7  Data

Published

2024-10-15

Data files in your app-package:

  • data/: data files that will be used in your application (i.e., become part of your app-package namespace and accessed via pkg::data) should in stored in data/

    • Add data to the data/ directory using usethis::use_data()

    • Include the LazyData: true field in the DESCRIPTION

  • data-raw/: scripts used to prepare data files can be created with usethis::use_data_raw()

    • Store intermediate data files in data-raw/

    • Store output files in data/ (or inst/extdata/)

  • inst/extdata/: ‘External’ data files (i.e., non-R formatted data files) can be stored in inst/extdata and accessed using system.file().

Workflow: start with the script that creates/downloads/wrangles your data using usethis::use_data_raw(), keep any intermediate or non-R formatted files in inst/extdata/, then export the final object to data/ with usethis::use_data()

In the previous chapters we covered how to document functions and manage dependencies. In this chapter, we’re going to cover how make sure our data file (movie.RData) becomes part of our app-package and can be loaded into our application. We’ll also discuss other locations and purposes for app-package data files.

I’ve created the shinypak R package In an effort to make each section accessible and easy to follow:

Install shinypak using pak (or remotes):

# install.packages('pak')
pak::pak('mjfrigaard/shinypak')

Review the chapters in each section:

library(shinypak)
list_apps(regex = '^07')
## # A tibble: 1 × 2
##   branch  last_updated       
##   <chr>   <dttm>             
## 1 07_data 2024-09-03 22:14:49

Launch an app:

launch(app = "07_data")

Data in R packages are typically stored in one of three folders: data/, data-raw/, and inst/extdata/.1 The folder you use will depend on the format, accessibility, and intended purpose of the data file.2

7.1 data/

The primary location for data is the data/ folder. Objects in data/ folder are available in your package namespace when it’s installed and loaded, and can be accessed with the :: syntax. See the example below of the storms data from dplyr:

library(dplyr)
head(dplyr::storms)
## # A tibble: 6 × 13
##   name   year month   day  hour   lat  long status
##   <chr> <dbl> <dbl> <int> <dbl> <dbl> <dbl> <fct> 
## 1 Amy    1975     6    27     0  27.5 -79   tropi…
## 2 Amy    1975     6    27     6  28.5 -79   tropi…
## 3 Amy    1975     6    27    12  29.5 -79   tropi…
## 4 Amy    1975     6    27    18  30.5 -79   tropi…
## 5 Amy    1975     6    28     0  31.5 -78.8 tropi…
## 6 Amy    1975     6    28     6  32.4 -78.7 tropi…
## # ℹ 5 more variables: category <dbl>, wind <int>,
## #   pressure <int>,
## #   tropicalstorm_force_diameter <int>,
## #   hurricane_force_diameter <int>

7.1.1 LazyData

Data files become part of a package when they’re added to the data/ folder and LazyData: true is added to the DESCRIPTION file.

  • LazyData: true: this means the data are only loaded into memory if they are explicitly accessed by the user or a function in the package. Until then, only the dataset names is loaded. This user-friendly practice is the default for most R packages.

  • LazyData: false (or omitted): accessing a data file from the package requires explicitly loading it using the data() function.

Files in data/ should be in the .rda or .RData format. Below are the steps for adding movies to sap:

  1. Move the movies.RData file into a newly created the data/ folder:
sap/
    └──data/
        └── movies.RData
  1. Include LazyData: true in the DESCRIPTION file (I’ve added it above Imports:):
Package: sap
Version: 0.0.0.9000
Type: Package
Title: Shiny App-Packages
Description: An R package with a collection of Shiny applications.
Author: John Smith [aut, cre]
Maintainer: John Smith <John.Smith@email.io>
License: GPL-3
RoxygenNote: 7.2.3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
LazyData: true
Imports:
  shiny,
  ggplot2,
  rlang,
  stringr,
  tools
  1. Load, document, and install.


Ctrl/Cmd + Shift + L

ℹ Loading sap


Ctrl/Cmd + Shift + D

==> devtools::document(roclets = c('rd', 'collate', 'namespace'))

ℹ Updating sap documentation
ℹ Loading sap
Documentation completed


Ctrl/Cmd + Shift + B

In the Build pane, you’ll notice a few new ** data lines of output after adding data:

** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading

The diagram below captures what happens to the package files and namespace after adding LazyData: true to the DESCRIPTION file and exporting movies from sap.

