scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

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  1. scientific_writer/.claude/WRITER.md +748 -0
  2. scientific_writer/.claude/settings.local.json +30 -0
  3. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  4. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  5. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  6. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  7. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  8. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  9. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  10. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  16. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  17. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  18. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  19. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  31. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  39. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  47. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  48. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  49. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  50. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  98. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  106. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  118. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  174. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  177. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  182. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  183. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  184. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  188. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  189. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  192. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  193. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  194. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  195. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  196. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  197. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  200. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  201. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  202. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  203. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  204. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  205. scientific_writer/.claude/skills/markitdown/README.md +184 -0
  206. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  207. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  208. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  209. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  210. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  213. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  214. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  219. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  220. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  221. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  222. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  223. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  224. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  225. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  227. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  228. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  229. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  230. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  231. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  232. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  233. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  234. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
  235. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  236. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  237. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  238. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  239. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  242. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  249. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  250. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  255. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  259. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  263. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  264. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  269. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  270. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  271. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  278. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  283. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  287. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  288. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  294. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  295. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  296. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  297. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  298. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  301. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  302. scientific_writer/__init__.py +1 -1
  303. scientific_writer/api.py +9 -5
  304. scientific_writer/cli.py +9 -5
  305. scientific_writer/core.py +28 -5
  306. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/METADATA +1 -1
  307. scientific_writer-2.2.3.dist-info/RECORD +312 -0
  308. scientific_writer-2.2.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,720 @@
1
+ # Citation Styles Guide
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+
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+ ## Overview
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+
5
+ Citation styles provide standardized formats for acknowledging sources in scientific writing. Different disciplines prefer different styles, and journals typically specify which style to use. The five most common citation styles in science are AMA, Vancouver, APA, Chicago, and IEEE.
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+
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+ ## Choosing the Right Style
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+
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+ | Style | Primary Disciplines | In-Text Format |
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+ |-------|-------------------|----------------|
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+ | AMA | Medicine, health sciences | Superscript numbers¹ |
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+ | Vancouver | Biomedical sciences | Numbers in brackets [1] |
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+ | APA | Psychology, social sciences, education | Author-date (Smith, 2023) |
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+ | Chicago | Humanities, history, some sciences | Notes-bibliography or author-date |
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+ | IEEE | Engineering, computer science | Numbers in brackets [1] |
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+ | ACS | Chemistry | Superscript numbers¹ or (1) |
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+ | NLM | Life sciences, PubMed | Numbers in brackets [1] |
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+
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+ **Default recommendation**: When in doubt, check the journal's author guidelines. Most biomedical journals use Vancouver or AMA style.
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+
21
+ ## AMA Style (American Medical Association)
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+
23
+ ### Overview
24
+ - Used primarily in medical research
25
+ - Based on the *AMA Manual of Style* (11th edition, 2020)
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+ - Numbered citations appearing as superscripts
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+ - References listed numerically in order of appearance
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+
29
+ ### In-Text Citations
30
+
31
+ **Basic format**: Superscript numerals outside periods and commas, inside semicolons and colons.
32
+
33
+ **Examples:**
34
+ ```
35
+ Several studies have demonstrated this effect.¹
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+
37
+ The results were inconclusive,² although Smith et al³ reported otherwise.
38
+
39
+ These findings³⁻⁵ suggest a correlation.
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+
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+ One meta-analysis⁶ found significant heterogeneity; however, the pooled effect was significant.⁷
42
+ ```
43
+
44
+ **Multiple citations**: Use commas or hyphens for ranges
45
+ ```
46
+ Multiple studies¹,³,⁵⁻⁷ have confirmed this.
47
+ ```
48
+
49
+ **Same source cited multiple times**: Use the same number throughout
50
+
51
+ ### Reference List Format
52
+
53
+ **Journal Articles:**
54
+ ```
55
+ 1. Author AA, Author BB, Author CC. Title of article. Journal Name. Year;Volume(Issue):Page range. doi:xx.xxxx
56
+ ```
57
+
58
+ **Example:**
59
+ ```
60
+ 1. Smith JD, Johnson AB, Williams CD. Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry. 2023;80(5):456-464. doi:10.1001/jamapsychiatry.2023.0123
61
+ ```
62
+
63
+ **Books:**
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+ ```
65
+ 2. Author AA. Book Title. Edition. Publisher; Year.
66
+ ```
67
+
68
+ **Book Chapters:**
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+ ```
70
+ 3. Chapter Author AA. Chapter title. In: Editor AA, Editor BB, eds. Book Title. Edition. Publisher; Year:Page range.
71
+ ```
72
+
73
+ **Online Resources:**
74
+ ```
75
+ 4. Organization Name. Page title. Website name. Published date. Updated date. Accessed date. URL
76
+ ```
77
+
78
+ ### Special Cases
79
+
80
+ **More than 6 authors**: List first 3, then "et al"
81
+ ```
82
+ Smith JD, Jones AB, Williams CD, et al.
