Changelog • papercheck

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

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

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

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

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

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

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

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()