dplyr and pipes: the basics

The dplyr R package is awesome. Pipes from the magrittr R package are awesome. Put the two together and you have one of the most exciting things to happen to R in a long time.

dplyr is Hadley Wickham’s re-imagined plyr package (with underlying C++ secret sauce co-written by Romain Francois). plyr 2.0 if you will. It does less than dplyr, but what it does it does more elegantly and much more quickly.

dplyr is built around 5 verbs. These verbs make up the majority of the data manipulation you tend to do. You might need to:

Select certain columns of data.

Filter your data to select specific rows.

Arrange the rows of your data into an order.

Mutate your data frame to contain new columns.

Summarise chunks of you data in some way.

Let’s look at how those work.

The data

We’re going to work with a dataset of mammal life-history, geography, and ecology traits from the PanTHERIA database:

Jones, K.E., et al. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648. http://esapubs.org/archive/ecol/E090/184/

First we’ll download the data:

pantheria <-
  "http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt"
download.file(pantheria, destfile = "mammals.txt")

Next we’ll read it in and simplify it. This gets a bit ugly, but you can safely just run this code chunk and ignore the details:

mammals <- read.table("mammals.txt", sep = "\t", header = TRUE, 
  stringsAsFactors = FALSE)
names(mammals) <- sub("X[0-9._]+", "", names(mammals))
names(mammals) <- sub("MSW05_", "", names(mammals))
mammals <- dplyr::select(mammals, Order, Binomial, AdultBodyMass_g, 
  AdultHeadBodyLen_mm, HomeRange_km2, LitterSize)
names(mammals) <- gsub("([A-Z])", "_\\L\\1", names(mammals), perl = TRUE)
names(mammals) <- gsub("^_", "", names(mammals), perl = TRUE)
mammals[mammals == -999] <- NA
names(mammals)[names(mammals) == "binomial"] <- "species"
mammals <- dplyr::tbl_df(mammals) # for prettier printing

Next we’ll load the dplyr package:

library(dplyr)

Looking at the data

Data frames look a bit different in dplyr. Above, I called the tbl_df() function on our data. This provides more useful printing of data frames in the console. Ever accidentally printed a massive data frame in the console before? Yeah… this avoids that. You don’t need to change your data to a data frame tbl first — the dplyr functions will automatically convert your data when you call them. This is what the data look like on the console:

mammals
## # A tibble: 5,416 x 6
##    order    species     adult_body_mass… adult_head_body_l… home_range_km2
##    <chr>    <chr>                  <dbl>              <dbl>          <dbl>
##  1 Artioda… Camelus dr…          492714.                NA          196.  
##  2 Carnivo… Canis adus…           10392.               745.           1.01
##  3 Carnivo… Canis aure…            9659.               828.           2.95
##  4 Carnivo… Canis latr…           11989.               872.          18.9 
##  5 Carnivo… Canis lupus           31757.              1055.         160.  
##  6 Artioda… Bos fronta…          800143.              2700.          NA   
##  7 Artioda… Bos grunni…          500000.                NA           NA   
##  8 Artioda… Bos javani…          635974.              2075.          NA   
##  9 Primates Callicebus…            1117.               355.          NA   
## 10 Primates Callicebus…              NA                 NA           NA   
## # ... with 5,406 more rows, and 1 more variable: litter_size <dbl>

dplyr also provides a function glimpse() that makes it easy to look at our data in a transposed view. It’s similar to the str() (structure) function, but has a few advantages (see ?glimpse).

glimpse(mammals)
## Observations: 5,416
## Variables: 6
## $ order                  <chr> "Artiodactyla", "Carnivora", "Carnivora...
## $ species                <chr> "Camelus dromedarius", "Canis adustus",...
## $ adult_body_mass_g      <dbl> 492714.47, 10392.49, 9658.70, 11989.10,...
## $ adult_head_body_len_mm <dbl> NA, 745.32, 827.53, 872.39, 1055.00, 27...
## $ home_range_km2         <dbl> 1.963200e+02, 1.010000e+00, 2.950000e+0...
## $ litter_size            <dbl> 0.98, 4.50, 3.74, 5.72, 4.98, 1.22, 1.0...