83
+ ```
84
+
85
+ **No author**: Begin with title
86
+
87
+ **Advance online publication**:
88
+ ```
89
+ Published online Month Day, Year. doi:xx.xxxx
90
+ ```
91
+
92
+ ## Vancouver Style
93
+
94
+ ### Overview
95
+ - Developed by the International Committee of Medical Journal Editors (ICMJE)
96
+ - Described in *Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals*
97
+ - Also called "author-number style"
98
+ - Numbered citations in square brackets
99
+ - References listed numerically
100
+
101
+ ### In-Text Citations
102
+
103
+ **Basic format**: Numbers in square brackets after the relevant text, before periods and commas.
104
+
105
+ **Examples:**
106
+ ```
107
+ Several studies have shown this effect [1].
108
+
109
+ The results were inconclusive [2], although Smith et al [3] reported otherwise.
110
+
111
+ These findings [3-5] suggest a correlation.
112
+
113
+ Multiple studies [1,3,5-7] have confirmed this.
114
+ ```
115
+
116
+ ### Reference List Format
117
+
118
+ **Journal Articles:**
119
+ ```
120
+ 1. Author AA, Author BB, Author CC. Title of article. Journal Name. Year;Volume(Issue):Page range.
121
+ ```
122
+
123
+ **Example:**
124
+ ```
125
+ 1. Smith JD, Johnson AB, Williams CD. Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry. 2023;80(5):456-464.
126
+ ```
127
+
128
+ **Books:**
129
+ ```
130
+ 2. Author AA, Author BB. Book title. Edition. Place of publication: Publisher; Year.
131
+ ```
132
+
133
+ **Book Chapters:**
134
+ ```
135
+ 3. Chapter Author AA, Chapter Author BB. Chapter title. In: Editor AA, Editor BB, editors. Book title. Edition. Place: Publisher; Year. p. Page range.
136
+ ```
137
+
138
+ **Electronic Sources:**
139
+ ```
140
+ 4. Author AA. Title of page [Internet]. Place: Publisher; Date of publication [cited Date of citation]. Available from: URL
141
+ ```
142
+
143
+ ### Special Cases
144
+
145
+ **More than 6 authors**: List first 6, then "et al."
146
+
147
+ **Journal title abbreviations**: Use PubMed/Index Medicus abbreviations
148
+ - *The Journal of the American Medical Association* → *JAMA*
149
+ - *Nature Medicine* → *Nat Med*
150
+
151
+ **No volume or issue**: Use year and page numbers only
152
+
153
+ **Article in press**: Use "[Epub ahead of print]" notation
154
+
155
+ ## APA Style (American Psychological Association)
156
+
157
+ ### Overview
158
+ - Widely used in psychology, education, and social sciences
159
+ - Based on the *Publication Manual of the APA* (7th edition, 2020)
160
+ - Author-date format for in-text citations
161
+ - References listed alphabetically by author surname
162
+
163
+ ### In-Text Citations
164
+
165
+ **Basic format**: (Author, Year)
166
+
167
+ **Examples:**
168
+ ```
169
+ One study found significant effects (Smith, 2023).
170
+
171
+ Smith (2023) found significant effects.
172
+
173
+ Multiple studies (Jones, 2020; Smith, 2023; Williams, 2024) support this conclusion.
174
+ ```
175
+
176
+ **Two authors**: Use "&" in parentheses, "and" in narrative
177
+ ```
178
+ (Smith & Jones, 2023)
179
+ Smith and Jones (2023) demonstrated...
180
+ ```
181
+
182
+ **Three or more authors**: Use "et al." after first author
183
+ ```
184
+ (Smith et al., 2023)
185
+ Smith et al. (2023) reported...
186
+ ```
187
+
188
+ **Multiple works by same author(s) in same year**: Add letters
189
+ ```
190
+ (Smith, 2023a, 2023b)
191
+ ```
192
+
193
+ **Direct quotations**: Include page numbers
194
+ ```
195
+ (Smith, 2023, p. 45)
196
+ "Quote text" (Smith, 2023, p. 45).
197
+ Smith (2023) stated, "Quote text" (p. 45).
198
+ ```
199
+
200
+ ### Reference List Format
201
+
202
+ **Journal Articles:**
203
+ ```
204
+ Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. Journal Name, Volume(Issue), page range. https://doi.org/xx.xxxx
205
+ ```
206
+
207
+ **Example:**
208
+ ```
209
+ Smith, J. D., Johnson, A. B., & Williams, C. D. (2023). Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry, 80(5), 456-464. https://doi.org/10.1001/jamapsychiatry.2023.0123
210
+ ```
211
+
212
+ **Books:**
213
+ ```
214
+ Author, A. A. (Year). Book title: Subtitle (Edition). Publisher. https://doi.org/xx.xxxx
215
+ ```
216
+
217
+ **Book Chapters:**
218
+ ```
219
+ Chapter Author, A. A., & Chapter Author, B. B. (Year). Chapter title. In E. E. Editor & F. F. Editor (Eds.), Book title (pp. page range). Publisher.
