This function prints a notification message when some or all of
the data used in a project are synthetic (see closed_data and
synthetic). See details for important information.
Arguments
- ...
Objects of class
worcs_data. The function will check if these are original or synthetic data.- msg
Expression containing the message to print in case not all
worcs_dataare original.- worcs_directory
Character, indicating the WORCS project directory to which to save data. The default value
"."points to the current directory.
Value
No return value. This function is called for its side effect of printing a notification message.
Details
The preferred way to use this function is to provide specific data
objects in the function call, using the ... argument.
If no such objects are provided, notify_synthetic will scan the
parent environment for objects of class worcs_data.
This function is emphatically designed to be included in an 'R Markdown' file, to dynamically generate a notification message when a third party 'Knits' such a document without having access to all original data.
Examples
if(requireNamespace("withr", quietly = TRUE)){
withr::with_tempdir({
file.create(".worcs")
df <- iris
class(df) <- c("worcs_data", class(df))
attr(df, "type") <- "synthetic"
result <- capture.output(notify_synthetic(df, msg = "it is synthetic"))
if(!grepl("synthetic", result)) stop()
df <- df[1:10, ]
closed_data(df, codebook = NULL)
file.remove("df.csv")
result <- capture.output(notify_synthetic(msg = "synthetic"))
if(!grepl("synthetic", result)) stop()
if(requireNamespace("rmarkdown", quietly = TRUE)){
add_manuscript(manuscript = "github_document")
print(readLines("manuscript/manuscript.Rmd"))
rmarkdown::render("manuscript/manuscript.Rmd")
if(!any(grepl("reproduced using synthetic",
readLines("manuscript/manuscript.html")))) stop()
}
})
}
#> ✔ Storing original data in 'df.csv' and updating the checksum in '.worcs'.
#> ✔ Generating synthetic data for public use. Ensure that no identifying
#> information is included.
#>
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#> Warning: Dropped unused factor level(s) in dependent variable: versicolor, virginica.
#>
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|======================================================================| 100%
#> ℹ Storing synthetic data in "fn_write_synth_rel" and updating the checksum in "…
#> ✔ Updating '.gitignore'.
#> ℹ Storing synthetic data in "fn_write_synth_rel" and updating the checksum in "…
#> ✔ Storing synthetic data in "fn_write_synth_rel" and updating the checksum in "…
#>
#> ✔ Updating '.gitignore'.
#> ✔ Storing value labels in 'value_labels_df.yml'.
#> ✔ Creating manuscript files.
#> [1] "---"
#> [2] "title: \"Untitled\""
#> [3] "output: github_document"
#> [4] "date: '`r format(Sys.time(), \"%d %B, %Y\")`'"
#> [5] "bibliography: references.bib"
#> [6] "knit: worcs::cite_all"
#> [7] "---"
#> [8] ""
#> [9] "```{r setup, include=FALSE}"
#> [10] "library(\"worcs\")"
#> [11] "# We recommend that you prepare your raw data for analysis in 'prepare_data.R',"
#> [12] "# and end that file with either open_data(yourdata), or closed_data(yourdata)."
#> [13] "# Then, uncomment the line below to load the original or synthetic data"
#> [14] "# (whichever is available), to allow anyone to reproduce your code:"
#> [15] "# load_data()"
#> [16] "knitr::opts_chunk$set(echo = TRUE)"
#> [17] "```"
#> [18] ""
#> [19] "This manuscript uses the Workflow for Open Reproducible Code in Science [WORCS version 0.1.2, @vanlissaWORCSWorkflowOpen2021] to ensure reproducibility and transparency."
#> [20] ""
#> [21] ""
#> [22] "This is an example of a non-essential citation [@@vanlissaWORCSWorkflowOpen2021]. If you change the rendering function to `worcs::cite_essential`, it will be removed."
#> [23] ""
#> [24] "<!--The function below inserts a notification if the manuscript is knit using synthetic data.-->"
#> [25] "`r notify_synthetic()`"
#> [26] ""
#> [27] "## GitHub Documents"
#> [28] ""
#> [29] "This is an R Markdown format used for publishing markdown documents to GitHub. When you click the **Knit** button all R code chunks are run and a markdown file (.md) suitable for publishing to GitHub is generated."
#> [30] ""
#> [31] "## Including Code"
#> [32] ""
#> [33] "You can include R code in the document as follows:"
#> [34] ""
#> [35] "```{r cars}"
#> [36] "summary(cars)"
#> [37] "```"
#> [38] ""
#> [39] "## Including Plots"
#> [40] ""
#> [41] "You can also embed plots, for example:"
#> [42] ""
#> [43] "```{r pressure, echo=FALSE}"
#> [44] "plot(pressure)"
#> [45] "```"
#> [46] ""
#> [47] "Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot."
#>
#>
#> processing file: manuscript.Rmd
#> 1/7
#> 2/7 [setup]
#> 3/7
#> 4/7 [cars]
#> 5/7
#> 6/7 [pressure]
#> 7/7
#> output file: manuscript.knit.md
#> /opt/hostedtoolcache/pandoc/3.1.11/x64/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm+tex_math_dollars-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/runner/work/_temp/Library/rmarkdown/rmarkdown/templates/github_document/resources/default.md --citeproc
#> /opt/hostedtoolcache/pandoc/3.1.11/x64/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm+tex_math_dollars --output manuscript.html --embed-resources --standalone --highlight-style pygments --template /home/runner/work/_temp/Library/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/runner/work/_temp/Library/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax
#>
#> Preview created: manuscript.html
#>
#> Output created: manuscript.md