NEWS.md

metacheck 0.0.0.9069

• New logging functions: logger() and lastlog() inspired by @levibaruch
• New test_paper() for creating paper objects with specfic test text

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

• Lots of changes for how reports are formatted
• In module output, summary is now summary_table
• Fixed a bug where some .docx file wouldn't read in (support for Word files is still patchy -- ideally render to PDF)
• New pubpeer_comments() function (now vectorised)
• Module helpers: scroll_table(), collapse_section(), link(), plural(), pb()

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)

papercheck 0.0.0.9058

• openalex() results now include abstract, which parses the abstract_inverted_index for you

papercheck 0.0.0.9057

New functions/modules

• New module: miscitation to detect commonly mis-cited papers (a proof-of-concept)
• New module: power to detect and classify power analyses (currently being validated)
• New module: aspredicted to get structured data from AsPredicted preregistrations (mainly for info)
• module_template() creates a module file from a template
• orcid_person() gets details from an ORCiD, such as name, emails, country
• osf_preprint_list() returns a table of preprints from the OSF optionally filtered by archive and dates created or modified
• Added an API wrapper - it is now possible to run papercheck functions and modules via a REST API. See inst/plumber/README.md for details.
• Added documentation and plumber/Docker quickstart for the API

Changes

• Changes to module_find() to find potential modules in the working directory and ./modules/
• Changes to effectsize module so text of the potential effect size is given in mod_output$table$es (mod_output$summary$ttests_n and mod_output$summary$Ftests_n columns removed, as they are just the sum of *tests_with_es and *tests_without_es)
• pdf2grobid() now gives more useful information in the warning if some files do not convert when converting more than one PDF
• Changed parameter names in pdf2grobid to be consistently snake_case (consolidate_headers etc.) whilst keeping backward compatibility for the old camelCase (consolidateHeaders etc.)

Bug Fixes

• Fixed warning messages in osf_check module when there are no OSF links
• Fixed a problem in module_report() that happens when the table returned from module_run() has no rows
• Fixed a bug that crashed stat_table() function by generating a summary table in case of empty stat table

papercheck 0.0.0.9056

• If expand_text() doesn't find a text match because sentence location info is missing, it now returns the original text instead of NA
• Fixed a bug that prevented matching xrefs sentences under some circumstances (when there was an initial with a full stop in the citation) -- re-run read() on XMLs to update any saved paper objects
• psychsci updated for these fixes
• Changed retractionwatch internal data to retractionwatch() function (alias rw()) to support user updating.
• Added new function rw_date() so you can find out when retractionwatch was last updated
• New function rw_update() lets you update retractionwatch yourself

papercheck 0.0.0.9055

• pdf2grobid() handles save_path batter if any path components don't exist yet. The argument save_path also now can take a vector of the same length as the number of PDFs to convert, so you can specify the name of each output XML.
• read() now skips any imports with errors and warns you about them after importing all files
• Fixed a bug that errored on read() when bibentry files don't format correctly
• Function osf_get_all_pages() now has a new argument page_end to limit the number of pages retrieved (mainly for testing purposes), and is external (previously internal)
• Fixed a bug in osf_files() that failed on paths with spaces
• Fixed a bug in read() that duplicated entries in xrefs

papercheck 0.0.0.9054

• osf_file_download() now also retrieves files from linked storage
• Removed the last dependency to {osfr} and updated osf_check_id() to return expected IDs from various URLs
• OSF functions added to getting started vignette
• Functions that require and API are now tested using httptest
• module_list() doesn't fail if there are any errors in the modules

papercheck 0.0.0.9053

• Updated read() to parse more stupid date formats that turn up in the submission string (and added the unparsed submission string back just in case)
• Completely overhauled how paper objects handle references.
  • the paper$reference table is now paper$bib
  • the paper$citations table is now paper$xrefs and also contains information for internal cross-references to figures, tables, footnotes, and formulae
  • the ref_id and bib_id in both tables is now xref_id
  • the xrefs table also contains location information (section, div, p, s) for the sentence containing the cross-ref, so you can use expand_text()
  • The read() function now returns paper objects with these new tables, so you will need to re-read any XML files (if you have stored the papercheck list as Rdata)
  • The psychsci object has been updated for this new format
  • Modules and vignettes have been updated as well