%%{init: {'theme': 'base', 'themeVariables': { 'fontFamily': 'Inconsolata'}}}%%

flowchart TD
  AddLazyData("Add <code>LazyData: true</code> to <code>DESCRIPTION</code>")
  LoadAll("Run <code>devtools::load_all()</code>")
  Document("Run <code>devtools::document()</code>")
  Install("Run <code>devtools::install()</code>")
  UpdateNamespace("Update <code>NAMESPACE</code> with <code>LazyData</code>")
  BuildBinary("Build package binary")
  LoadData("Load data into namespace")
  UpdateDocs("Update documentation files")
  InstallPackage("Install package")

  AddLazyData --> LoadAll
  AddLazyData --> Document
  AddLazyData --> Install
  LoadAll --> UpdateNamespace
  UpdateNamespace --> LoadData
  Document --> UpdateDocs
  Install --> BuildBinary
  BuildBinary --> LoadData
  LoadData --> InstallPackage
  UpdateDocs --> InstallPackage
  
  style AddLazyData fill:#8dd38d,stroke:none,rx:10,ry:10;
  style LoadAll fill:#89D6FB,stroke:none,rx:10,ry:10;
  style Document fill:#89D6FB,stroke:none,rx:10,ry:10;
  style Install fill:#89D6FB,stroke:none,rx:10,ry:10;
  style UpdateNamespace fill:#FFDD67,stroke:none,rx:10,ry:10;
  style BuildBinary fill:#FFDD67,stroke:none,rx:10,ry:10;
  style LoadData fill:#FFDD67,stroke:none,rx:10,ry:10;
  style UpdateDocs fill:#FFDD67,stroke:none,rx:10,ry:10;
  style InstallPackage fill:#FFDD67,stroke:none,rx:10,ry:10;

Adding LazyData: true to the DESCRIPTION file

We can check to see if movies has been included in sap using the package::data syntax:

Figure 7.1: movies is now part of sap

7.1.2 usethis::use_data()

If you’d prefer to store data using the .rda format, the usethis package has the use_data() function that will automatically store an object in data/ in the .rda format.

To use usethis::use_data(), we can load the movies data into the global environment with load("movies.RData"), then run usethis::use_data(movies):

usethis::use_data(movies)
✔ Setting active project to '/path/to/sap'
✔ Adding 'R' to Depends field in DESCRIPTION
✔ Creating 'data/'
✔ Saving 'movies' to 'data/movies.rda'
• Document your data (see 'https://r-pkgs.org/data.html')

The Depends: field is added to the DESCRIPTION file with an R version (this ensures the data files will be loaded)

Depends: 
    R (>= 2.10)

use_data() will also add LazyData: true to the DESCRIPTION

7.2 Documenting data/

Documenting data can be tedious, but it’s worth the effort if you’ll be sharing your package with collaborators. There are multiple ways to store dataset documentation. A common approach is to create a data.R file in the R/ folder.3

fs::file_create("R/data.R")

In data.R, we provide a @title, @description, and @details for the data (with or without the tags), followed by @format:

#' @title IMDB movies data 
#'
#' @description
#' Movie review data. Note: these data come from the [Building Web Applications with Shiny course](https://rstudio-education.github.io/shiny-course/). 
#' 
#' @details
#' Read more about acquiring these data in the ['Web Scraping and programming' section of Data science in a box](https://datasciencebox.org/02-exploring-data#web-scraping-and-programming)   
#'
#' @format

7.2.1 @format

The text following @format is a one-sentence description of the data (with it’s dimensions).

#' @title IMDB movies data 
#'
#' @description
#' Movie review data. Note: these data come from the [Building Web Applications with Shiny course](https://rstudio-education.github.io/shiny-course/). 
#' 
#' @details
#' Read more about acquiring these data in the ['Web Scraping and programming' section of Data science in a box](https://datasciencebox.org/02-exploring-data#web-scraping-and-programming) 
#' 
#' @format A data frame with [] rows and [] variables:

7.2.2 \describe & \item

Each variable (column) in the data is documented with a combination of \describe and \item (pay close attention to the curly brackets):

#' \describe{
#'  \item{variable}{description}
#' }

After closing the curly brackets in \describe, place the name of the data in quotes ("movies") on the following line.

