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Merged
chainsawriot merged 6 commits into from
Aug 6, 2025
Merged

Adding (.qs2) functionality - Fix #471 #472

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97f4d28
Adding (.qs2) functionality - Fix #471
jmears-at-acespower-dot-com Aug 6, 2025
110ae87
Added as contributor
jmears-at-acespower-dot-com Aug 6, 2025
ade8596
Removing per suggestion
jmears-at-acespower-dot-com Aug 6, 2025
97a8b37
Made error on DESCRIPTION file for ctb, fixed now
jmears-at-acespower-dot-com Aug 6, 2025
1e65077
Updating sysdata.rds and re-rendering README
jmears-at-acespower-dot-com Aug 6, 2025
88647ef
Final Touches: Re-render REAME, updating datatype descriptions to fix…
jmears-at-acespower-dot-com Aug 6, 2025
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7 changes: 4 additions & 3 deletions DESCRIPTION
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Expand Up @@ -27,8 +27,8 @@ Authors@R: c(person("Jason", "Becker", role = "aut", email = "[email protected]")
comment=c(ORCID="0000-0002-5759-428X")),
person("Alex", "Bokov", email = "[email protected]", role = "ctb",
comment=c(ORCID="0000-0002-0511-9815")),
person("Hugo", "Gruson", role = "ctb", comment = c(ORCID = "0000-0002-4094-1476"))
)
person("Hugo", "Gruson", role = "ctb", comment = c(ORCID = "0000-0002-4094-1476")),
person("Jacob", "Mears", role = "ctb"))
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
Expand Down Expand Up @@ -74,7 +74,8 @@ Suggests:
arrow (>= 0.17.0),
stringi,
withr,
nanoparquet
nanoparquet,
qs2 (>= 0.1.5)
License: GPL-2
VignetteBuilder: knitr
Encoding: UTF-8
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -20,6 +20,7 @@ S3method(.export,rio_parquet)
S3method(.export,rio_psv)
S3method(.export,rio_pzfx)
S3method(.export,rio_qs)
S3method(.export,rio_qs2)
S3method(.export,rio_r)
S3method(.export,rio_rda)
S3method(.export,rio_rdata)
Expand Down Expand Up @@ -58,6 +59,7 @@ S3method(.import,rio_parquet)
S3method(.import,rio_psv)
S3method(.import,rio_pzfx)
S3method(.import,rio_qs)
S3method(.import,rio_qs2)
S3method(.import,rio_r)
S3method(.import,rio_rda)
S3method(.import,rio_rdata)
Expand Down
5 changes: 3 additions & 2 deletions R/export.R
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Expand Up @@ -28,6 +28,7 @@
#' \item Serialized R objects (.qs), using [qs::qsave()], which is
#' significantly faster than .rds. This can be any R
#' object (not just a data frame).
#' \item Serialized R objects (.qs2), using [qs2::qs_save()]. This is the future-proof successor to using (.qs).
#' \item "XBASE" database files (.dbf), using [foreign::write.dbf()]
#' \item Weka Attribute-Relation File Format (.arff), using [foreign::write.arff()]
#' \item Fixed-width format data (.fwf), using [utils::write.table()] with `row.names = FALSE`, `quote = FALSE`, and `col.names = FALSE`
Expand Down Expand Up @@ -100,10 +101,10 @@ export <- function(x, file, format, ...) {
x <- as.data.frame(x)
}
if (!is.data.frame(x) && is.list(x) && length(x) == 1 && is.data.frame(x[[1]]) &&
!format %in% c("xlsx", "html", "rdata", "rds", "json", "qs", "fods", "ods")) {
!format %in% c("xlsx", "html", "rdata", "rds", "json", "qs", "qs2", "fods", "ods")) {
x <- x[[1]] ## fix 385
}
if (!is.data.frame(x) && !format %in% c("xlsx", "html", "rdata", "rds", "json", "qs", "fods", "ods")) {
if (!is.data.frame(x) && !format %in% c("xlsx", "html", "rdata", "rds", "json", "qs", "qs2", "fods", "ods")) {
stop("'x' is not a data.frame or matrix", call. = FALSE)
}
if (format == "gz") {
Expand Down
6 changes: 6 additions & 0 deletions R/export_methods.R
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Expand Up @@ -290,3 +290,9 @@ export_delim <- function(file, x, fwrite = lifecycle::deprecated(), sep = "\t",
.check_pkg_availability("qs")
.docall(qs::qsave, ..., args = list(x = x, file = file))
}