Selecting columns

select() lets you subset by columns. This is similar to subset() in base R, but it also allows for some fancy use of helper functions such as contains(), starts_with() and, ends_with(). I think these examples are self explanatory, so I’ll just include them here:

select(mammals, adult_head_body_len_mm)
## # A tibble: 5,416 x 1
##    adult_head_body_len_mm
##                     <dbl>
##  1                    NA 
##  2                   745.
##  3                   828.
##  4                   872.
##  5                  1055.
##  6                  2700.
##  7                    NA 
##  8                  2075.
##  9                   355.
## 10                    NA 
## # ... with 5,406 more rows
select(mammals, adult_head_body_len_mm, litter_size)
## # A tibble: 5,416 x 2
##    adult_head_body_len_mm litter_size
##                     <dbl>       <dbl>
##  1                    NA        0.980
##  2                   745.       4.50 
##  3                   828.       3.74 
##  4                   872.       5.72 
##  5                  1055.       4.98 
##  6                  2700.       1.22 
##  7                    NA        1.00 
##  8                  2075.       1.22 
##  9                   355.       1.01 
## 10                    NA       NA    
## # ... with 5,406 more rows
select(mammals, adult_head_body_len_mm:litter_size)
## # A tibble: 5,416 x 3
##    adult_head_body_len_mm home_range_km2 litter_size
##                     <dbl>          <dbl>       <dbl>
##  1                    NA          196.         0.980
##  2                   745.           1.01       4.50 
##  3                   828.           2.95       3.74 
##  4                   872.          18.9        5.72 
##  5                  1055.         160.         4.98 
##  6                  2700.          NA          1.22 
##  7                    NA           NA          1.00 
##  8                  2075.          NA          1.22 
##  9                   355.          NA          1.01 
## 10                    NA           NA         NA    
## # ... with 5,406 more rows
select(mammals, -adult_head_body_len_mm)
## # A tibble: 5,416 x 5
##    order        species        adult_body_mass… home_range_km2 litter_size
##    <chr>        <chr>                     <dbl>          <dbl>       <dbl>
##  1 Artiodactyla Camelus drome…          492714.         196.         0.980
##  2 Carnivora    Canis adustus            10392.           1.01       4.50 
##  3 Carnivora    Canis aureus              9659.           2.95       3.74 
##  4 Carnivora    Canis latrans            11989.          18.9        5.72 
##  5 Carnivora    Canis lupus              31757.         160.         4.98 
##  6 Artiodactyla Bos frontalis           800143.          NA          1.22 
##  7 Artiodactyla Bos grunniens           500000.          NA          1.00 
##  8 Artiodactyla Bos javanicus           635974.          NA          1.22 
##  9 Primates     Callicebus cu…            1117.          NA          1.01 
## 10 Primates     Callicebus di…              NA           NA         NA    
## # ... with 5,406 more rows
select(mammals, contains("body"))
## # A tibble: 5,416 x 2
##    adult_body_mass_g adult_head_body_len_mm
##                <dbl>                  <dbl>
##  1           492714.                    NA 
##  2            10392.                   745.
##  3             9659.                   828.
##  4            11989.                   872.
##  5            31757.                  1055.
##  6           800143.                  2700.
##  7           500000.                    NA 
##  8           635974.                  2075.
##  9             1117.                   355.
## 10               NA                     NA 
## # ... with 5,406 more rows
select(mammals, starts_with("adult"))
## # A tibble: 5,416 x 2
##    adult_body_mass_g adult_head_body_len_mm
##                <dbl>                  <dbl>
##  1           492714.                    NA 
##  2            10392.                   745.
##  3             9659.                   828.
##  4            11989.                   872.
##  5            31757.                  1055.
##  6           800143.                  2700.
##  7           500000.                    NA 
##  8           635974.                  2075.
##  9             1117.                   355.
## 10               NA                     NA 
## # ... with 5,406 more rows
select(mammals, ends_with("g"))
## # A tibble: 5,416 x 1
##    adult_body_mass_g
##                <dbl>
##  1           492714.
##  2            10392.
##  3             9659.
##  4            11989.
##  5            31757.
##  6           800143.
##  7           500000.
##  8           635974.
##  9             1117.
## 10               NA 
## # ... with 5,406 more rows
select(mammals, 1:3)
## # A tibble: 5,416 x 3
##    order        species             adult_body_mass_g
##    <chr>        <chr>                           <dbl>
##  1 Artiodactyla Camelus dromedarius           492714.
##  2 Carnivora    Canis adustus                  10392.
##  3 Carnivora    Canis aureus                    9659.
##  4 Carnivora    Canis latrans                  11989.
##  5 Carnivora    Canis lupus                    31757.
##  6 Artiodactyla Bos frontalis                 800143.
##  7 Artiodactyla Bos grunniens                 500000.
##  8 Artiodactyla Bos javanicus                 635974.
##  9 Primates     Callicebus cupreus              1117.
## 10 Primates     Callicebus discolor               NA 
## # ... with 5,406 more rows

