readxl
Read Excel Files
Import excel files into R. Supports '.xls' via the embedded 'libxls' C library < https://github.com/libxls/libxls> and '.xlsx' via the embedded 'RapidXML' C++ library < http://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.
Overview
The readxl package makes it easy to get data out of Excel and into R. Compared to many of the existing packages (e.g. gdata, xlsx, xlsReadWrite) readxl has no external dependencies, so it’s easy to install and use on all operating systems. It is designed to work with tabular data.
readxl supports both the legacy .xls format and the modern xml-based
.xlsx format. The libxls C
library is used to support .xls, which abstracts away many of the
complexities of the underlying binary format. To parse .xlsx, we use
the RapidXML C++ library.
Installation
The easiest way to install the latest released version from CRAN is to install the whole tidyverse.
install.packages("tidyverse")
NOTE: you will still need to load readxl explicitly, because it is not a
core tidyverse package loaded via library(tidyverse).
Alternatively, install just readxl from CRAN:
install.packages("readxl")
Or install the development version from GitHub:
# install.packages("devtools")devtools::install_github("tidyverse/readxl")
Usage
library(readxl)
readxl includes several example files, which we use throughout the
documentation. Use the helper readxl_example() with no arguments to
list them or call it with an example filename to get the path.
readxl_example()#> [1] "clippy.xls" "clippy.xlsx" "datasets.xls" "datasets.xlsx"#> [5] "deaths.xls" "deaths.xlsx" "geometry.xls" "geometry.xlsx"#> [9] "type-me.xls" "type-me.xlsx"readxl_example("clippy.xls")#> [1] "/Users/jenny/resources/R/library/readxl/extdata/clippy.xls"
read_excel() reads both xls and xlsx files and detects the format from
the extension.
xlsx_example <- readxl_example("datasets.xlsx")read_excel(xlsx_example)#> # A tibble: 150 x 5#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species#> <dbl> <dbl> <dbl> <dbl> <chr>#> 1 5.1 3.5 1.4 0.2 setosa#> 2 4.9 3 1.4 0.2 setosa#> 3 4.7 3.2 1.3 0.2 setosa#> # … with 147 more rowsxls_example <- readxl_example("datasets.xls")read_excel(xls_example)#> # A tibble: 150 x 5#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species#> <dbl> <dbl> <dbl> <dbl> <chr>#> 1 5.1 3.5 1.4 0.2 setosa#> 2 4.9 3 1.4 0.2 setosa#> 3 4.7 3.2 1.3 0.2 setosa#> # … with 147 more rows
List the sheet names with excel_sheets().
excel_sheets(xlsx_example)#> [1] "iris" "mtcars" "chickwts" "quakes"
Specify a worksheet by name or number.
read_excel(xlsx_example, sheet = "chickwts")#> # A tibble: 71 x 2#> weight feed#> <dbl> <chr>#> 1 179 horsebean#> 2 160 horsebean#> 3 136 horsebean#> # … with 68 more rowsread_excel(xls_example, sheet = 4)#> # A tibble: 1,000 x 5#> lat long depth mag stations#> <dbl> <dbl> <dbl> <dbl> <dbl>#> 1 -20.4 182. 562 4.8 41#> 2 -20.6 181. 650 4.2 15#> 3 -26 184. 42 5.4 43#> # … with 997 more rows
There are various ways to control which cells are read. You can even specify the sheet here, if providing an Excel-style cell range.
read_excel(xlsx_example, n_max = 3)#> # A tibble: 3 x 5#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species#> <dbl> <dbl> <dbl> <dbl> <chr>#> 1 5.1 3.5 1.4 0.2 setosa#> 2 4.9 3 1.4 0.2 setosa#> 3 4.7 3.2 1.3 0.2 setosaread_excel(xlsx_example, range = "C1:E4")#> # A tibble: 3 x 3#> Petal.Length Petal.Width Species#> <dbl> <dbl> <chr>#> 1 1.4 0.2 setosa#> 2 1.4 0.2 setosa#> 3 1.3 0.2 setosaread_excel(xlsx_example, range = cell_rows(1:4))#> # A tibble: 3 x 5#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species#> <dbl> <dbl> <dbl> <dbl> <chr>#> 1 5.1 3.5 1.4 0.2 setosa#> 2 4.9 3 1.4 0.2 setosa#> 3 4.7 3.2 1.3 0.2 setosaread_excel(xlsx_example, range = cell_cols("B:D"))#> # A tibble: 150 x 3#> Sepal.Width Petal.Length Petal.Width#> <dbl> <dbl> <dbl>#> 1 3.5 1.4 0.2#> 2 3 1.4 0.2#> 3 3.2 1.3 0.2#> # … with 147 more rowsread_excel(xlsx_example, range = "mtcars!B1:D5")#> # A tibble: 4 x 3#> cyl disp hp#> <dbl> <dbl> <dbl>#> 1 6 160 110#> 2 6 160 110#> 3 4 108 93#> # … with 1 more row
If NAs are represented by something other than blank cells, set the
na argument.
