Importing data with the tidyverse

One of the first steps of a project is to import outside data into R. Data is often stored in tabular formats, like csv files or spreadsheets.

• The first half of this cheatsheet shows how to import and save text files into R using readr.
• The second half shows how to import spreadsheet data from Excel files using readxl or Google Sheets using googlesheets4.

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library(readr)
library(readxl)
library(googlesheets4)

For importing other types of data try one of the following packages:

• haven: SPSS, Stata, and SAS files
• DBI: databases
• jsonlite: json
• xml2: XML
• httr: Web APIs
• rvest: HTML (Web Scraping)
• readr::read_lines(): text data

Read Tabular Data with readr

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#| include: false
library(readr)

See ?read_delim.

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read_*(
  file, 
  col_names = TRUE, col_types = NULL, col_select = NULL, 
  show_col_types = TRUE
  id = NULL, locale, 
  n_max = Inf, skip = 0, guess_max = min(1000, n_max), 
  na = c("", "NA")
)

Examples

• Read files with any delimiter: read_delim(). If no delimiter is specified, it will automatically guess.

  • If the file you want to import is the following:

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    A|B|C 1|2|3 4|5|NA

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    #| label: write-file-txt #| echo: false write_file("A|B|C\n1|2|3\n4|5|NA", file = "file.txt")

  • Read it with read_delim() and it will look like the following when imported:

    1 2	read_delim("file.txt", delim = "|", show_col_types = FALSE)

  • To make file.txt, run:

    1 2	#| ref.label: write-file-txt #| eval: false

• Read a comma delimited file with period decimal marks: read_csv().

  • If the file you want to import is the following:

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    A,B,C 1,2,3 4,5,NA

    1 2 3 4

    #| label: write-file-csv #| echo: false write_file("A,B,C\n1,2,3\n4,5,NA", file = "file.csv")

  • Read it with read_csv() and it will look like the following when imported:

    1	read_csv("file.csv", show_col_types = FALSE)

  • To make file.csv, run:

    1 2	#| ref.label: write-file-csv #| eval: false

• Read semicolon delimited files with comma decimal marks: read_csv2().

  • If the file you want to import is the following:

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    A;B;C 1,5;2;3 4,5;5;NA

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    #| label: write-file-csv2 #| echo: false write_file("A;B;C\n1,5;2;3\n4,5;5;NA", file = "file2.csv")

  • Read it with read_csv2() and it will look like the following when imported:

    1	read_csv2("file2.csv", show_col_types = FALSE)

  • To make file2.csv, run:

    1 2	#| ref.label: write-file-csv2 #| eval: false

• Read a tab delimited file: read_tsv() or read_table().

  Read a fixed width file: read_fwf("file.tsv", fwf_widths(c(2, 2, NA))).

  • If the file you want to import is the following:

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    A B C 1 2 3 4 5 NA

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    #| label: write-file-tsv #| echo: false write_file("A\tB\tC\n1\t2\t3\n4\t5\tNA\n", file = "file.tsv")

  • Read it with read_tsv() and it will look like the following when imported:

    1	read_tsv("file.tsv", show_col_types = FALSE)

  • To make tsv, run:

    1 2	#| ref.label: write-file-tsv #| eval: false

Useful read arguments

Suppose you have the following CSV files that you want to read in, called file.csv:

file.csv

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A,B,C
1,2,3
4,5,NA

file3.csv

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A,B,C
7,8,9
NA,11,12

To make these files, run:

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write_file("A,B,C\n1,2,3\n4,5,NA", file = "file.csv")
write_file("A,B,C\n7,8,9\nNA,11,12", file = "file3.csv")

• No header: col_names = FALSE

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  #| message: false read_csv("file.csv", col_names = FALSE)

• Provide header: col_names = c("x", "y", "z")

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  #| message: false read_csv("file.csv", col_names = c("x", "y", "z"))

• Skip lines:

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  #| message: false read_csv("file.csv", skip = 1)

• Read a subset of lines:

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  #| message: false read_csv("file.csv", n_max = 1)