Filtering rows

filter() lets you subset by rows. You can use any valid logical statements:

filter(mammals, adult_body_mass_g > 1e7)[ , 1:3]
## # A tibble: 12 x 3
##    order   species                adult_body_mass_g
##    <chr>   <chr>                              <dbl>
##  1 Cetacea Caperea marginata              32000000.
##  2 Cetacea Balaenoptera musculus         154321304.
##  3 Cetacea Balaenoptera physalus          47506008.
##  4 Cetacea Balaena mysticetus             79691179.
##  5 Cetacea Balaenoptera borealis          22106252.
##  6 Cetacea Balaenoptera edeni             20000000.
##  7 Cetacea Berardius bairdii              11380000.
##  8 Cetacea Eschrichtius robustus          27324024.
##  9 Cetacea Eubalaena australis            23000000.
## 10 Cetacea Eubalaena glacialis            23000000.
## 11 Cetacea Megaptera novaeangliae         30000000.
## 12 Cetacea Physeter catodon               14540960.
filter(mammals, species == "Balaena mysticetus")
## # A tibble: 1 x 6
##   order  species       adult_body_mass… adult_head_body_le… home_range_km2
##   <chr>  <chr>                    <dbl>               <dbl>          <dbl>
## 1 Cetac… Balaena myst…        79691179.              12187.             NA
## # ... with 1 more variable: litter_size <dbl>
filter(mammals, order == "Carnivora" & adult_body_mass_g < 200)
## # A tibble: 3 x 6
##   order    species     adult_body_mass… adult_head_body_le… home_range_km2
##   <chr>    <chr>                  <dbl>               <dbl>          <dbl>
## 1 Carnivo… Mustela al…            180.                 244.        NA     
## 2 Carnivo… Mustela fr…            190.                 229.         0.210 
## 3 Carnivo… Mustela ni…             78.4                188.         0.0700
## # ... with 1 more variable: litter_size <dbl>