read_excel(xlsx_example, na = "setosa")#> # A tibble: 150 x 5#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species#> <dbl> <dbl> <dbl> <dbl> <chr>#> 1 5.1 3.5 1.4 0.2 <NA>#> 2 4.9 3 1.4 0.2 <NA>#> 3 4.7 3.2 1.3 0.2 <NA>#> # … with 147 more rows
If you are new to the tidyverse conventions for data import, you may want to consult the data import chapter in R for Data Science. readxl will become increasingly consistent with other packages, such as readr.
Articles
Broad topics are explained in these articles:
- Cell and Column Types
- Sheet Geometry: how to specify which cells to read
- readxl Workflows: Iterating over multiple tabs or worksheets, stashing a csv snapshot
We also have some focused articles that address specific aggravations presented by the world’s spreadsheets:
Features
-
No external dependency on, e.g., Java or Perl.
-
Re-encodes non-ASCII characters to UTF-8.
-
Loads datetimes into POSIXct columns. Both Windows (1900) and Mac (1904) date specifications are processed correctly.
-
Discovers the minimal data rectangle and returns that, by default. User can exert more control with
range,skip, andn_max. -
Column names and types are determined from the data in the sheet, by default. User can also supply via
col_namesandcol_typesand control name repair via.name_repair. -
Returns a tibble, i.e. a data frame with an additional
tbl_dfclass. Among other things, this provide nicer printing.
Other relevant packages
Here are some other packages with functionality that is complementary to readxl and that also avoid a Java dependency.
Writing Excel files: The example files datasets.xlsx and
datasets.xls were created with the help of
openxlsx (and Excel).
openxlsx provides “a high level interface to writing, styling and
editing
worksheets”.
l <- list(iris = iris, mtcars = mtcars, chickwts = chickwts, quakes = quakes)openxlsx::write.xlsx(l, file = "inst/extdata/datasets.xlsx")
writexl is a new option in this space, first released on CRAN in August 2017. It’s a portable and lightweight way to export a data frame to xlsx, based on libxlsxwriter. It is much more minimalistic than openxlsx, but on simple examples, appears to be about twice as fast and to write smaller files.
Non-tabular data and formatting: tidyxl is focused on importing awkward and non-tabular data from Excel. It also “exposes cell content, position and formatting in a tidy structure for further manipulation”.
Please note that the readxl project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
News
readxl 1.3.1
Pragmatic patch release to update some tests in advance of v2.1.0 of the tibble package. That release updates name repair: standard suffix becomes ...j, instead of ..j, partially motivated by user experience in readxl.
readxl 1.3.0
Dependency changes
readxl embeds libxls v1.5.0. This is the first official release of libxls in several years, although readxl has been tracking the development version in the interim. The libxls project is now officially hosted at https://github.com/libxls/libxls. In particular, libxls v1.5.0 addresses these two CVEs:
readxl 1.2.0
Column name repair
readxl exposes the .name_repair argument that is coming to version 2.0.0 of the tibble package. The readxl default is .name_repair = "unique", keeping with the readxl convention to ensure column names are neither missing nor duplicated.
- Column Names is a new article about this feature.
- readxl delegates name repair to tibble, therefore the installed tibble version determines how names are repaired.
- If tibble >= v2.0.0, the full power of
.name_repairis available, defaulting to.name_repair = "unique". Otherwise, the legacy functiontibble::repair_names(prefix = "X", sep = "__")is used, replicating the behaviour of readxl v1.1.0.- Consider a spreadsheet with three columns: one unnamed and two named
x. - Content of cells in Excel:
"",x,x - New style column names:
..1,x..2,x..3 - Legacy column names:
X__1,x,x__1
- Consider a spreadsheet with three columns: one unnamed and two named
- Once per session, readxl emits a message stating that it works best with tibble >= v2.0.0. It is anticipated that this will become a hard minimum version requirement in a future version of readxl.