papercheck 0.0.0.9052

• Fixed a bug in expand_text() where expanded sentences were duplicated if there are multiple matches from the same sentence in the data frame.
• Updated the retractionwatch table
• Fixed a bug in read() that omitted paper DOIs from paper$info
• Updated read() to add correctly parsed "accepted" and "received" dates to paper$info (replaces paper$submission string) (ISO 8601 is the only correct date format!)
• Updated psychsci for new info structure

papercheck 0.0.0.9051

• Small bug fixes to osf_file_download()
• osf_file_download() now returns a table of file info, including info for files not downloaded because of file size limits

papercheck 0.0.0.9050

• Added read() function, which superceeds read_grobid(), read_cermine() and read_text() (they are still available, but are now just aliases to read()). This should work with XML files in TEI (grobid), JATS APA-DTD, NLM-DTD and cermine formats, plus full text-only parsing of .docx and plain text files.
• Added osf_file_download() function, which downloads all files under a project or node and structures them the same as the project.

papercheck 0.0.0.9049

• Updated read_grobid() to classify headers as intro, method, results, discussion with better accuracy (to handle garbled headers)
• Updated pdf2grobid() to allow some grobid parameters
• Updated the module "all_p_values" to handle more scientific notation formats

papercheck 0.0.0.9048

• Functions to check ResearchBox.org (rbox_links() and rbox_retrieve()) -- very preliminary
• The module "all_p_values" now returns the p-value as a numeric column p_value and the comparator as p_comp, like "exact_p"

papercheck 0.0.0.9047

• fixed some bugs in osf and aspredicted functions (mainly around dealing with private or empty projects)
• added rvest dependency for better webpage parsing
• changed name of resulting column from summarize_contents() from best_guess to file_category

papercheck 0.0.0.9046

• New aspredicted_links() and aspredicted_retrieve() functions
• New related blog post
• General bug fixes in newer stuff
• Updated license to AGPL (GNU Affero General Public License)

papercheck 0.0.0.9045

• When reading a paper with read_grobid(), the paper$references table now contains new columns for bibtype, title, journal, year, and authors to facilitate reference checks, and more reliably pulls DOIs.
• The psychsci set has been updated for the new reference tables
• fixed bug in info_table() where adding "id" to the items argument borked the id column
• Added json_expand() function to expand JSON-formatted LLM responses
• Updated the LLM examples in the vignettes
• Added find_project argument to osf_retrieve() to make searching for the parent project optional (it takes 1+ API calls)
• Added emojis for convenience

papercheck 0.0.0.9044

• Revised the OSF functions again!
• Organised the Reference section of the website
• Added some blog posts to the website
• Upgraded the "osf_check" module to give more info

papercheck 0.0.0.9043

• Totally re-wrote the OSF functions

papercheck 0.0.0.9042

• New OSF functions and vignette
• Build pkgdown manually

papercheck 0.0.0.9041

• Fixed a bug in validate() that returned incorrect summary stats if the data type of an expected column didn't match the data type of an observed column (e.g., double vs integer)
• Combined the two effect size modules into "effect_size"
• Renamed the module "imprecise_p" to "exact_p" (I keep typo-ing "imprecise")
• Added a loading message
• Added code coverage at https://app.codecov.io/gh/scienceverse/papercheck
• updated "all_p_values" to handle unicode operators like <=or >>

papercheck 0.0.0.9040

• Updated default llm model to llama-3.3-70b-versatile (old one is being deprecated in August)
• Updated reporting function for modules to show the summary table
• Fixes a bug in validate() that returned FALSE for matches if the expected and observed results were both NA
• Added two preliminary modules: "effect_size_ttest" and "effect_size_ftest"