Arranging rows

arrange() lets you order the rows by one or more columns in ascending or descending order. I’m selecting the first three columns only to make the output easier to read:

arrange(mammals, adult_body_mass_g)[ , 1:3]
## # A tibble: 5,416 x 3
##    order        species                     adult_body_mass_g
##    <chr>        <chr>                                   <dbl>
##  1 Chiroptera   Craseonycteris thonglongyai              1.96
##  2 Chiroptera   Kerivoula minuta                         2.03
##  3 Soricomorpha Suncus etruscus                          2.26
##  4 Soricomorpha Sorex minutissimus                       2.46
##  5 Soricomorpha Suncus madagascariensis                  2.47
##  6 Soricomorpha Crocidura lusitania                      2.48
##  7 Soricomorpha Crocidura planiceps                      2.50
##  8 Chiroptera   Pipistrellus nanulus                     2.51
##  9 Soricomorpha Sorex nanus                              2.57
## 10 Soricomorpha Sorex arizonae                           2.70
## # ... with 5,406 more rows
arrange(mammals, desc(adult_body_mass_g))[ , 1:3]
## # A tibble: 5,416 x 3
##    order   species                adult_body_mass_g
##    <chr>   <chr>                              <dbl>
##  1 Cetacea Balaenoptera musculus         154321304.
##  2 Cetacea Balaena mysticetus             79691179.
##  3 Cetacea Balaenoptera physalus          47506008.
##  4 Cetacea Caperea marginata              32000000.
##  5 Cetacea Megaptera novaeangliae         30000000.
##  6 Cetacea Eschrichtius robustus          27324024.
##  7 Cetacea Eubalaena australis            23000000.
##  8 Cetacea Eubalaena glacialis            23000000.
##  9 Cetacea Balaenoptera borealis          22106252.
## 10 Cetacea Balaenoptera edeni             20000000.
## # ... with 5,406 more rows
arrange(mammals, order, adult_body_mass_g)[ , 1:3]
## # A tibble: 5,416 x 3
##    order        species                adult_body_mass_g
##    <chr>        <chr>                              <dbl>
##  1 Afrosoricida Microgale pusilla                   3.40
##  2 Afrosoricida Microgale parvula                   3.53
##  3 Afrosoricida Geogale aurita                      6.69
##  4 Afrosoricida Microgale fotsifotsy                7.70
##  5 Afrosoricida Microgale longicaudata              8.08
##  6 Afrosoricida Microgale brevicaudata              8.99
##  7 Afrosoricida Microgale principula               10.2 
##  8 Afrosoricida Microgale drouhardi                10.5 
##  9 Afrosoricida Microgale cowani                   12.3 
## 10 Afrosoricida Microgale taiva                    12.4 
## # ... with 5,406 more rows

Mutating columns

mutate() lets you add new columns. Notice that the new columns you create can build on each other. I will wrap these in glimpse() to make the new columns easy to see:

glimpse(mutate(mammals, adult_body_mass_kg = adult_body_mass_g / 1000))
## Observations: 5,416
## Variables: 7
## $ order                  <chr> "Artiodactyla", "Carnivora", "Carnivora...
## $ species                <chr> "Camelus dromedarius", "Canis adustus",...
## $ adult_body_mass_g      <dbl> 492714.47, 10392.49, 9658.70, 11989.10,...
## $ adult_head_body_len_mm <dbl> NA, 745.32, 827.53, 872.39, 1055.00, 27...
## $ home_range_km2         <dbl> 1.963200e+02, 1.010000e+00, 2.950000e+0...
## $ litter_size            <dbl> 0.98, 4.50, 3.74, 5.72, 4.98, 1.22, 1.0...
## $ adult_body_mass_kg     <dbl> 492.71447, 10.39249, 9.65870, 11.98910,...
glimpse(mutate(mammals, 
    g_per_mm = adult_body_mass_g / adult_head_body_len_mm))
## Observations: 5,416
## Variables: 7
## $ order                  <chr> "Artiodactyla", "Carnivora", "Carnivora...
## $ species                <chr> "Camelus dromedarius", "Canis adustus",...
## $ adult_body_mass_g      <dbl> 492714.47, 10392.49, 9658.70, 11989.10,...
## $ adult_head_body_len_mm <dbl> NA, 745.32, 827.53, 872.39, 1055.00, 27...
## $ home_range_km2         <dbl> 1.963200e+02, 1.010000e+00, 2.950000e+0...
## $ litter_size            <dbl> 0.98, 4.50, 3.74, 5.72, 4.98, 1.22, 1.0...
## $ g_per_mm               <dbl> NA, 13.9436618, 11.6717219, 13.7428214,...
glimpse(mutate(mammals, 
    g_per_mm = adult_body_mass_g / adult_head_body_len_mm,
    kg_per_mm = g_per_mm / 1000))
## Observations: 5,416
## Variables: 8
## $ order                  <chr> "Artiodactyla", "Carnivora", "Carnivora...
## $ species                <chr> "Camelus dromedarius", "Canis adustus",...
## $ adult_body_mass_g      <dbl> 492714.47, 10392.49, 9658.70, 11989.10,...
## $ adult_head_body_len_mm <dbl> NA, 745.32, 827.53, 872.39, 1055.00, 27...
## $ home_range_km2         <dbl> 1.963200e+02, 1.010000e+00, 2.950000e+0...
## $ litter_size            <dbl> 0.98, 4.50, 3.74, 5.72, 4.98, 1.22, 1.0...
## $ g_per_mm               <dbl> NA, 13.9436618, 11.6717219, 13.7428214,...
## $ kg_per_mm              <dbl> NA, 0.0139436618, 0.0116717219, 0.01374...