• Read values as missing:

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  #| message: false read_csv("file.csv", na = c("1"))

• Specify decimal marks:

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  #| message: false read_delim("file2.csv", locale = locale(decimal_mark = ","))

• Read multiple files into a single table:

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  #| message: false read_csv(c("file.csv", "file3.csv"), id = "origin_file")

Save data with readr

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write_*(
  x, file, 
  na = "NA", 
  append, col_names, quote, escape, eol, num_threads, progress
)

• Write files with any delimiter: write_delim(x, file, delim = " ")
• Write a comma delimited file: write_csv(x, file)
• Write a semicolon delimited file: write_csv2(x, file)
• Write a tab delimited file: write_tsv(x, file)

Column specification with readr

Column specifications define what data type each column of a file will be imported as. By default readr will generate a column spec when a file is read and output a summary.

spec(df): Extract the full column specification for the given imported data frame.

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#| eval: false

spec(df)
# cols(
#   age = col_integer(),   # age is an integer
#   edu = col_character(), # edu is a character
#   earn = col_double()    # earn is a double (numeric)
# )

Column types

Each column type has a function and corresponding string abbreviation.

• col_logical() - "l"
• col_integer() - "i"
• col_double() - "d"
• col_number() - "n"
• col_character() - "c"
• col_factor(levels, ordered = FALSE) - "f"
• col_datetime(format = "") - "T"
• col_date(format = "") - "D"
• col_time(format = "") - "t"
• col_skip() - "-", "_"
• col_guess() - "?"

Useful column arguments

• Hide col spec message:

  1	read_*(file, show_col_types = FALSE)

• Select columns to import: Use names, position, or selection helpers.

  1	read_*(file, col_select = c(age, earn))

• Guess column types: To guess a column type, read_ *() looks at the first 1000 rows of data. Increase with guess_max.

  1	read_*(file, guess_max = Inf)

Define column specification

• Set a default type:

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  #| eval: false read_csv( file, col_type = list(.default = col_double()) )

• Use column type or string abbreviation:

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  #| eval: false read_csv( file, col_type = list(x = col_double(), y = "l", z = "_") )

• Use a single string of abbreviations:

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  #| eval: false # col types: skip, guess, integer, logical, character read_csv( file, col_type = "_?ilc" )

Import spreadsheets with readxl

Read Excel files

Read a .xls or .xlsx file based on the file extension, e.g. read_excel("excel_file.xlsx"). See [Useful read arguments] for more read arguments. Also read_xls() and read_xlsx().

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#| eval: false

read_excel(path, sheet = NULL, range = NULL)

• If the Google sheet you want to import is the following:

  A	B	C	D	E
  x1	x2	x3	x4	x5
  x		z	8
  y	7		9	10

  : Spreadsheet with 5 columns (A through E) and three rows. First row reads x1 through x5. Second and third row have some missing values.

• It will look like the following when imported:

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  #| echo: false write_file("x1,x2,x3,x4,x5\nx, ,z,8, \ny,7, ,9,10", file = "excel.csv") read_csv("excel.csv", show_col_types = FALSE)

Read sheets

• Specify which sheet to read by position or name: read_excel(path, sheet = NULL)

  • read_excel(path, sheet = 1)
  • read_excel(path, sheet = "s1")

• Get a vector of sheet names: excel_sheets(path)

  excel_sheets("excel_file.xlsx")

• To read multiple sheets:

  1. Get a vector of sheet names from the file path.

  2. Set the vector names to be the sheet names.

  3. Use purrr::map() and purrr::list_rbind() to read multiple files into one data frame.

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     #| eval: false path <- "your_file_path.xlsx" path |> excel_sheets() |> set_names() |> map(read_excel, path = path) |> list_rbind()

readxl column specification

• Column specifications define what data type each column of a file will be imported as.

• Use the col_types argument of read_excel() to set the column specification.

• Guess column types: To guess a column type, read_excel() looks at the first 1000 rows of data. Increase with the guess_max argument.