papercheck 0.0.0.9039

• removed the llm_summarise module
• updated papercheck_app() to show all modules
• removed the LLM tab from the shiny app
• fixed a bug in pdf2grobid() where a custom grobid_url was not used in batch processing
• psychsci object updated to use XMLs from grobid 0.8.2, which fixes some grobid-related errors in PDF import

papercheck 0.0.0.9038

• validate() function is updated for the new module structure
• the validation, metascience, and text_model vignettes are updated
• modules can now use relative paths (to their own location) to access helper files

papercheck 0.0.0.9037

• The way modules are created has been majorly changed -- it is now very similar to R package functions, using roxygen for documentation, instead of JSON format. There is no longer a need to distinguish text search, code, and LLM types of modules, they all use code. The vignettes have been updated to reflect this.
• Modules now return a summary table that is appended to a master summary table if you chain modules like psychsci |> module_run("all_p_values") |> module_run("marginal")
• The validate() function is temporarily removed to adapt the workflow to the new summary tables.
• new module_help() function and some help/examples in modules
• new module_info() helper function
• new paperlist() function to create paper list objects
• paper lists now print as a table of IDs, titles, and DOIs
• updated read_grobid() to have fewer false positives for citations
• updated retractionwatch

papercheck 0.0.0.9036

• Now reads in grobid XMLs that have badly parsed figures

papercheck 0.0.0.9035

• updated the shiny app for recent changes

papercheck 0.0.0.9034

• openalex() takes paper objects, paper lists, and vectors of DOIs as input, not just a single DOI
• fixed paper object naming problem when nested files are not all at the same depth

papercheck 0.0.0.9033

• added read_cermine() as associated internal functions for reading cermine-formatted XMLs

papercheck 0.0.0.9032

• New functions for exploring github repositories: github_repo(), github_readme(), github_languages(), github_files(), github_info()
• A new vignette about github functions

papercheck 0.0.0.9031

• read_grobid() now includes figure and table captions, plus footnotes, in the full_text table
• the psychsci paper list object is updated to include the above
• The functions that module_run() delegates to now check and only pass valid arguments

papercheck 0.0.0.9030 (2025-03-01)

• modules are now updated for clearer output, and added a new module vignette
• llm() no longer returns NA when the rate limit is hit, but slows down queries accordingly
• read_grobid() now includes back matter (e.g., acknowledgements, COI statements) in the full_text, so is searchable with search_text()
• references are now converted to bibtex format, so are more complete and consistent
• Machine-learning module types are removed (the python/reticulate setup was too complex for many users), and instructions for how to create simple text feature models is included in the metascience vignette

papercheck 0.0.0.9029 (2025-02-26)

• added author_table() to get a dataframe of author info from a list of paper objects
• fixed a bunch of tests now that multiple matches in a sentence are possible
• added back text (acknowledgements, annex, funding notes) to the full_text of a paper
• Fixed a bug in search_text() that omitted duplicate matches in the same sentence when using results = "match"
• Upgraded the search string for the "all-p-values" module to not error when a numeric value is followed by "-"
• Error catching for stats() related to the above problem (and filed an issue on statcheck)
• URLs in grobid XML are now converted to "" using the source url, not the text url, which is often mangled

papercheck 0.0.0.9028 (2025-02-18)

• added psychsci dataset of 250 open access papers from Psychological Science
• added "all" option the the return argument of search_text()
• added info_table() to get a dataframe of info from a list of paper objects
• experimental functions for text prediction: distinctive_words() and text_features()

papercheck 0.0.0.9027 (2025-02-07)

• Removed ChatGPT and added groq support
• Updated llm() and associated functions like llm_models()
• Working on div vs section aggregation for search_text()

papercheck 0.0.0.9026 (2025-02-06)

• metascience and batch vignettes
• removed scienceverse as a dependency
• revised validation functions
• added tl_accuracy()

papercheck 0.0.0.9025 (2025-02-04)

• Added expand_text()

papercheck 0.0.0.9024 (2025-01-31)

• Added validate() function and vignette