Other changes
-
read_excel()and friends gain aprogressargument that controls a progress spinner (#243, #538). -
read_xls()andread_xlsx()pass thetrim_wsargument along (#514). -
readxl has a new article on reading Excel files with multiple header rows (#486, #492 @apreshill).
-
xlsx files that do not have a "styles" part can now be read (#505, #506 @jt6)
-
All paths are passed through
normalizePath()(#498, #499, new behaviour for xlsx but not xls) andenc2native()(#370).
Dependency changes
readxl is now tested back to R >= 3.1.
Embedded libxls has been updated, using the source in https://github.com/evanmiller/libxls. readxl's DESCRIPTION now records the SHA associated to the embedded libxls in a Note.
readxl 1.1.0
-
read_excel()andexcel_sheets()associate a larger set of file extensions with xlsx and are better able to guess the format of a file with a nonstandard or missing extension. This is about deciding whether to treat a file as xls or xlsx. (#342, #411, #457)excel_format()is the newly-exported format-guessing function.format_from_ext()is a low-level helper, also exported, that only consults file extension. In addition to the obvious interpretation of.xlsand.xlsx, the extensions.xlsm,.xltx, and.xltmare now associated with xlsx.format_from_signature()is a low-level helper, also exported, that consults the file's signature (a.k.a. magic number). It's handy for files that lack an extension.
-
Embedded libxls has been updated to address security vulnerabilitities identified in late 2017 (#441, #442).
- CVE-2017-12110, CVE-2017-2896, and CVE-2017-2897 were demonstrated to affect readxl v1.0.0. These have been addressed in libxls and the embedded version of libxls incorporates those fixes.
- Although CVE-2017-12111 and CVE-2017-2919 mention readxl, the notices clarify that these CVEs do not actually affect readxl. Both have been fixed in libxls for quite a while: CVE-2017-12111 since 2014 and CVE-2017-2919 since 2012.
-
xlsx structured as a "minimal conformant SpreadsheetML package" can be read. Most obvious feature of such sheets is the lack of an
xl/directory in the unzipped form. (xlsx, #435, #437) -
Reading xls sheet with exactly 65,536 rows no longer enters an infinite loop. (xls, #373, #416, #432 @vkapartzianis)
-
Doubles, including datetimes, coerced to character from xls now have much higher precision, comparable to the xlsx behaviour. (xls, #430, #431)
-
Integer-y numbers larger than 2^31 are coerced properly to string (xls, #346)
-
Shared strings are only compared to NA strings after lookup, never on the basis of their index. (xlsx, #401)
-
Better checks and messaging around nonexistent files. (#392)
-
Add
$(C_VISIBILITY)to compiler flags to hide internal symbols from the dll. (#385 @jeroen) -
Numeric data in a logical column now coerces properly to logical. (xlsx, #385 @nacnudus)
readxl 1.0.0
Sheet geometry
-
rangeis a new argument for reading a rectangular range, possibly open. (#314, #8) -
n_maxis a new argument that limits the number of data rows read. (#306, #281) -
Empty cells, rows, columns (xlsx #248 and #240, xls #271): Cells with no content are no longer loaded, even if they appear in the file. Affects cells that have no data but that carry explicit formatting, detectable in Excel as seemingly empty cells with a format other than "General". Such cells may still exist in the returned tibble, with value
NA, depending on the sheet geometry.- Eliminates a source of trailing rows (#203) and columns (#236, #162, #146) consisting entirely of
NA. - Eliminates a subtle source of disagreement between user-provided column names and guessed column types (#169, #81).
