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Changelog

Source: NEWS.md

metacheck 0.0.1.0

Our beta release! We’ve made so many changes, and we’re sure there are still many bugs to ctach and things to improve, but we need other people to start using metacheck to help us.

metacheck 0.0.0.9107

  • code_check now checks if code is parseable (thanks @Raphael-Merz!)
  • many new code_*() functions abstracted out from the code_check module. These may eventually move to a new package specifically for codecheck

metacheck 0.0.0.9106

  • Added functions from svutils back in.
  • Reorganised some ML read-in functions (internal).
  • Ollama further support in llm() and vignette.
  • The code_check module handles local file with the argument local_path
  • New local_files() function (thanks @lakens!)
  • Updated vignettes

metacheck 0.0.0.9105

  • Much less buggy .grobid_to_bibr() conversion, handling URLs in text, xrefs, url, and eq tables better.
  • extract_equations() renamed to extract_eq() and now extracts degrees of freedom (df column)
  • Improvements to .tei_text() to fix common problems with grobid handling of equations (e.g., ““)
  • Corresponding paper schema changes
  • Updated psychsci and demopaper() and demofile() for new schema and read

metacheck 0.0.0.9104

  • Updated file_types to fix a bug that prepended X to all extensions starting with a number.
  • paper_id() now returns a vector, not a table, fixing modules that used it that way
  • read() no longer errors when reading an empty directory, just messages and returns an empty paperlist
  • read() only reads in the .json version if a .json and .xml file with the same name exist
  • read() has a new argument recursive (default FALSE) to recursively read a directory. This does not handle it well if individual files have the same paper_id, so don’t do that.

metacheck 0.0.0.9103

  • converting grobid xml to bibr json now saves the file after each conversion, instead of at the end, making it better for large batches (although slightly less efficient by potentially duplicating crossref lookups shared between papers)
  • convert() has new arguments crossref_lookup (default FALSE) and keep_xml (default TRUE). It also saves XML and/or JSON files as they are converted, rather than at the end, in case of breaking failure.
  • Updated the “open_practices” module, which is much faster than the ODDPub version of this module (about 40x faster), also returns open materials and registrations, and has a lower false negative rate, but also a higher false positive rate. This removes the oddpub dependency.
  • Restructured file names (not function names) for functions so all archive helper (e.g., osf, github, zenodo) start with “archive-” and database helpers (e.g., pubpeer, retractionwatch) start with “db-”.
  • Restructured text functions to start with text_, so search_text() is now text_search() and expand_text() is now text_expand(). The old names will exist as aliases.
  • Internal functions now prefaced with . to make it clearer for developers.
  • All {archive}_retrieve() functions now renamed to {archive}_info() and the old {archive}_info() internal functions are now .{archive}_info()

metacheck 0.0.0.9102

  • Shiny app improvements: you can now view HTML reports in the browser
  • Fixes the “prereg_check” module to address an error when there are more than 10 OSF registrations in a batch that caused unmergable data frames.
  • Fixes the “code_check” module to address an error when checking multiple files that have no repositories with code.
  • The module “code_check” now has an argument “file_limit” to control how many code files per repo are downloaded and processed. The default is 20.
  • Fixed a problem where invisible figures in grobid would mess up the text section ids

metacheck 0.0.0.9101

metacheck 0.0.0.9100

  • So many updates to fix things that broke with the new structure
  • Using httptest2 to mock tests that access external APIs

metacheck 0.0.0.9070

  • Major updates to replace grobid functions with bibr
  • Remove author_table(), as this is just concat_tables() now

metacheck 0.0.0.9069

  • Updated osf_* and rb_* functions to use progress bars instead of messages
  • New logging functions: logger() and lastlog() inspired by @levibaruch
  • New test_paper() for creating paper objects with specific test text
  • summarize_contents() changed to file_category() and now works with a vector of file names, as well as a data frame
  • compare_tables(), text_features() and distinctive_words() now deprecated
  • validate() function simplified

metacheck 0.0.0.9068

  • FReD replication database and associated functions now renamed to FLoRA()
  • Various bug fixes discovered when running modules on large numbers of papers (e.g., handling when zero references have DOIs)
  • Modules “function_check” and “coi_check” reverted to the rtransparent versions (the re-written version were overinclusive and need more development).

metacheck 0.0.0.9067

  • reports() now takes a paperlist and makes a report from each
  • New report_module_run() and report_qmd() break down the report() function to allow separation of module output lists and creation of QMD report from them (might be changed to internal functions).
  • Ability to select returned columns in crossref_query()
  • Module “ref_accuracy” now returns info for references with missing DOIs that were found by ref_doi_check
  • Module “code_check” split into “repo_check” and “code_check”

metacheck 0.0.0.9066

  • lmm() allows you to set the model to any provider or provider/model supported by ellmer (must have appropriate *****_API_KEY set in your Renviron)
  • lmm() arguments have changed to align with ellmer::chat() arguments
  • lmm_models() now returns models from all platforms for which you have a valid API key set
  • The power module uses a new prompt that utilises a JSON schema for power
  • Updated report styles

metacheck 0.0.0.9065

  • New github_links() function to find github references in a paper.
  • code_check module very much improved - checks SAS and STATA code in OSF, researchbox, and github repos.
  • power module much improved
  • New modules: coi_check, funding_check
  • New functions extract_p_values() and extract_urls(), so now no need to use all_p_values and all_urls modules to get their tables. These modules remain because they are used in demos, but may be deprecated soon.

metacheck 0.0.0.9064

  • Enhanced module help
  • “ref_replication” module no longer warns about replications if you have cited them.
  • Extensive chenges to clen up tests.

metacheck 0.0.0.9063

  • get_doi() has been removed in favour of crossref_query(), to look up crossref info by bibliographic query, and crossref_doi(), to look up crossref info by DOI.
  • scroll_table() changed arguments. height is removed and scroll_above changed to maxrows. It not paginates above maxrows (default = 2), rather than scrolling within a fixed height. This is a more accessible solution, since scrolling is hard with touchscreens and it’s often hard to copy text in a scroll window. We will continually improve this with further user feedback.
  • Fixed a bunch of small problems with modules and let the report render even with errors
  • Updated the report template with light and dark themes (set to user preference)
  • The module reference_check is split into ref_doi_check and ref_accuracy.
  • Lots of modules got renamed so they have a consistent format.

metacheck 0.0.0.9062

  • json_expand() updated to handle LLM JSON errors more gracefully.
  • You can pass arguments to modules via report() now with the new args argument.
  • New get_prev_outputs() module helper function
  • Updated the vignettes.
  • Modules aspredicted and retractionwatch are removed, as they are superseded by prereg_check and reference_check.
  • The module nonsignificant_pvalue has changed to nonsig_p
  • The default modules in a report have changed.
  • A new module report helper, format_ref() for displaying references in bibentry or bibtex formats
  • The ref column of the bib table in paper objects is now the bibentry for a reference, not just the formatted text. This will allow for more formatting options.

metacheck 0.0.0.9061

  • Efficiency improvements to the OSF functions
  • Fixed some confusing parts of the articles that changed when the module output report structure changed.
  • Modules are now categorised by section: general, intro, method, results, discussion, reference
  • Reports are organised by section
  • Display improvement in reports
  • Module report improvement (e.g., fixing broken links)
  • New example report on the pkgdown website

metacheck 0.0.0.9060

metacheck 0.0.0.9059

  • Package name changed to metacheck!
  • Fixed a bug in osf_file_download() when multiple files have the same name and ignore_folder_structure = TRUE.
  • osf_file_download() should handle errors more gracefully (with warnings, but not fail)