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  #| eval: false read_excel(path, guess_max = Inf)

• Set all columns to same type, e.g. character:

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  #| eval: false read_excel(path, col_types = "text")

• Set each column individually:

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  #| eval: false read_excel( path, col_types = c("text", "guess", "guess","numeric") )

• Column types:

  logical	numeric	text	date	list
  TRUE	2	hello	1947-01-08	hello
  FALSE	3.45	world	1956-10-21	1

  : Table with 5 columns. Column headers are various data types (logical, numeric, text, date, and list). The data in two rows show examples of data for the given column type.

  • skip

  • guess

  • logical

  • date

  • numeric

  • text

  • Use listfor columns that include multiple data types. See tidyr and purrr for list-column data.

Other useful Excel packages

• For functions to write data to Excel files: openxlsx and writexl
• For working with non-tabular Excel data: tidyxl

Import spreadsheets with googlesheets4

Read sheets

Read a sheet from a URL, a Sheet ID, or a dribble samefrom the googledrive package. See [Useful read arguments] for more read arguments.

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#| eval: false

read_sheet(ss, sheet = NULL, range = NULL)

Same as range_read().

• If the Google sheet you want to import is the following:

  A	B	C	D	E
  x1	x2	x3	x4	x5
  x		z	8
  y	7		9	10

  : Spreadsheet with 5 columns (A through E) and three rows. First row reads x1 through x5. Second and third row have some missing values.

• It will look like the following when imported:

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  #| echo: false write_file("x1,x2,x3,x4,x5\nx, ,z,8, \ny,7, ,9,10", file = "googlesheet.csv") read_csv("googlesheet.csv", show_col_types = FALSE)

Sheet metadata

• URLs are in the form:

  1 2	https://docs.google.com/spreadsheets/d/             SPREADSHEET_ID/edit#gid=SHEET_ID

• Get spreadsheet meta data: gs4_get(ss)

• Get data on all spreadsheet files: gs4_find(...)

• Get a tibble of properties for each worksheet: sheet_properties(ss). Also sheet_names().

Write sheets

• write_sheet(data, ss = NULL, sheet = NULL): Write a data frame into a new or existing Sheet. 
• gs4_create(name, ..., sheets = NULL): Create a new Sheet with a vector of names, a data frame, or a (named) list of data frames.
• sheet_append(ss, data, sheet = 1): Add rows to the end of a worksheet.

googlesheets4 column specification

Column specifications define what data type each column of a file will be imported as.

Use the col_types argument of read_sheet()/range_read() to set the column specification.

• Guess column types: To guess a column type read_sheet()/range_read() looks at the first 1000 rows of data. Increase with guess_max.

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  #| eval: false read_sheet(path, guess_max = Inf)

• Set all columns to same type, e.g. character:

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  #| eval: false read_sheet(path, col_types = "c")

• Set each column individually:

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  #| eval: false # col types: skip, guess, integer, logical, character read_sheets(ss, col_types = "_?ilc")

• Column types:

  • skipped my lunch 🥙 🍱 and: “_” or “-”

  • guess: “?”

  • logical: “l”

  • integer: “i”

  • double: “d”

  • numeric: “n”

  • date: “D”

  • datetime: “T”

  • character: “c”

  • list-column: “L”

  • cell: “C” (returns list of raw cell data)

  • Use list for columns that include multiple data types. See tidyr and purrr for list-column data.

File level operations

• googlesheets4 also offers ways to modify other aspects of Sheets (e.g. freeze rows, set column width, manage (work)sheets). Go to googlesheets4.tidyverse.org to read more.
• For whole-file operations (e.g. renaming, sharing, placing within a folder), see the tidyverse package googledrive at googledrive.tidyverse.org .

Cell specification for readxl and googlesheets4

Use the range argument of readxl::read_excel() or googlesheets4::read_sheet() to read a subset of cells from a sheet.

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#| eval: false

read_excel(path, range = "Sheet1!B1:D2")
read_sheet(ss, range = "B1:D2")

Also use the range argument with cell specification functions cell_limits(), cell_rows(), cell_cols(), and anchored().