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
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$submission string) (ISO 8601 is the only correct date format!)
osf_file_download() now returns a table of file info, including info for files not downloaded because of file size limits
papercheck 0.0.0.9050
Added read() function, which superceeds read_grobid(), read_cermine() and read_text() (they are still available, but are now just aliases to read()). This should work with XML files in TEI (grobid), JATS APA-DTD, NLM-DTD and cermine formats, plus full text-only parsing of .docx and plain text files.
Added osf_file_download() function, which downloads all files under a project or node and structures them the same as the project.
papercheck 0.0.0.9049
Updated read_grobid() to classify headers as intro, method, results, discussion with better accuracy (to handle garbled headers)
Updated pdf2grobid() to allow some grobid parameters
Updated the module “all_p_values” to handle more scientific notation formats
Updated license to AGPL (GNU Affero General Public License)
papercheck 0.0.0.9045
When reading a paper with read_grobid(), the paper$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”)
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
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