Below is the documentation for the first five columns in the movies dataset:

#' @title IMDB movies data 
#'
#' @description
#' Movie review data. Note: these data come from the [Building Web Applications with shiny course](https://rstudio-education.github.io/shiny-course/). 
#' 
#' @details
#' Read more about acquiring these data in the ['Web Scraping and programming' section of Data science in a box](https://datasciencebox.org/02-exploring-data#web-scraping-and-programming) 
#'
#' @format A data frame with 651 rows and 34 variables:
#' \describe{
#'  \item{title}{movie title}
#'  \item{title_type}{type, fct (Documentary, Feature Film, TV Movie)}
#'  \item{genre}{movie genre, fct (Action & Adventure, Animation, etc.}
#'  \item{runtime}{movie length in minutes, num, avg = 106, sd = 19.4}
#'  \item{mpaa_rating}{movie rating, fct (G, NC-17, PG, PG-13, R, Unrated)}
#' }
#'
"movies"

If we load and document sap, we can see a preview of the help file:


Ctrl/Cmd + Shift + L

ℹ Loading sap


Ctrl/Cmd + Shift + D

==> devtools::document(roclets = c('rd', 'collate', 'namespace'))

ℹ Updating sap documentation
ℹ Loading sap
Writing movies.Rd
Documentation completed

We can view the documentation using the following in the Console:

?movies
(a) The movies help file
Figure 7.2: Documentation for the movies dataset

I’ve provided documentation for the full movies dataset below.

show/hide full movies data documenation 
#' @title IMDB movies data 
#'
#' @description
#' Movie review data. Note: these data come from the [Building Web Applications with Shiny course](https://rstudio-education.github.io/shiny-course/). 
#' 
#' @details
#' Read more about acquiring these data in the ['Web Scraping and programming' section of Data science in a box](https://datasciencebox.org/02-exploring-data#web-scraping-and-programming) 
#'
#' @format A data frame with 651 rows and 34 variables:
#' \describe{
#'  \item{title}{movie title}
#'  \item{title_type}{type, fct (Documentary, Feature Film, TV Movie)}
#'  \item{genre}{movie genre, fct (Action & Adventure, Animation, etc.}
#'  \item{runtime}{movie length in minutes, num, avg = 106, sd = 19.4}
#'  \item{mpaa_rating}{movie rating, fct (G, NC-17, PG, PG-13, R, Unrated)}
#'  \item{studio}{name of studio, chr}
#'  \item{thtr_rel_date}{Theatre release date, POSIXct, min = 1970-05-19 21:00:00, max = 2014-12-24 21:00:00}
#'  \item{thtr_rel_year}{Theatre release year, num, min = 1970, max = 2014}
#'  \item{thtr_rel_month}{Theatre release month, num, min = 1, max =12}
#'  \item{thtr_rel_day}{Theatre release day, num, min = 1, max =31}
#'  \item{dvd_rel_date}{DVD release date, POSIXct, min = 1991-03-27 21:00:00, max = 2015-03-02 21:00:00}
#'  \item{dvd_rel_year}{DVD release year, num, min = 1991, max = 2015}
#'  \item{dvd_rel_month}{DVD release month, num, min = 1, max = 12}
#'  \item{dvd_rel_day}{DVD release day, num, min = 1, max = 31}
#'  \item{imdb_rating}{Internet movie database rating, avg = 6.49, sd = 1.08}
#'  \item{imdb_num_votes}{Internet movie database votes, avg = 57533, sd = 112124}
#'  \item{critics_rating}{Rotten tomatoes rating, fct (Certified Fresh, Fresh, Rotten)}
#'  \item{critics_score}{Rotten tomatoes score, avg = 57.7, sd = 28.4}
#'  \item{audience_rating}{Audience rating, fct (Spilled, Upright)}
#'  \item{audience_score}{Audience score, avg = 62.4, sd = 20.2}
#'  \item{best_pic_nom}{Best picture nomination, fct (no, yes)}
#'  \item{best_pic_win}{Best picture win, fct (no, yes)}
#'  \item{best_actor_win}{Best actor win, fct (no, yes)}
#'  \item{best_actress_win}{Best actress win, fct (no, yes)}
#'  \item{best_dir_win}{Best director win, fct (no, yes)}
#'  \item{top200_box}{Top 20 box-office, fct (no, yes)}
#'  \item{director}{Name of director, chr}
#'  \item{actor1}{Name of leading actor, chr}
#'  \item{actor2}{Name of supporting actor, chr}
#'  \item{actor3}{Name of #3 actor, chr}
#'  \item{actor4}{Name of #4 actor, chr}
#'  \item{actor5}{Name of #5 actor, chr}
#'  \item{imdb_url}{IMDB URL}
#'  \item{rt_url}{Rotten tomatoes URL}
#' }
#'
"movies"