#' @export
.export.rio_qs2 <- function(file, x, ...) {
.check_pkg_availability("qs2")
.docall(qs2::qs_save, ..., args = list(object = x, file = file))
}
3 changes: 2 additions & 1 deletion R/import.R
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Expand Up @@ -33,6 +33,7 @@
#' \item Serialized R objects (.qs), using [qs::qread()], which is
#' significantly faster than .rds. This can be any R
#' object (not just a data frame).
#' \item Serialized R objects (.qs2), using [qs2::qs_read()]. This is the future-proof successor to using (.qs).
#' \item Epiinfo (.rec), using [foreign::read.epiinfo()]
#' \item Minitab (.mtp), using [foreign::read.mtp()]
#' \item Systat (.syd), using [foreign::read.systat()]
Expand Down Expand Up @@ -154,7 +155,7 @@ import <- function(file, format, setclass = getOption("rio.import.class", "data.
}

# if R serialized object, just return it without setting object class
if (inherits(file, c("rio_rdata", "rio_rds", "rio_json", "rio_qs")) && !inherits(x, "data.frame")) {
if (inherits(file, c("rio_rdata", "rio_rds", "rio_json", "rio_qs", "rio_qs2")) && !inherits(x, "data.frame")) {
return(x)
}
# otherwise, make sure it's a data frame (or requested class)
Expand Down
6 changes: 6 additions & 0 deletions R/import_methods.R
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Expand Up @@ -425,3 +425,9 @@ extract_html_row <- function(x, empty_value) {
.check_pkg_availability("qs")
.docall(qs::qread, ..., args = list(file = file))
}

#' @export
.import.rio_qs2 <- function(file, which = 1, ...) {
.check_pkg_availability("qs2")
.docall(qs2::qs_read, ..., args = list(file = file))
}
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140 changes: 70 additions & 70 deletions README.md
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Expand Up @@ -14,11 +14,11 @@ coverage](https://codecov.io/gh/gesistsa/rio/graph/badge.svg)](https://app.codec
The aim of **rio** is to make data file I/O in R as easy as possible by
implementing two main functions in Swiss-army knife style:

- `import()` provides a painless data import experience by
automatically choosing the appropriate import/read function based on
file extension (or a specified `format` argument)
- `export()` provides the same painless file recognition for data
export/write functionality
- `import()` provides a painless data import experience by automatically
choosing the appropriate import/read function based on file extension
(or a specified `format` argument)
- `export()` provides the same painless file recognition for data
export/write functionality

## Installation

Expand Down Expand Up @@ -135,54 +135,55 @@ install_formats()

The full list of supported formats is below:

