Computing by groups within data.frames with plyr

Install and load plyr

If you have not already done so, you’ll need to install plyr.

install.packages("plyr", dependencies = TRUE)

We also need to load it.

library(plyr)

Note: if you are using both plyr and dplyr in a script, you should always load plyr first, then dplyr.

Load the Gapminder data

As usual, load the Gapminder excerpt.

library(gapminder)

Introduction to ddply()

Let’s say we want the maximum life expectancy for each continent. We’re providing a data.frame as input and we want a data.frame as output. Therefore this is a job for ddply(). We want to divide the data.frame into pieces based on continent. Here’s the call

(max_le_by_cont <-
   ddply(gapminder, ~ continent, summarize, max_le = max(lifeExp)))
##   continent max_le
## 1    Africa 76.442
## 2  Americas 80.653
## 3      Asia 82.603
## 4    Europe 81.757
## 5   Oceania 81.235

Let’s study the return value.

str(max_le_by_cont)
## 'data.frame':    5 obs. of  2 variables:
##  $ continent: Factor w/ 5 levels "Africa","Americas",..: 1 2 3 4 5
##  $ max_le   : num  76.4 80.7 82.6 81.8 81.2
levels(max_le_by_cont$continent)
## [1] "Africa"   "Americas" "Asia"     "Europe"   "Oceania"

We got a data.frame back, with one observation per continent, and two variables: the maximum life expectancies and the continent, as a factor, with the same levels in the same order, as for the input data.frame gapminder. If you have sweated to do such things with base R, this minor miracle might make you cry tears of joy (or anguish over all the hours you have wasted.)

summarize() or its synonym summarise() is a function provided by plyr that creates a new data.frame from an old one. It is related to the built-in function transform() that transforms variables in a data.frame or adds new ones. Feel free to play with it a bit in some top-level commands; you will use it alot inside plyr calls.

The two variables in max_le_by_cont come from two sources. The continent factor is provided by ddply() and represents the labelling of the life expectancies with their associated continent. This is the book-keeping associated with dividing the input into little bits, computing on them, and gluing the results together again in an orderly, labelled fashion. We can take more credit for the other variable max_le, which has a name we chose and arises from applying a function we specified (max()) to a variable of our choice (lifeExp).

You try: compute the minimum GDP per capita by continent. Here’s what I get:

##   continent  min_gdppc
## 1    Africa   241.1659
## 2  Americas  1201.6372
## 3      Asia   331.0000
## 4    Europe   973.5332
## 5   Oceania 10039.5956

You might have chosen a different name for the minimum GDP/capita’s, but your numerical results should match.

The function you want to apply to the continent-specific data.frames can be built-in, like max() above, or a custom function you’ve written. This custom function can be written in advance or specified ‘on the fly’. Here’s one way to count the number of countries in this dataset for each continent.

ddply(gapminder, ~ continent,
      summarize, n_uniq_countries = length(unique(country)))
##   continent n_uniq_countries
## 1    Africa               52
## 2  Americas               25
## 3      Asia               33
## 4    Europe               30
## 5   Oceania                2

Here is another way to do the same thing that doesn’t use summarize() at all:

ddply(gapminder, ~ continent,
      function(x) c(n_uniq_countries = length(unique(x$country))))
##   continent n_uniq_countries
## 1    Africa               52
## 2  Americas               25
## 3      Asia               33
## 4    Europe               30
## 5   Oceania                2

In pseudo pseudo-code, here’s what’s happening above:

returnValue <- an empty receptacle with one "slot" per country
for each possible country i {
    x  <- subset(gapminder, subset = country == i)
    returnValue[i] <- length(unique(x$country))
    name or label for returnValue[i] is set to country i
}
ddply packages returnValue and associated names/labels as a nice data.frame

You don’t have to compute just one thing for each sub-data.frame, nor are you limited to computing on just one variable. Check this out.

ddply(gapminder, ~ continent, summarize,
      min_le = min(lifeExp), max_le = max(lifeExp),
      med_gdppc = median(gdpPercap))
##   continent min_le max_le med_gdppc
## 1    Africa 23.599 76.442  1192.138
## 2  Americas 37.579 80.653  5465.510
## 3      Asia 28.801 82.603  2646.787
## 4    Europe 43.585 81.757 12081.749
## 5   Oceania 69.120 81.235 17983.304

Recall the function we wrote to fit a linear model

We recently learned how to write our own R functions (Part 1, Part 2, Part 3). We then wrote a function to use on the Gapminder dataset. This function le_lin_fit() takes a data.frame and expects to find variables for life expectancy and year. It returns the estimated coefficients from a simple linear regression. We wrote it with the goal of applying it to the data from each country in Gapminder. That’s what we do here.

Make the function available in the workspace

Define the function developed elsewhere:

le_lin_fit <- function(dat, offset = 1952) {
  the_fit <- lm(lifeExp ~ I(year - offset), dat)
  setNames(coef(the_fit), c("intercept", "slope"))
}

Let’s try it out on the data for one country, just to reacquaint ourselves with it.

le_lin_fit(subset(gapminder, country == "Canada"))
##  intercept      slope 
## 68.8838462  0.2188692

Apply our function inside ddply

We are ready to scale up to all countries by placing this function inside a ddply() call.

j_coefs <- ddply(gapminder, ~ country, le_lin_fit)
str(j_coefs)
## 'data.frame':    142 obs. of  3 variables:
##  $ country  : Factor w/ 142 levels "Afghanistan",..: 1 2 3 4 5 6 7 8 9 10 ...
##  $ intercept: num  29.9 59.2 43.4 32.1 62.7 ...
##  $ slope    : num  0.275 0.335 0.569 0.209 0.232 ...
tail(j_coefs)
##                country intercept       slope
## 137          Venezuela  57.51332  0.32972168
## 138            Vietnam  39.01008  0.67161538
## 139 West Bank and Gaza  43.79840  0.60110070
## 140        Yemen, Rep.  30.13028  0.60545944
## 141             Zambia  47.65803 -0.06042517
## 142           Zimbabwe  55.22124 -0.09302098

We did it! By the time we’ve packaged the computation in a function, the call itself is deceptively simple. To review, here’s the script I would save from our work in this tutorial:

library(plyr)
library(gapminder)
le_lin_fit <- function(dat, offset = 1952) {
  the_fit <- lm(lifeExp ~ I(year - offset), dat)
  setNames(coef(the_fit), c("intercept", "slope"))
}
j_coefs <- ddply(gapminder, ~ country, le_lin_fit)

That’s all. After we’ve developed the le_lin_fit() function and gotten to know ddply(), this task requires about 5 lines of R code.

Reflect on how incredibly convenient this is. If you’re coming from another analytical environment, how easy would this task have been? If you had been asked to do this with R a week ago, would you have written a for loop or given up? The take away message is this: if you are able to write custom functions, the plyr package can make you extremely effective at computing on pieces of a data structure and reassembling the results.

References

plyr paper: The split-apply-combine strategy for data analysis, Hadley Wickham, Journal of Statistical Software, vol. 40, no. 1, pp. 1–29, 2011. Go here for supplements, such as example code from the paper.