7.2.3 Using movies

After documenting the movies data in R/data.R, we’ll remove the call to load() in the mod_scatter_display_server() function and replace it with a direct call to the dataset:

mod_scatter_display_server <- function(id, var_inputs) {
  shiny::moduleServer(id, function(input, output, session) {

  inputs <- reactive({
    plot_title <- tools::toTitleCase(var_inputs()$plot_title)
      list(
        x = var_inputs()$x,
        y = var_inputs()$y,
        z = var_inputs()$z,
        alpha = var_inputs()$alpha,
        size = var_inputs()$size,
        plot_title = plot_title
      )
  })
  output$scatterplot <- renderPlot({
    plot <- scatter_plot(
      df = movies,
      x_var = inputs()$x,
      y_var = inputs()$y,
      col_var = inputs()$z,
      alpha_var = inputs()$alpha,
      size_var = inputs()$size
    )
    plot +
      ggplot2::labs(
        title = inputs()$plot_title,
        x = stringr::str_replace_all(tools::toTitleCase(inputs()$x), "_", " "),
        y = stringr::str_replace_all(tools::toTitleCase(inputs()$y), "_", " ")
      ) +
      ggplot2::theme_minimal() +
      ggplot2::theme(legend.position = "bottom")
  })
})
}
1
The movies data from our package namespace

After loading, documenting, and installing the package, we see the following application:

Figure 7.3: launch_app() with movies data file

7.2.4 More examples

To illustrate other options for data documentation, we’ll use the dplyr package. dplyr stores its data in the data/ folder:

data/
├── band_instruments.rda
├── band_instruments2.rda
├── band_members.rda
├── starwars.rda
└── storms.rda

The documentation for the datasets in dplyr are stored in R/ using a data- prefix:

R/
├── data-bands.R
├── data-starwars.R
└── data-storms.R

The three band_ datasets have documented in a single file, data-bands.R:

show/hide documentation for dplyr::band_ datasets 
# from the dplyr github repo: 
# https://github.com/tidyverse/dplyr/blob/main/R/data-bands.R
# 
#' Band membership
#'
#' These data sets describe band members of the Beatles and Rolling Stones. They
#' are toy data sets that can be displayed in their entirety on a slide (e.g. to
#' demonstrate a join).
#'
#' `band_instruments` and `band_instruments2` contain the same data but use
#' different column names for the first column of the data set.
#' `band_instruments` uses `name`, which matches the name of the key column of
#' `band_members`; `band_instruments2` uses `artist`, which does not.
#'
#' @format Each is a tibble with two variables and three observations
#' @examples
#' band_members
#' band_instruments
#' band_instruments2
"band_members"

#' @rdname band_members
#' @format NULL
"band_instruments"

#' @rdname band_members
#' @format NULL
"band_instruments2"

In the example above, note that two of the datasets (band_instruments and band_instruments2) have the @format set to NULL, and define the help search name with @rdname. The @examples tag can be used to view the dataset when users click ‘Run Examples’

Either method works–what’s important is that each dataset in your package has documentation.

Documenting data requires the following roxygen2 structure:

#' 
#' @title single-sentence describing [data]
#' 
#' @description
#' Single-paragraph describing [data]
#' 
#' @format [data] number of rows and columns:
#' \describe{
#'  \item{variable}{description}
#'  \item{variable}{description}
#' }
#'
"[data]"

Replace [data] with the name of your dataset.

7.3 data-raw/

The data-raw folder is not an official directory in the standard R package structure, but it’s a common location for any data processing or cleaning scripts, and the raw data file for datasets stored in data/.4

The code used to produce the movies dataset in the data/ directory might* come from this GitHub repo. If so, the data-raw folder is where the data processing and preparation scritps would be stored (along with a copy of the data in .csv format) before saving a copy in the data/ folder.

*I say ‘might’ because it’s not clear if the movies.RData is the output from these .R files (although many of the column names match).

7.3.1 More examples

If we look at the data in the dplyr package again, we can see the data-raw/ folder contains a combination of .R and .csv files:

data-raw/
├── band_members.R
├── starwars.R
├── starwars.csv
└── storms.R

1 directory, 4 files

In this example, the starwars.R script downloads & prepares starwars, then saves a .csv copy of the data in data-raw.

7.4 inst/extdata/

The extdata folder (inside inst/) can be used for external datasets in other file formats (.csv, .tsv, .txt, .xlsx, etc).5 The data files in inst/extdata/ aren’t directly loadable using the package::data syntax or the data() function like with the data/ directory. These files can be imported using the file path accessor function, system.file().