| Name | Extensions / “format” | Import Package | Export Package | Type | Note |
| :---------------------------------- | :---------------------------------- | :------------- | :------------- | :------ | :----------------------------- |
| Archive files (handled by tar) | tar / tar.gz / tgz / tar.bz2 / tbz2 | utils | utils | Default | |
| Bzip2 | bz2 / bzip2 | base | base | Default | |
| Gzip | gz / gzip | base | base | Default | |
| Zip files | zip | utils | utils | Default | |
| Ambiguous file format | dat | data.table | | Default | Attempt as delimited text data |
| CSVY (CSV + YAML metadata header) | csvy | data.table | data.table | Default | |
| Comma-separated data | csv | data.table | data.table | Default | |
| Comma-separated data (European) | csv2 | data.table | data.table | Default | |
| Data Interchange Format | dif | utils | | Default | |
| Epiinfo | epiinfo / rec | foreign | | Default | |
| Excel | excel / xlsx | readxl | writexl | Default | |
| Excel (Legacy) | xls | readxl | | Default | |
| Excel (Read only) | xlsm / xltx / xltm | readxl | | Default | |
| Fixed-width format data | fwf | readr | utils | Default | |
| Fortran data | fortran | utils | | Default | No recognized extension |
| Google Sheets | googlesheets | data.table | | Default | As comma-separated data |
| Minitab | minitab / mtp | foreign | | Default | |
| Pipe-separated data | psv | data.table | data.table | Default | |
| R syntax | r | base | base | Default | |
| SAS | sas / sas7bdat | haven | haven | Default | Export is deprecated |
| SAS XPORT | xport / xpt | haven | haven | Default | |
| SPSS | sav / spss | haven | haven | Default | |
| SPSS (compressed) | zsav | haven | haven | Default | |
| SPSS Portable | por | haven | | Default | |
| Saved R objects | rda / rdata | base | base | Default | |
| Serialized R objects | rds | base | base | Default | |
| Stata | dta / stata | haven | haven | Default | |
| Systat | syd / systat | foreign | | Default | |
| Tab-separated data | / tsv / txt | data.table | data.table | Default | |
| Text Representations of R Objects | dump | base | base | Default | |
| Weka Attribute-Relation File Format | arff / weka | foreign | foreign | Default | |
| XBASE database files | dbf | foreign | foreign | Default | |
| Apache Arrow (Parquet) | parquet | nanoparquet | nanoparquet | Suggest | |
| Clipboard | clipboard | clipr | clipr | Suggest | default is tsv |
| EViews | eviews / wf1 | hexView | | Suggest | |
| Fast Storage | fst | fst | fst | Suggest | |
| Feather R/Python interchange format | feather | arrow | arrow | Suggest | |
| Graphpad Prism | pzfx | pzfx | pzfx | Suggest | |
| HTML Tables | htm / html | xml2 | xml2 | Suggest | |
| JSON | json | jsonlite | jsonlite | Suggest | |
| Matlab | mat / matlab | rmatio | rmatio | Suggest | |
| OpenDocument Spreadsheet | ods | readODS | readODS | Suggest | |
| OpenDocument Spreadsheet (Flat) | fods | readODS | readODS | Suggest | |
| Serialized R objects (Quick) | qs | qs | qs | Suggest | |
| Shallow XML documents | xml | xml2 | xml2 | Suggest | |
| YAML | yaml / yml | yaml | yaml | Suggest | |
| Name | Extensions / “format” | Import Package | Export Package | Type | Note |
|:---|:---|:---|:---|:---|:---|
| Archive files (handled by tar) | tar / tar.gz / tgz / tar.bz2 / tbz2 | utils | utils | Default | |
| Bzip2 | bz2 / bzip2 | base | base | Default | |
| Gzip | gz / gzip | base | base | Default | |
| Zip files | zip | utils | utils | Default | |
| Ambiguous file format | dat | data.table | | Default | Attempt as delimited text data |
| CSVY (CSV + YAML metadata header) | csvy | data.table | data.table | Default | |
| Comma-separated data | csv | data.table | data.table | Default | |
| Comma-separated data (European) | csv2 | data.table | data.table | Default | |
| Data Interchange Format | dif | utils | | Default | |
| Epiinfo | epiinfo / rec | foreign | | Default | |
| Excel | excel / xlsx | readxl | writexl | Default | |
| Excel (Legacy) | xls | readxl | | Default | |
| Excel (Read only) | xlsm / xltx / xltm | readxl | | Default | |
| Fixed-width format data | fwf | readr | utils | Default | |
| Fortran data | fortran | utils | | Default | No recognized extension |
| Google Sheets | googlesheets | data.table | | Default | As comma-separated data |
| Minitab | minitab / mtp | foreign | | Default | |
| Pipe-separated data | psv | data.table | data.table | Default | |
| R syntax | r | base | base | Default | |
| SAS | sas / sas7bdat | haven | haven | Default | Export is deprecated |
| SAS XPORT | xport / xpt | haven | haven | Default | |
| SPSS | sav / spss | haven | haven | Default | |
| SPSS (compressed) | zsav | haven | haven | Default | |
| SPSS Portable | por | haven | | Default | |
| Saved R objects | rda / rdata | base | base | Default | |
| Serialized R objects | rds | base | base | Default | |
| Stata | dta / stata | haven | haven | Default | |
| Systat | syd / systat | foreign | | Default | |
| Tab-separated data | / tsv / txt | data.table | data.table | Default | |
| Text Representations of R Objects | dump | base | base | Default | |
| Weka Attribute-Relation File Format | arff / weka | foreign | foreign | Default | |
| XBASE database files | dbf | foreign | foreign | Default | |
| Apache Arrow (Parquet) | parquet | nanoparquet | nanoparquet | Suggest | |
| Clipboard | clipboard | clipr | clipr | Suggest | default is tsv |
| EViews | eviews / wf1 | hexView | | Suggest | |
| Fast Storage | fst | fst | fst | Suggest | |
| Feather R/Python interchange format | feather | arrow | arrow | Suggest | |
| Graphpad Prism | pzfx | pzfx | pzfx | Suggest | |
| HTML Tables | htm / html | xml2 | xml2 | Suggest | |
| JSON | json | jsonlite | jsonlite | Suggest | |
| Matlab | mat / matlab | rmatio | rmatio | Suggest | |
| OpenDocument Spreadsheet | ods | readODS | readODS | Suggest | |
| OpenDocument Spreadsheet (Flat) | fods | readODS | readODS | Suggest | |
| Serialized R objects (qs) | qs | qs | qs | Suggest | |
| Serialized R objects (qs2) | qs2 | qs2 | qs2 | Suggest | Replaces {qs} package which will be deprecated. |
| Shallow XML documents | xml | xml2 | xml2 | Suggest | |
| YAML | yaml / yml | yaml | yaml | Suggest | |

