Report Metadata Compliance

Helper functions to generate a metacheck report.

path_copied_report_rmd(...)

draft_report(lang = mc_langs, ...)

render_report(dois = doi_examples$good, translator = mc_translator(), ...)

Arguments

...	Arguments passed on to rmarkdown::draft, rmarkdown::render file File name for the draft template Template to use as the basis for the draft. This is either the full path to a template directory or the name of a template directory within the rmarkdown/templates directory of a package. package (Optional) Name of package where the template is located. create_dir TRUE to create a new directory for the document (the "default" setting leaves this behavior up to the creator of the template). edit TRUE to edit the template immediately input The input file to be rendered. This can be an R script (.R), an R Markdown document (.Rmd), or a plain markdown document. output_format The R Markdown output format to convert to. The option "all" will render all formats defined within the file. The option can be the name of a format (e.g. "html_document") and that will render the document to that single format. One can also use a vector of format names to render to multiple formats. Alternatively, you can pass an output format object (e.g. html_document()). If using NULL then the output format is the first one defined in the YAML frontmatter in the input file (this defaults to HTML if no format is specified there). If you pass an output format object to output_format, the options specified in the YAML header or _output.yml will be ignored and you must explicitly set all the options you want when you construct the object. If you pass a string, the output format will use the output parameters in the YAML header or _output.yml. output_file The name of the output file. If using NULL then the output filename will be based on filename for the input file. If a filename is provided, a path to the output file can also be provided. Note that the output_dir option allows for specifying the output file path as well, however, if also specifying the path, the directory must exist. If output_file is specified but does not have a file extension, an extension will be automatically added according to the output format. To avoid the automatic file extension, put the output_file value in I(), e.g., I('my-output'). output_dir The output directory for the rendered output_file. This allows for a choice of an alternate directory to which the output file should be written (the default output directory of that of the input file). If a path is provided with a filename in output_file the directory specified here will take precedence. Please note that any directory path provided will create any necessary directories if they do not exist. output_options List of output options that can override the options specified in metadata (e.g. could be used to force self_contained or mathjax = "local"). Note that this is only valid when the output format is read from metadata (i.e. not a custom format object passed to output_format). output_yaml Paths to YAML files specifying output formats and their configurations. The first existing one is used. If none are found, then the function searches YAML files specified to the output_yaml top-level parameter in the YAML front matter, _output.yml or _output.yaml, and then uses the first existing one. intermediates_dir Intermediate files directory. If a path is specified then intermediate files will be written to that path. If NULL, intermediate files are written to the same directory as the input file. knit_root_dir The working directory in which to knit the document; uses knitr's root.dir knit option. If NULL then the behavior will follow the knitr default, which is to use the parent directory of the document. runtime The runtime target for rendering. The static option produces output intended for static files; shiny produces output suitable for use in a Shiny document (see run). The default, auto, allows the runtime target specified in the YAML metadata to take precedence, and renders for a static runtime target otherwise. clean Using TRUE will clean intermediate files that are created during rendering. params A list of named parameters that override custom params specified within the YAML front-matter (e.g. specifying a dataset to read or a date range to confine output to). Pass "ask" to start an application that helps guide parameter configuration. knit_meta (This option is reserved for expert use.) Metadata generated by knitr. envir The environment in which the code chunks are to be evaluated during knitting (can use new.env() to guarantee an empty new environment). run_pandoc An option for whether to run pandoc to convert Markdown output. quiet An option to suppress printing during rendering from knitr, pandoc command line and others. To only suppress printing of the last "Output created: " message, you can set rmarkdown.render.message to FALSE encoding Ignored. The encoding is always assumed to be UTF-8.
lang	Character scalar giving the anguage of the report. Not reactive as in mcControlsServer().
dois	Vector of DOIs, as created by, or coerceable to biblids::doi().
translator	A shiny.i18n::Translator object or NULL for english-only defaults. Strings inside the module UI are marked as translateable. You can pass a translator object included in the package, or can create your own translator using shiny.i18n::Translator. This must not be a reactive, it is only set at shiny startup. To update the language reactively during a shiny session, see lang.

Related Functions and Methods

Functions

• path_copied_report_rmd: Path to rmd in temp folder. Has a side effect: copies the template to the temp folder. Safer to render because some runtimes (shinyapps.io) cannot write to folders in R_HOME.

• draft_report: Create a draft report from the template. Useful for manual edits; equivalent to opening a new template in RStudio.

• render_report: Render a parametrised metacheck report.

Note

Metacheck supports your workflows to check OA metadata deposited by publishers, but it cannot conclusively check funding eligibility of OA publications. Please consult the funding conditions of the respective funder.

See also

Other communicate: emailReport(), email, mcApp(), mcControls, md_data_attachment(), runMetacheck()