For example, if we create the inst/extdata/ and save a copy of movies as a .fst file:

library(fs)
library(tibble)
library(fst)
fst package v0.9.8
fs::dir_create("inst/extdata/")
fst::write_fst(
  x = movies, 
  path = "inst/extdata/movies.fst", 
  compress = 75)
fstcore package v0.9.14
(OpenMP was not detected, using single threaded mode)

Then load, document, and install sap:



Ctrl/Cmd + Shift + L / D / B

We can import movies.fst using system.file() to create a path to the file:

tibble::as_tibble(
  fst::read_fst(path = 
      system.file("extdata/", "movies.fst", package = "sap")
    )
  )
show/hide 
## A tibble: 651 × 34
#    title  title_type genre runtime mpaa_rating studio thtr_rel_date      
#    <chr>  <fct>      <fct>   <dbl> <fct>       <fct>  <dttm>             
#  1 Filly… Feature F… Drama      80 R           Indom… 2013-04-18 21:00:00
#  2 The D… Feature F… Drama     101 PG-13       Warne… 2001-03-13 21:00:00
#  3 Waiti… Feature F… Come…      84 R           Sony … 1996-08-20 21:00:00
#  4 The A… Feature F… Drama     139 PG          Colum… 1993-09-30 21:00:00
#  5 Malev… Feature F… Horr…      90 R           Ancho… 2004-09-09 21:00:00
#  6 Old P… Documenta… Docu…      78 Unrated     Shcal… 2009-01-14 21:00:00
#  7 Lady … Feature F… Drama     142 PG-13       Param… 1985-12-31 21:00:00
#  8 Mad D… Feature F… Drama      93 R           MGM/U… 1996-11-07 21:00:00
#  9 Beaut… Documenta… Docu…      88 Unrated     Indep… 2012-09-06 21:00:00
# 10 The S… Feature F… Drama     119 Unrated     IFC F… 2012-03-01 21:00:00
## ℹ 641 more rows
## ℹ 27 more variables: thtr_rel_year <dbl>, thtr_rel_month <dbl>,
##   thtr_rel_day <dbl>, dvd_rel_date <dttm>, dvd_rel_year <dbl>,
##   dvd_rel_month <dbl>, dvd_rel_day <dbl>, imdb_rating <dbl>,
##   imdb_num_votes <int>, critics_rating <fct>, critics_score <dbl>,
##   audience_rating <fct>, audience_score <dbl>, best_pic_nom <fct>,
##   best_pic_win <fct>, best_actor_win <fct>, best_actress_win <fct>, …
## ℹ Use `print(n = ...)` to see more rows

We’ll cover inst/ and system.file() in more detail in the next chapter.

See the 07_data branch of sap.

Recap

It’s common for Shiny apps to require data, so knowing how to store and access these files in your app-package will make it easier to load and reproducible in other environments. Here are a few other things to consider when including data in your app-package:

Recap: Package data files

  • data/: All data files stored in data/ will be ‘lazy loaded’ (see below) when the package is installed and loaded.

  • Loading: include the LazyData: true field in the DESCRIPTION file so the data is only loaded when it’s used (and it increases package loading speed).

  • Size: large data files can inflate the size of your app-package, making it harder for users to download and install. CRAN also has a size limit for packages (if you plan on submitting your app-package).

  • Format: data files in data/ must be either .rda or .RData format.

  • Documentation: document the data files in either a single R/data.R file or individual .R files. Documentation should include the following roxygen2 format:

    #' 
#' @title 
#' 
#' @description
#' 
#' @format 
#' \describe{
#'  \item{variable}{description}
#' }
#'
'data'

  • inst/extdata/: Store external data in the inst/extdata/ directory and access it using system.file(). This can be helpful if your app-package needs access to data files that are not R objects. For faster loading, consider the fst or feather formats.

Please open an issue on GitHub

  1. Read more about the data folder in the ‘Data in packages’ section of Writing R Extenstions and the ‘Data’ chapter of R Packages, 2ed.↩︎

  2. For information on how to store and retrieve inside your application, see the chapter on app Data.↩︎

  3. The ggplot2 package has a great example of documenting datasets in the R/data.R file↩︎

  4. Read more about the data-raw folder in R Packages, 2ed↩︎

  5. Read more about the inst/extdata/ folder in R Packages, 2ed↩︎