├── .Rbuildignore ├── .Rprofile ├── .gitattributes ├── .gitignore ├── .travis.yml ├── CITATION.cff ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── ODDPub.Rproj ├── R ├── ODDPub.R ├── load_txt.R ├── parse_pdf.R └── screen_text.R ├── README.md ├── inst ├── CITATION ├── extdata │ └── keywords_patterns.yaml └── previous_versions │ ├── ODDPub_Ver4.R │ ├── ODDPub_Ver4_functions.R │ ├── ODDPub_functions_ver6.R │ └── ODDPub_ver6.R ├── man ├── open_data_search.Rd ├── pdf_convert.Rd ├── pdf_load.Rd └── splice_margin_text.Rd ├── renv.lock ├── renv ├── .gitignore ├── activate.R ├── settings.dcf └── settings.json └── tests ├── testthat.R └── testthat ├── test_higher_level_functions.R ├── test_individual_keywords.R ├── test_parse_pdf.R ├── test_pdfs ├── 10.1001+jama.2020.7172.pdf ├── 10.1002+acm2.14114.pdf ├── 10.1007+s00424-021-02582-7.pdf ├── 10.1016+j.celrep.2022.110564.pdf ├── 10.1016+j.ssmph.2022.101285.pdf ├── 10.1029+2025sw004559.pdf ├── 10.1038+s41526-020-00129-1.pdf ├── 10.1073+pnas.2123476119.pdf ├── 10.1080+21678421.2022.2104649.pdf ├── 10.1093+ndt+gfaa294.pdf ├── 10.1097+as9.0000000000000095.pdf ├── 10.1098+rsif.2022.0070.pdf ├── 10.1126+science.abm8668.pdf ├── 10.1128+spectrum.02839-23.pdf ├── 10.1159+000521415.pdf ├── 10.1177+00207640231162277.pdf ├── 10.1186+s42466-019-0022-4.pdf ├── 10.1200+JCO.2017.74.7642.pdf ├── 10.1212+NXI.0000000000000763.pdf ├── 10.1371+journal.pmed.1003873.pdf ├── 10.1515+jpm-2019-0153.pdf ├── 10.15252+embr.202154000.pdf ├── 10.21037+jgo-20-203.pdf ├── 10.21203+rs.3.rs-2838995+v1.pdf ├── 10.3233+TAD-190227.pdf ├── 10.3324+haematol.2017.168716.pdf ├── 10.3389+fimmu.2022.915001.pdf ├── 10.3390+toxins8070200.pdf └── 10.7554+elife.59907.pdf ├── test_section_extraction.R ├── test_tokenization.R └── testthat-problems.rds /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/quest-bih/oddpub/HEAD/.Rbuildignore 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