Additionally, any format that is not supported by **rio** but that has a
known R implementation will produce an informative error message
Expand Down Expand Up @@ -253,23 +254,22 @@ c("mtcars.tsv", "iris.tsv") %in% dir()

### GUIs

- [**datamods**](https://cran.r-project.org/package=datamods) provides
Shiny modules for importing data via `rio`.
- [**rioweb**](https://github.com/lbraglia/rioweb) that provides
access to the file conversion features of `rio`.
- [**GREA**](https://github.com/Stan125/GREA/) is an RStudio add-in
that provides an interactive interface for reading in data using
`rio`.
- [**datamods**](https://cran.r-project.org/package=datamods) provides
Shiny modules for importing data via `rio`.
- [**rioweb**](https://github.com/lbraglia/rioweb) that provides access
to the file conversion features of `rio`.
- [**GREA**](https://github.com/Stan125/GREA/) is an RStudio add-in that
provides an interactive interface for reading in data using `rio`.

### Similar packages

- [**reader**](https://cran.r-project.org/package=reader) handles
certain text formats and R binary files
- [**io**](https://cran.r-project.org/package=io) offers a set of
custom formats
- [**ImportExport**](https://cran.r-project.org/package=ImportExport)
focuses on select binary formats (Excel, SPSS, and Access files) and
provides a Shiny interface.
- [**SchemaOnRead**](https://cran.r-project.org/package=SchemaOnRead)
iterates through a large number of possible import methods until one
works successfully
- [**reader**](https://cran.r-project.org/package=reader) handles
certain text formats and R binary files
- [**io**](https://cran.r-project.org/package=io) offers a set of custom
formats
- [**ImportExport**](https://cran.r-project.org/package=ImportExport)
focuses on select binary formats (Excel, SPSS, and Access files) and
provides a Shiny interface.
- [**SchemaOnRead**](https://cran.r-project.org/package=SchemaOnRead)
iterates through a large number of possible import methods until one
works successfully
11 changes: 10 additions & 1 deletion data-raw/single.json
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Expand Up @@ -624,11 +624,20 @@
"input": "qs",
"format": "qs",
"type": "suggest",
"format_name": "Serialized R objects (Quick)",
"format_name": "Serialized R objects (qs)",
"import_function": "qs::qread",
"export_function": "qs::qsave",
"note": ""
},
{
"input": "qs2",
"format": "qs2",
"type": "suggest",
"format_name": "Serialized R objects (qs2)",
"import_function": "qs2::qs_save",
"export_function": "qs2::qs_read",
"note": "Replaces {qs} package which will be deprecated."
},
{
"input": "xml",
"format": "xml",
Expand Down
1 change: 1 addition & 0 deletions man/export.Rd
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