rio (version 1.3.0)

import: Import

Description

Read in a data.frame from a file. Exceptions to this rule are Rdata, RDS, and JSON input file formats, which return the originally saved object without changing its class.

Usage

import(
  file,
  format,
  setclass = getOption("rio.import.class", "data.frame"),
  which,
  ...
)

Value

A data frame. If setclass is used, this data frame may have additional class attribute values, such as “tibble” or “data.table”.

Arguments

file

A character string naming a file, URL, or single-file (can be Gzip or Bzip2 compressed), .zip or .tar archive.

format

An optional character string code of file format, which can be used to override the format inferred from file. Shortcuts include: “,” (for comma-separated values), “;” (for semicolon-separated values), and “|” (for pipe-separated values).

setclass

An optional character vector specifying one or more classes to set on the import. By default, the return object is always a “data.frame”. Allowed values include “tbl_df”, “tbl”, or “tibble” (if using tibble), “arrow”, “arrow_table” (if using arrow table; the suggested package arrow must be installed) or “data.table” (if using data.table). Other values are ignored, such that a data.frame is returned. The parameter takes precedents over parameters in ... which set a different class.

which

This argument is used to control import from multi-object files; as a rule import only ever returns a single data frame (use import_list() to import multiple data frames from a multi-object file). If file is an archive format (zip and tar), which can be either a character string specifying a filename or an integer specifying which file (in locale sort order) to extract from the compressed directory. But please see the section which below. For Excel spreadsheets, this can be used to specify a sheet name or number. For .Rdata files, this can be an object name. For HTML files, it identifies which table to extract (from document order). Ignored otherwise. A character string value will be used as a regular expression, such that the extracted file is the first match of the regular expression against the file names in the archive.

...

Additional arguments passed to the underlying import functions. For example, this can control column classes for delimited file types, or control the use of haven for Stata and SPSS or readxl for Excel (.xlsx) format. See details below.

Trust

For serialization formats (.R, .RDS, and .RData), please note that you should only load these files from trusted sources. It is because these formats are not necessarily for storing rectangular data and can also be used to store many things, e.g. code. Importing these files could lead to arbitary code execution. Please read the security principles by the R Project (Plummer, 2024). When importing these files via rio, you should affirm that you trust these files, i.e. trust = TRUE. See example below. If this affirmation is missing, the current version assumes trust to be true for backward compatibility and a deprecation notice will be printed. In the next major release (2.0.0), you must explicitly affirm your trust when importing these files.

Which

For compressed archives (zip and tar, where a compressed file can contain multiple files), it is possible to come to a situation where the parameter which is used twice to indicate two different concepts. For example, it is unclear for .xlsx.zipwhether which refers to the selection of an exact file in the archive or the selection of an exact sheet in the decompressed Excel file. In these cases, rio assumes that which is only used for the selection of file. After the selection of file with which, rio will return the first item, e.g. the first sheet.

Please note, however, .gz and .bz2 (e.g. .xlsx.gz) are compressed, but not archive format. In those cases, which is used the same way as the non-compressed format, e.g. selection of sheet for Excel.

Details

This function imports a data frame or matrix from a data file with the file format based on the file extension (or the manually specified format, if format is specified).

import supports the following file formats:

• Comma-separated data (.csv), using data.table::fread()

• Pipe-separated data (.psv), using data.table::fread()

• Tab-separated data (.tsv), using data.table::fread()

• SAS (.sas7bdat), using haven::read_sas()

• SAS XPORT (.xpt), using haven::read_xpt()

• SPSS (.sav), using haven::read_sav()

• SPSS compressed (.zsav), using haven::read_sav().

• Stata (.dta), using haven::read_dta()

• SPSS Portable Files (.por), using haven::read_por().

• Excel (.xls and .xlsx), using readxl::read_xlsx() or readxl::read_xls(). Use which to specify a sheet number.

• R syntax object (.R), using base::dget(), see trust below.

• Saved R objects (.RData,.rda), using base::load() for single-object .Rdata files. Use which to specify an object name for multi-object .Rdata files. This can be any R object (not just a data frame), see trust below.

• Serialized R objects (.rds), using base::readRDS(). This can be any R object (not just a data frame), see trust below.

