1.3 Reading Tabular Data with the readr Package | Mastering Software Development in R

1.3 Reading Tabular Data with the `readr` Package

The learning objectives for this section are to:

Read tabular data into R and read in web data via web scraping tools and APIs

The readr package is the primary means by which we will read tablular data, most notably, comma-separated-value (CSV) files. The readr package has a few functions in it for reading and writing tabular data—we will focus on the read_csv function. The readr package is available on CRAN and the code for the package is maintained on GitHub.

The importance of the read_csv function is perhaps better understood from an historical perspective. R’s built in read.csv function similarly reads CSV files, but the read_csv function in readr builds on that by removing some of the quirks and “gotchas” of read.csv as well as dramatically optimizing the speed with which it can read data into R. The read_csv function also adds some nice user-oriented features like a progress meter and a compact method for specifying column types.

The only required argument to read_csv is a character string specifying the path to the file to read. A typical call to read_csv will look as follows.

library(readr)
teams <- read_csv("data/team_standings.csv")

── Column specification ────────────────────────────────────────────────────────
cols(
  Standing = col_double(),
  Team = col_character()
)
teams
# A tibble: 32 x 2
   Standing Team       
      <dbl> <chr>      
 1        1 Spain      
 2        2 Netherlands
 3        3 Germany    
 4        4 Uruguay    
 5        5 Argentina  
 6        6 Brazil     
 7        7 Ghana      
 8        8 Paraguay   
 9        9 Japan      
10       10 Chile      
# … with 22 more rows

By default, read_csv will open a CSV file and read it in line-by-line. It will also (by default), read in the first few rows of the table in order to figure out the type of each column (i.e. integer, character, etc.). In the code example above, you can see that read_csv has correctly assigned an integer class to the “Standing” variable in the input data and a character class to the “Team” variable. From the read_csv help page:

If [the argument for col_types is] ‘NULL,’ all column types will be imputed from the first 1000 rows on the input. This is convenient (and fast), but not robust. If the imputation fails, you’ll need to supply the correct types yourself.

You can also specify the type of each column with the col_types argument. In general, it’s a good idea to specify the column types explicitly. This rules out any possible guessing errors on the part of read_csv. Also, specifying the column types explicitly provides a useful safety check in case anything about the dataset should change without you knowing about it.

teams <- read_csv("data/team_standings.csv", col_types = "cc")

Note that the col_types argument accepts a compact representation. Here "cc" indicates that the first column is character and the second column is character (there are only two columns). Using the col_types argument is useful because often it is not easy to automatically figure out the type of a column by looking at a few rows (especially if a column has many missing values).

The read_csv function will also read compressed files automatically. There is no need to decompress the file first or use the gzfile connection function. The following call reads a gzip-compressed CSV file containing download logs from the RStudio CRAN mirror.

logs <- read_csv("data/2016-07-19.csv.gz", n_max = 10)

── Column specification ────────────────────────────────────────────────────────
cols(
  date = col_date(format = ""),
  time = col_time(format = ""),
  size = col_double(),
  r_version = col_character(),
  r_arch = col_character(),
  r_os = col_character(),
  package = col_character(),
  version = col_character(),
  country = col_character(),
  ip_id = col_double()
)

Note that the message (“Parse with column specification …”) printed after the call indicates that read_csv may have had some difficulty identifying the type of each column. This can be solved by using the col_types argument.

logs <- read_csv("data/2016-07-20.csv.gz", col_types = "ccicccccci", n_max = 10)
logs
# A tibble: 10 x 10
   date    time      size r_version r_arch r_os   package  version country ip_id
   <chr>   <chr>    <int> <chr>     <chr>  <chr>  <chr>    <chr>   <chr>   <int>
 1 2016-0… 06:04…  144723 3.3.1     i386   mingw… gtools   3.5.0   US          1
 2 2016-0… 06:04… 2049711 3.3.0     i386   mingw… rmarkdo… 1.0     DK          2
 3 2016-0… 06:04…   26252 <NA>      <NA>   <NA>   R.metho… 1.7.1   AU          3
 4 2016-0… 06:04…  556091 2.13.1    x86_64 mingw… tibble   1.1     CN          4
 5 2016-0… 06:03…  313363 2.13.1    x86_64 mingw… iterato… 1.0.5   US          5
 6 2016-0… 06:03…  378892 3.3.1     x86_64 mingw… foreach  1.3.2   US          5
 7 2016-0… 06:04…   41228 3.3.1     x86_64 linux… moments  0.14    US          6
 8 2016-0… 06:04…  403177 <NA>      <NA>   <NA>   R.oo     1.20.0  AU          3
 9 2016-0… 06:04…     525 3.3.0     x86_64 linux… rgl      0.95.1… KR          7
10 2016-0… 06:04…  755720 3.2.5     x86_64 mingw… geosphe… 1.5-5   US          8

You can specify the column type in a more detailed fashion by using the various col_* functions. For example, in the log data above, the first column is actually a date, so it might make more sense to read it in as a Date variable. If we wanted to just read in that first column, we could do

logdates <- read_csv("data/2016-07-20.csv.gz", 
                     col_types = cols_only(date = col_date()),
                     n_max = 10)
logdates
# A tibble: 10 x 1
   date      
   <date>    
 1 2016-07-20
 2 2016-07-20
 3 2016-07-20
 4 2016-07-20
 5 2016-07-20
 6 2016-07-20
 7 2016-07-20
 8 2016-07-20
 9 2016-07-20
10 2016-07-20

Now the date column is stored as a Date object which can be used for relevant date-related computations (for example, see the lubridate package).

A> The read_csv function has a progress option that defaults to TRUE. This options provides a nice progress meter while the CSV file is being read. However, if you are using read_csv in a function, or perhaps embedding it in a loop, it’s probably best to set progress = FALSE.

The readr package includes a variety of functions in the read_* family that allow you to read in data from different formats of flat files. The following table gives a guide to several functions in the read_* family.

`readr` function	Use
`read_csv`	Reads comma-separated file
`read_csv2`	Reads semicolon-separated file
`read_tsv`	Reads tab-separated file
`read_delim`	General function for reading delimited files
`read_fwf`	Reads fixed width files
`read_log`	Reads log files