Summarising columns

Finally, summarise() lets you calculate summary statistics. On its own summarise() isn’t that useful, but when combined with group_by() you can summarise by chunks of data. This is similar to what you might be familiar with through ddply() and summarise() from the plyr package:

summarise(mammals, mean_mass = mean(adult_body_mass_g, na.rm = TRUE))
## # A tibble: 1 x 1
##   mean_mass
##       <dbl>
## 1   177810.
# summarise with group_by:
head(summarise(group_by(mammals, order),
  mean_mass = mean(adult_body_mass_g, na.rm = TRUE)))
## # A tibble: 6 x 2
##   order        mean_mass
##   <chr>            <dbl>
## 1 Afrosoricida      94.8
## 2 Artiodactyla  121329. 
## 3 Carnivora      47386. 
## 4 Cetacea      7373065. 
## 5 Chiroptera        57.7
## 6 Cingulata       4699.

Piping data

Pipes take the output from one function and feed it to the first argument of the next function. You may have encountered the Unix pipe | before.

The magrittr R package contains the pipe function %>%. Yes it might look bizarre at first but it makes more sense when you think about it. The R language allows symbols wrapped in % to be defined as functions, the > helps imply a chain, and you can hit these 2 characters one after the other very quickly on a keyboard by holding down the Shift key. Try it!

Try pronouncing %>% “then” whenever you see it. If you want to see the help page, you’ll need to wrap it in back ticks like so:

?magrittr::`%>%`

A trivial pipe example

Pipes can work with nearly any functions. Let’s start with a non-dplyr example:

x <- rnorm(10)
x %>% max
## [1] 1.546282
# is the same thing as:
max(x)
## [1] 1.546282

So, we took the value of x (what would have been printed on the console), captured it, and fed it to the first argument of max(). It’s probably not clear why this is cool yet, but hang on.

A silly dplyr example with pipes

Let’s try a single-pipe dplyr example. We’ll pipe the mammals data frame to the arrange function’s first argument, and choose to arrange by the adult_body_mass_g column:

mammals %>% arrange(adult_body_mass_g)
## # A tibble: 5,416 x 6
##    order   species       adult_body_mass… adult_head_body_… home_range_km2
##    <chr>   <chr>                    <dbl>             <dbl>          <dbl>
##  1 Chirop… Craseonycter…             1.96              31.0             NA
##  2 Chirop… Kerivoula mi…             2.03              NA               NA
##  3 Sorico… Suncus etrus…             2.26              NA               NA
##  4 Sorico… Sorex minuti…             2.46              52.0             NA
##  5 Sorico… Suncus madag…             2.47              NA               NA
##  6 Sorico… Crocidura lu…             2.48              31.0             NA
##  7 Sorico… Crocidura pl…             2.50              NA               NA
##  8 Chirop… Pipistrellus…             2.51              NA               NA
##  9 Sorico… Sorex nanus               2.57              52.0             NA
## 10 Sorico… Sorex arizon…             2.70              58.0             NA
## # ... with 5,406 more rows, and 1 more variable: litter_size <dbl>

