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Changelog

Source: NEWS.md

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

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

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

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)

papercheck 0.0.0.9024 (2025-01-31)