The aim of the dataset package is to make tidy datasets easier to release, exchange and reuse. It organizes and formats data frame R objects into well-referenced, well-described, interoperable datasets into release and reuse ready form.
- Increase FAIR use of your datasets: Offer a way to better
utilise the
utils:bibentrybibliographic entry objects and working with the ROpenSci package RefManageR extending their fields of the Dublin Core and DataCite standards, and making them detachable from the data, i.e., including the bibliographic entries into the attributes of a data frame-like object. See for more information the Bibentry for FAIR datasets vignette. 2.Interoperability outside R: Extending thehaven_labelledclass of thetidyversefor consistently labelled categorical variables with linked (standard) definitions and units of measures in our defined class; this enables to share exact definitions, units of measures across computers and systems, and increasing the interoperability of the data set from an R data.frame to any standardised statistical or library system. - Tidy data tidier, richer: Offering a new data frame format,
dataset_dfthat extends tibbles with semantically rich metadata, ready to be shared on open data exchange platforms and in data repositories. This s3 class is aimed at developers and we are working on several packages that provide interoperability with SDMX statistical data exchange platforms, Wikidata, or the EU Open Data portal. Read more in the Create Datasets that are Easy to Share Exchange and Extend vignette. - R+RDF=global interoperability: The From R to RDF vignette shows how to leverage the capabilities of the dataset package with rdflib, an R-user-friendly wrapper on ROpenSci to work with the redland Python library for performing common tasks on rdf data, such as parsing and converting between formats including rdfxml, turtle, nquads, ntriples, and trig, creating rdf graphs, and performing SPARQL queries.
You can install the latest CRAN release with
install.packages("dataset"), and the latest development version of
dataset with remotes::install_github():
install.packages("dataset")
remotes::install_github("dataobservatory-eu/dataset", build = FALSE)The current version of the dataset package is in an early,
experimental stage. You can follow the discussion of this package on
rOpenSci.
library(dataset)
iris_ds <- dataset_df(
x = iris,
dataset_bibentry = dublincore(
title = "Iris Dataset",
creator = person("Edgar", "Anderson", role = "aut"),
publisher = "American Iris Society",
datasource = "https://doi.org/10.1111/j.1469-1809.1936.tb02137.x",
dataset_date = 1935,
language = "en",
description = "This famous (Fisher's or Anderson's) iris data set."
)
)It is mandatory to add a title, author to a dataset, and if the
date is not specified, the current date will be added.
As the dataset_df at this point is just created, if it is not
published yet, the identifer receives the default :tba value, a
version of 0.1.0 and the :unas (unassigned) publisher field.
The dataset_df behaves as expected from a data.frame-like object. See
more information about the enhanced semantic capabilities of these data
frames in the vignette article Create Datasets that are Easy to Share
Exchange and
Extend
summary(iris_ds)
#> [1] E. Anderson. _Iris Dataset_. En. DCMITYPE:Dataset. 1935.
#> rowid
#> Length:150
#> Class :character
#> Mode :character
#>
#>
#>
#> x.Sepal.Length x.Sepal.Width x.Petal.Length x.Petal.Width x.Species
#> Min. :4.300000 Min. :2.000000 Min. :1.000 Min. :0.1000000 setosa :50
#> 1st Qu.:5.100000 1st Qu.:2.800000 1st Qu.:1.600 1st Qu.:0.3000000 versicolor:50
#> Median :5.800000 Median :3.000000 Median :4.350 Median :1.3000000 virginica :50
#> Mean :5.843333 Mean :3.057333 Mean :3.758 Mean :1.1993333 NA
#> 3rd Qu.:6.400000 3rd Qu.:3.300000 3rd Qu.:5.100 3rd Qu.:1.8000000 NA
#> Max. :7.900000 Max. :4.400000 Max. :6.900 Max. :2.5000000 NAThe dataset_df A brief description of the extended metadata attributes:
print(get_bibentry(iris_ds), "Bibtex")
#> [1] E. Anderson. _Iris Dataset_. En. DCMITYPE:Dataset. 1935.paste0("Publisher:", publisher(iris_ds))
#> [1] "Publisher:American Iris Society"
paste0("Rights:", rights(iris_ds))
#> [1] "Rights::tba"The descriptive metadata are added to a utils::bibentry object which
has many printing options (see ?bibentry). (The utils package is
installed by default with every R system, so working with utils is not
an extra dependency.)
It is important to see that we do not only increase the semantics of the
dataset as a whole, but also the semantics of each variable. R users
often have a problem with the reusability of their data frames because,
by default, a variable is only described by a programmatically usable
name label; for example, in the famous iris dataset, the length of the
sepal for each observation (row) is in the iris$Sepal.Length column.
