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paper: cite the references supporting the impact and method claims (orig) - #337
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…style python type annotations
… into pyproject.toml
…-reflow-and-typing
… it from pylance.
…ly library and enables the missing type checks
…le used across 3 files
unimplemented code in documentation or create unimplemented code file placeholders.
…s, and runners files.
…cated and removed.
Addresses reviewer feedback in openjournals/joss-reviews#10489. - Cite the 12 applied studies backing the Research Impact Statement, grouped by domain (oncology and surgical recovery, neurology, spine and rehabilitation, psychiatry). Previously the section claimed published applications without citing any. - Cite Barnett & Onnela 2020 and Liu & Onnela 2021 where Jasmine and the mobility methods are introduced, in the Summary and Software Design sections. - Add Straczkiewicz et al. 2023 and Huang et al. 2022 to paper.bib and cite them for the accelerometry methods. Both were listed in CITATION.cff but missing from the bibliography entirely. - Replace mora2017edaravone with Cedarbaum et al. 1999 as the source for the ALSFRS-R instrument. The former is a drug trial paper and did not support the claim it was attached to. - Fix four instances of an em dash followed by a stray hyphen. Uncited entries drop from 16 to 3. The remaining three (github_ears, wiki_sensing, mora2017edaravone) belong in the State of the Field section, which is being rewritten separately. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Addresses reviewer point 5 in openjournals/joss-reviews#10489, which noted that paper.md, CITATION.cff and pyproject.toml listed different author sets. CITATION.cff and pyproject.toml now match the author list in paper.md exactly, in the same order. The docs byline in docs/source/conf.py named only three of the authors and is replaced with the lab name, so the list is maintained in one place rather than four. Verified: all three author lists are identical, 13 entries in matching order. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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This branch was out of date with the state of develop, I have merged in the current state of develop, tests are running. |
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changed the title
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Can't work out how to resurrect this pull, cloned it over at #341 |
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Fixes the reference problems raised in the JOSS review.
The Research Impact Statement claimed the methods had been applied in published studies but cited none of them. It now cites the twelve studies that were already sitting in paper.bib.
The Summary said the methods were developed and published elsewhere, and Software Design described Jasmine. Neither cited Barnett & Onnela 2020 or Liu & Onnela 2021. Both are now cited where the methods are introduced.
Straczkiewicz et al. 2023 and Huang et al. 2022 were listed in CITATION.cff but missing from paper.bib entirely. Both are added and cited for the accelerometry methods.
The ALSFRS-R description was cited to mora2017edaravone, which is a paper about edaravone rather than a source for the scale. Replaced with Cedarbaum et al. 1999.
CITATION.cff and pyproject.toml now match the author list in paper.md. The docs byline in conf.py named three of the authors and now uses the lab name instead.
Also fixed four instances of an em dash followed by a stray hyphen.
Uncited bibliography entries drop from sixteen to three. Every citation in the text has a matching entry.
The State of the Field section is handled separately. The AI usage disclosure still needs the specific tools and versions.