An awesome example

OK, here’s where it gets cool. We can chain dplyr functions in succession. This lets us write data manipulation steps in the order we think of them and avoid creating temporary variables in the middle to capture the output. This works because the output from every dplyr function is a data frame and the first argument of every dplyr function is a data frame.

Say we wanted to find the species with the highest body-mass-to-length ratio:

mammals %>%
  mutate(mass_to_length = adult_body_mass_g / adult_head_body_len_mm) %>%
  arrange(desc(mass_to_length)) %>%
  select(species, mass_to_length)
## # A tibble: 5,416 x 2
##    species                mass_to_length
##    <chr>                           <dbl>
##  1 Balaena mysticetus              6539.
##  2 Balaenoptera musculus           5063.
##  3 Megaptera novaeangliae          2334.
##  4 Eschrichtius robustus           2309.
##  5 Balaenoptera physalus           2302.
##  6 Elephas maximus                 1704.
##  7 Eubalaena glacialis             1654.
##  8 Eubalaena australis             1625.
##  9 Balaenoptera edeni              1444.
## 10 Balaenoptera borealis           1203.
## # ... with 5,406 more rows

So, we took mammals, fed it to mutate() to create a mass-length ratio column, arranged the resulting data frame in descending order by that ratio, and selected the columns we wanted to see. This is just the beginning. If you can imagine it, you can string it together. If you want to debug your code, just pull a pipe off the end and run the code down to that step. Or build your analysis up and add successive pipes.

The above is equivalent to:

select(
  arrange(
    mutate(mammals,
      mass_to_length = adult_body_mass_g / adult_head_body_len_mm),
    desc(mass_to_length)),
  species, mass_to_length)
## # A tibble: 5,416 x 2
##    species                mass_to_length
##    <chr>                           <dbl>
##  1 Balaena mysticetus              6539.
##  2 Balaenoptera musculus           5063.
##  3 Megaptera novaeangliae          2334.
##  4 Eschrichtius robustus           2309.
##  5 Balaenoptera physalus           2302.
##  6 Elephas maximus                 1704.
##  7 Eubalaena glacialis             1654.
##  8 Eubalaena australis             1625.
##  9 Balaenoptera edeni              1444.
## 10 Balaenoptera borealis           1203.
## # ... with 5,406 more rows

But the problem here is that you have to read it inside out, it’s easy to miss a bracket, and the arguments get separated from the function (e.g. see mutate() and desc(mass_to_length))). Plus, this is a rather trivial example. Chain together even more steps and it quickly gets out of hand.

Here’s one more example. Let’s ask what taxonomic orders have a median litter size greater than 3.

mammals %>% group_by(order) %>%
  summarise(median_litter = median(litter_size, na.rm = TRUE)) %>%
  filter(median_litter > 3) %>%
  arrange(desc(median_litter)) %>%
  select(order, median_litter)
## # A tibble: 5 x 2
##   order           median_litter
##   <chr>                   <dbl>
## 1 Didelphimorphia          6.60
## 2 Dasyuromorphia           6.19
## 3 Erinaceomorpha           3.87
## 4 Soricomorpha             3.66
## 5 Rodentia                 3.28

These examples don’t even highlight one of the best things about dplyr. It’s really fast. The internal C++ code makes quick work of massive data frames that would make plyr slow to a crawl.

dplyr can do much more, but the above are the basics of the 5 verbs and pipes. Try them for a bit. Once they click I think they’ll revolutionize your data analysis.