If we would like to add rows to this dataset, it is essential to know if
the numbers in the iris$Sepal.Length are measured in millimetres,
centimetres or inches.
When working with datasets that receive their components from different linked open data sources, it is particularly important to have a more precise semantic definition and description of each variable.
gdp_1 = defined(
c(3897, 7365),
label = "Gross Domestic Product",
unit = "million dollars",
definition = "http://data.europa.eu/83i/aa/GDP")
# Summarise this semantically better defined vector:
summary(gdp_1)
#> Gross Domestic Product (million dollars)
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 3897 4764 5631 5631 6498 7365
# See its attributes under the hood:
attributes(gdp_1)
#> $label
#> [1] "Gross Domestic Product"
#>
#> $class
#> [1] "haven_labelled_defined" "haven_labelled" "vctrs_vctr"
#> [4] "double"
#>
#> $unit
#> [1] "million dollars"
#>
#> $definition
#> [1] "http://data.europa.eu/83i/aa/GDP"The dataset package contains a semantically enriched version of the
iris dataset (which is installed with every R system.)
data("iris_dataset")
# Print the dataset_df object:
print(iris_dataset)
#> [1] E. Anderson. _Iris Dataset_. En. DCMITYPE:Dataset. 1935.
#> rowid Sepal.Length Petal.Length Sepal.Width Petal.Width Species
#> <hvn_lbl_> <hvn_lbl_> <hvn_lbl_> <hvn_lbl_> <hvn_lbl_> <hvn_lbl_>
#> 1 #1 5.1 1.4 3.5 0.2 1 [setosa]
#> 2 #2 4.9 1.4 3 0.2 1 [setosa]
#> 3 #3 4.7 1.3 3.2 0.2 1 [setosa]
#> 4 #4 4.6 1.5 3.1 0.2 1 [setosa]
#> 5 #5 5 1.4 3.6 0.2 1 [setosa]
#> 6 #6 5.4 1.7 3.9 0.4 1 [setosa]
#> 7 #7 4.6 1.4 3.4 0.3 1 [setosa]
#> 8 #8 5 1.5 3.4 0.2 1 [setosa]
#> 9 #9 4.4 1.4 2.9 0.2 1 [setosa]
#> 10 #10 4.9 1.5 3.1 0.1 1 [setosa]
#> # ℹ 140 more rows
# Summarise the Sepal.Length variable:
summary(iris_dataset$Sepal.Length)
#> Length of the sepal in cm (centimeter)
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 4.300 5.100 5.800 5.843 6.400 7.900
# Check the attributes of this variable:
attributes(iris_dataset$Sepal.Length)
#> $label
#> [1] "Length of the sepal in cm"
#>
#> $class
#> [1] "haven_labelled_defined" "haven_labelled" "vctrs_vctr"
#> [4] "double"
#>
#> $unit
#> [1] "centimeter"
#>
#> $definition
#> [1] "https://www.wikidata.org/wiki/Property:P2043"The constructor of the dataset_df objects also records the most
important processes that created or modified the dataset. This
experimental feature has not been fully developed in the current
dataset version. The aim is to provide a standard way of describing
the processes that help to understand what happened with your data using
the W3C PROV-O provenance ontology and
the RDF 1.1 N-Triples W3C standard
for describing these processes in a flat file.
provenance(iris_dataset)
#> [1] "<http://example.com/dataset_prov.nt> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Bundle> ."
#> [2] "<http://example.com/dataset#> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> ."
#> [3] "<http://example.com/dataset#> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/linked-data/cube#DataSet> ."
#> [4] "<http://viaf.org/viaf/6440526> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> ."
#> [5] "<https://doi.org/10.32614/CRAN.package.dataset> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> ."
#> [6] "<http://example.com/creation> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> ."
#> [7] "<http://example.com/creation> <http://www.w3.org/ns/prov#generatedAtTime> \"2024-12-24T23:43:45Z\"^^<xs:dateTime> ."The From R to RDF vignette shows how to leverage the capabilities of the dataset package with rdflib to share the history and other metadata of your dataset globally, or import data updates from standardised statistical data exchanges.
Please note that the dataset package is released with a Contributor
Code of
Conduct.
By contributing to this project, you agree to abide by its terms.
Furthermore, rOpenSci Community Contributing
Guide - A guide to help people
find ways to contribute to rOpenSci is also applicable, because
dataset is under software review for potential inclusion in
rOpenSci.