- Embedded empty columns are no longer automatically dropped, regardless of whether there is a column name. (#157, #261)
- Worksheets that are completely empty or that contain only column names no longer error, but return a tibble with zero rows. (#222, #144, #65)
- Improved handling of leading and embedded blank rows and explicit row skipping. (#224, #194, #178, #156, #101)
- Eliminates a source of trailing rows (#203) and columns (#236, #162, #146) consisting entirely of
-
User-supplied
col_namesare processed relative to user-suppliedcol_types, if given. Specifically,col_namesis considered valid if it has the same length ascol_types, before or after removing skipped columns. (#81, #261)
Column types and coercion
-
"list"is a new accepted value forcol_types. Loads data as a list of length-1 vectors, that are typed using the logic fromcol_types = NULL, but on a cell-by-cell basis (#262 @gergness). -
"logical"is a new accepted value forcol_types. Whencol_types = NULL, it is the guessed type for cells Excel advertises as Boolean. When a column has no data, it is now filled with logicalNA. (#277, #270) -
"guess"is a new accepted value forcol_types. Allows the user to specify some column types, while allowing others to be guessed (#286) -
A user-specified
col_typesof length one will be replicated to have length equal to the number of columns. (#127, #114, #261) -
"blank"has been deprecated in favor of the more descriptive and readr-compatible"skip", which is now the preferred way to request that a column be skipped. (#260, #193, #261) -
guess_maxis a new argument that lets user adjust the number of rows used to guess column types. (#223, #257 @tklebel and @jennybc) -
trim_wsis a new argument to remove leading and trailing whitespace. It defaults toTRUE. (#326, #211) -
nacan now hold multiple NA values, e.g.,read_excel("missing-values.xls", na = c("NA", "1")). (#13, #56, @jmarshallnz) -
Coercions and cell data:
- Numeric data that appears in a date column is coerced to a date. Throws a warning. (#277, #266)
- Dates that appear in a numeric column are converted to
NAinstead of their integer representation. Throws warning. (#277, #263) - "Number stored as text": when a text cell is found in a numeric column,
read_excel()attempts to coerce the string to numeric and falls back toNAif unsuccessful. Throws warning. (#277, #217, #106) - Cells in error are treated as blank and are imported as
NA(instead of the string"error"). (#277, #62) - BoolErr cells are now handled in xls. Suppresses message
"Unknown type: 517". (#274, #259) - Dates that arise from a formula are treated as dates (vs. numeric) in xls. (#277)
- Dates in .xlsx files saved with LibreOffice are now recognized as such. (#134, @zeehio)
Compatibility
Many 3rd party tools write xls and xlsx that comply with the spec, but that are quite different from files produced by Excel.
-
Namespace prefixes are now stripped from element names and attributes when parsing XML from xlsx. Workaround for the creative approach taken in some other s/w, coupled with rapidxml's lack of namespace support. (#295, #268, #202, #80)
-
Excel mixes 0- and 1-indexing in reported row and column dimensions for xls and libxls expects that. Other s/w may index from 0 for both, preventing libxls from reading the last column. Patched to restore access to those cells. (#273, #180, #152, #99)
-
More robust logic for sheet lookup in xlsx. Improves compatibility with xlsx written by a variety of tools and/or xlsx containing chartsheets. (#233, #104, #200, #168, #116, @jimhester and @jennybc)
-
The
numFmtIdattribute is no longer accessed when it does not exist (xlsx written by http://epplus.codeplex.com). (#191, #229) -
Location is inferred for cells that do not declare their location (xlsx written by JMP). (#240, #163, #102)
Other
-
read_xls()andread_xlsx()are now exposed, such that files without an.xlsor.xlsxextension can be read. (#85, @jirkalewandowski) -
The Lotus 1-2-3 leap year bug is now accounted for, i.e. date-times prior to March 1, 1900 import correctly. Date-times on the non-existent leap day February 29, 1900 import as NA and throw a warning. (#264, #148, #292)
-
The tibble package is now imported (#175, @krlmlr) and
tibble::repair_names()is used to prevent empty,NA, or duplicated column names. (#216, #208, #199 #182, #53, #247). -
Default column names for xlsx now start with X__1 instead of X__0. (#98, @zeehio, @krlmlr)
-
Fix compilation warnings/failures (FreeBSD 10.3 #221, gcc 4.9.3 #124) and/or problems reading xls (CentOS 6.6 #189). (#244, #245, #246 @jeroen)
-
Unwanted printed output (e.g.,
DEFINEDNAME: 21 00 00 ...) is suppressed when reading xls that contains a defined range. (#82, #188, @PedramNavid)
readxl 0.1.1
- Add support for correctly reading strings in .xlsx files containing escaped
unicode characters (e.g.
_x005F_). (#51, @jmarshallnz)