the processing part now:

tvin <- suppressMessages(readr::read_tsv(file))
dtin <- data.table::fread(file, showProgress=FALSE)
bsin <- read.delim(file)

library(tidyverse)
library(data.table)
library(zoo)

transformTV <- function(polls_2016) {
  polls_2016 <- polls_2016 %>%
    filter(sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters")) %>%
    right_join(data.frame(end_date = seq.Date(min(.$end_date), max(.$end_date), by="days")), by="end_date")
  
  rolling_average <- polls_2016 %>%
    group_by(end_date) %>%
    summarise(Clinton = mean(Clinton), Trump = mean(Trump)) %>%
    mutate(Clinton.Margin = Clinton-Trump,
           Clinton.Avg =  rollapply(Clinton.Margin,width=14,
                                    FUN=function(x){mean(x, na.rm=TRUE)},
                                    by=1, partial=TRUE, fill=NA, align="right"))
}

transformDT <- function(dtin) {
  pollsDT <- copy(dtin) ## extra work to protect from reference semantics for benchmark
  pollsDT <- pollsDT[sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters"), ]
  pollsDT[, end_date := as.IDate(end_date)]
  pollsDT <- pollsDT[ data.table(end_date = seq(min(pollsDT[,end_date]),
                                                max(pollsDT[,end_date]), by="days")), on="end_date"]
  
  pollsDT <- pollsDT[, .(Clinton=mean(Clinton), Trump=mean(Trump)), by=end_date]
  pollsDT[, Clinton.Margin := Clinton-Trump]
  pollsDT[, Clinton.Avg := rollapply(Clinton.Margin, width=14,
                                     FUN=function(x){mean(x, na.rm=TRUE)},
                                     by=1, partial=TRUE, fill=NA, align="right")]
}

transformBS <- function(pollsB) {
  pollsB <- pollsB[pollsB$sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters"), ]
  pollsB$end_date <- base::as.Date(pollsB$end_date)
  endDate <- data.frame(end_date = seq.Date(min(pollsB$end_date), max(pollsB$end_date), by="days"))
  pollsB <- merge(pollsB, endDate, by="end_date", all=TRUE)
  
  pollsB <- aggregate(cbind(Clinton, Trump) ~ end_date, data=pollsB, mean, na.action=na.pass)
  pollsB$Clinton.Margin <- pollsB$Clinton - pollsB$Trump
  pollsB$Clinton.Avg <- rollapply(pollsB$Clinton.Margin, width=14,
                                  FUN=function(x){mean(x, na.rm=TRUE)},
                                  by=1, partial=TRUE, fill=NA, align="right")
}

res <- microbenchmark(tidy=transformTV(tvin),
                      dt=transformDT(dtin),
                      base=transformBS(bsin))
res
## Unit: milliseconds
##  expr      min       lq     mean   median       uq       max neval
##  tidy 20.68435 22.58603 26.67459 24.56170 27.85844  84.55077   100
##    dt 17.25547 18.88340 21.43256 20.24450 22.26448  41.65252   100
##  base 28.39796 30.93722 34.94262 32.97987 34.98222 109.14005   100

I don’t see so much difference between the tidyverse and data.table as Dirk showed, perhaps because I’ve simplified the script a bit, and removed some redundant parts. Again, base R is the slowest option, but don’t set it aside: it is the shortest one, and it is always there, out of the box!

Update (2018-01-25): Use read.delim(file) instead of read.csv(file, sep="\t") as @JorisMeys suggested here.

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6 comentarios sobre “Tidyverse and data.table, sitting side by side… and then base R walks in

  1. Hola Iñaki,

    Good work. I think the base version can be simplified, relying on defaults, as:
    polls_2016 <- read.delim("http:…") as the url is parsed automatically and read.delim assumes a tab.

    Probably using subset is clearer
    polls_2016 <- subset(polls_2016,
    sample_subpopulation %in% c("Adults","Likely Voters","Registered Voters"))

    And, given that as.Date is part of base
    pollsB$end_date <- as.Date(pollsB$end_date)

    and using:
    pollsB <- within(pollsb, {
    Clinton.Margin <- Clinton – Trump
    Clinton.Avg <- rollapply(Clinton.Margin, width=14,
    FUN=function(x){mean(x, na.rm=TRUE)},
    by=1, partial=TRUE, fill=NA, align="right")
    })
    is less wordy.

    Overall, whichever way one codes the example doesn't make a difference to the user from the point of view of performance. Readability can be vastly different though, for which I'm partial to the tidyverse.

    Saludos

  2. Thanks, Luis, nice additions. But note that “as.Date” is masked by package zoo. So you really need to specify the namespace if you want to use the one from the base package. ;-)

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