• Serialized R objects (.qs2), using qs2::qs_read().

• Epiinfo (.rec), using foreign::read.epiinfo()

• Minitab (.mtp), using foreign::read.mtp()

• Systat (.syd), using foreign::read.systat()

• "XBASE" database files (.dbf), using foreign::read.dbf()

• Weka Attribute-Relation File Format (.arff), using foreign::read.arff()

• Data Interchange Format (.dif), using utils::read.DIF()

• Fortran data (no recognized extension), using utils::read.fortran()

• Fixed-width format data (.fwf), using a faster version of utils::read.fwf() that requires a widths argument and by default in rio has stringsAsFactors = FALSE

• CSVY (CSV with a YAML metadata header) using data.table::fread().

• Apache Arrow Parquet (.parquet), using nanoparquet::read_parquet()

• Feather R/Python interchange format (.feather), using arrow::read_feather()

• Fast storage (.fst), using fst::read.fst()

• JSON (.json), using jsonlite::fromJSON()

• Matlab (.mat), using rmatio::read.mat()

• EViews (.wf1), using hexView::readEViews()

• OpenDocument Spreadsheet (.ods, .fods), using readODS::read_ods() or readODS::read_fods(). Use which to specify a sheet number.

• Single-table HTML documents (.html), using xml2::read_html(). There is no standard HTML table and we have only tested this with HTML tables exported with this package. HTML tables will only be read correctly if the HTML file can be converted to a list via xml2::as_list(). This import feature is not robust, especially for HTML tables in the wild. Please use a proper web scraping framework, e.g. rvest.

• Shallow XML documents (.xml), using xml2::read_xml(). The data structure will only be read correctly if the XML file can be converted to a list via xml2::as_list().

• YAML (.yml), using yaml::yaml.load()

• Clipboard import, using utils::read.table() with row.names = FALSE

• Google Sheets, as Comma-separated data (.csv)

• GraphPad Prism (.pzfx) using pzfx::read_pzfx()

import attempts to standardize the return value from the various import functions to the extent possible, thus providing a uniform data structure regardless of what import package or function is used. It achieves this by storing any optional variable-related attributes at the variable level (i.e., an attribute for mtcars$mpg is stored in attributes(mtcars$mpg) rather than attributes(mtcars)). If you would prefer these attributes to be stored at the data.frame-level (i.e., in attributes(mtcars)), see gather_attrs().

After importing metadata-rich file formats (e.g., from Stata or SPSS), it may be helpful to recode labelled variables to character or factor using characterize() or factorize() respectively.

References

Plummer, M (2024). Statement on CVE-2024-27322. https://blog.r-project.org/2024/05/10/statement-on-cve-2024-27322/

See Also

import_list(), characterize(), gather_attrs(), export(), convert()

Examples

## For demo, a temp. file path is created with the file extension .csv
csv_file <- tempfile(fileext = ".csv")
## .xlsx
xlsx_file <- tempfile(fileext = ".xlsx")
## create CSV to import
export(iris, csv_file)
## specify `format` to override default format: see export()
export(iris, xlsx_file, format = "csv")

## basic
import(csv_file)

## You can certainly import your data with the file name, which is not a variable:
## import("starwars.csv"); import("mtcars.xlsx")

## Override the default format
## import(xlsx_file) # Error, it is actually not an Excel file
import(xlsx_file, format = "csv")

## import CSV as a `data.table`
import(csv_file, setclass = "data.table")

## import CSV as a tibble (or "tbl_df")
import(csv_file, setclass = "tbl_df")

## pass arguments to underlying import function
## data.table::fread is the underlying import function and `nrows` is its argument
import(csv_file, nrows = 20)

## data.table::fread has an argument `data.table` to set the class explicitely to data.table. The
## argument setclass, however, takes precedents over such undocumented features.
class(import(csv_file, setclass = "tibble", data.table = TRUE))

## the default import class can be set with options(rio.import.class = "data.table")
## options(rio.import.class = "tibble"), or options(rio.import.class = "arrow")

## Security
rds_file <- tempfile(fileext = ".rds")
export(iris, rds_file)

## You should only import serialized formats from trusted sources
## In this case, you can trust it because it's generated by you.
import(rds_file, trust = TRUE)