220
+ ```
221
+
222
+ **Websites:**
223
+ ```
224
+ Author, A. A. (Year, Month Day). Page title. Website Name. URL
225
+ ```
226
+
227
+ ### Capitalization Rules
228
+ - Sentence case for article and book titles (capitalize only first word and proper nouns)
229
+ - Title case for journal names (capitalize all major words)
230
+
231
+ **Example:**
232
+ ```
233
+ Smith, J. D. (2023). Effects of stress on cognitive performance: A meta-analysis. Journal of Experimental Psychology: General, 152(3), 456-478.
234
+ ```
235
+
236
+ ### Special Cases
237
+
238
+ **No author**: Move title to author position
239
+ ```
240
+ Title of work. (Year). Journal Name...
241
+ ```
242
+
243
+ **No date**: Use (n.d.)
244
+ ```
245
+ Smith, J. D. (n.d.). Title...
246
+ ```
247
+
248
+ **Up to 20 authors**: List all authors with "&" before last
249
+ **21 or more authors**: List first 19, then "...", then final author
250
+
251
+ ## Chicago Style
252
+
253
+ ### Overview
254
+ - Based on *The Chicago Manual of Style* (17th edition, 2017)
255
+ - Two systems: Notes-Bibliography and Author-Date
256
+ - Notes-Bibliography common in humanities
257
+ - Author-Date common in sciences
258
+
259
+ ### Notes-Bibliography System
260
+
261
+ **In-Text**: Superscript numbers for footnotes or endnotes
262
+ ```
263
+ One study demonstrated this effect.¹
264
+ ```
265
+
266
+ **Note format:**
267
+ ```
268
+ 1. John D. Smith, Alice B. Johnson, and Carol D. Williams, "Effectiveness of Cognitive Behavioral Therapy for Anxiety Disorders," JAMA Psychiatry 80, no. 5 (2023): 456-64.
269
+ ```
270
+
271
+ **Bibliography format:**
272
+ ```
273
+ Smith, John D., Alice B. Johnson, and Carol D. Williams. "Effectiveness of Cognitive Behavioral Therapy for Anxiety Disorders." JAMA Psychiatry 80, no. 5 (2023): 456-64.
274
+ ```
275
+
276
+ ### Author-Date System
277
+
278
+ **In-Text**: Similar to APA
279
+ ```
280
+ (Smith, Johnson, and Williams 2023)
281
+ Smith, Johnson, and Williams (2023) found...
282
+ ```
283
+
284
+ **Reference list**: Similar to APA but with different punctuation
285
+ ```
286
+ Smith, John D., Alice B. Johnson, and Carol D. Williams. 2023. "Effectiveness of Cognitive Behavioral Therapy for Anxiety Disorders." JAMA Psychiatry 80 (5): 456-64.
287
+ ```
288
+
289
+ ### Special Features
290
+ - Full names in bibliography (not just initials)
291
+ - Uses "and" not "&"
292
+ - Different punctuation from APA
293
+
294
+ ## IEEE Style
295
+
296
+ ### Overview
297
+ - Used in engineering, computer science, and technology
298
+ - Published by the Institute of Electrical and Electronics Engineers
299
+ - Numbered citations in square brackets
300
+ - References listed numerically
301
+
302
+ ### In-Text Citations
303
+
304
+ **Format**: Numbers in square brackets
305
+
306
+ **Examples:**
307
+ ```
308
+ Several studies have demonstrated this effect [1].
309
+
310
+ The algorithm was described by Smith [2] and later improved [3], [4].
311
+
312
+ Multiple implementations [1]-[4] have been proposed.
313
+ ```
314
+
315
+ ### Reference List Format
316
+
317
+ **Journal Articles:**
318
+ ```
319
+ [1] A. A. Author, B. B. Author, and C. C. Author, "Title of article," Journal Name, vol. X, no. X, pp. XX-XX, Month Year.
320
+ ```
321
+
322
+ **Example:**
323
+ ```
324
+ [1] J. D. Smith, A. B. Johnson, and C. D. Williams, "Effectiveness of cognitive behavioral therapy for anxiety disorders," JAMA Psychiatry, vol. 80, no. 5, pp. 456-464, May 2023.
325
+ ```
326
+
327
+ **Books:**
328
+ ```
329
+ [2] A. A. Author, Book Title, Edition. City, State: Publisher, Year.
330
+ ```
331
+
332
+ **Conference Papers:**
333
+ ```
334
+ [3] A. A. Author, "Paper title," in Proc. Conference Name, City, State, Year, pp. XX-XX.
335
+ ```
336
+
337
+ **Online Sources:**
338
+ ```
339
+ [4] A. A. Author. "Title." Website. URL (accessed Mon. Day, Year).
340
+ ```
341
+
342
+ ### Special Features
343
+ - Abbreviated first and middle names
344
+ - Uses "and" before last author (not comma)
345
+ - Month abbreviations (Jan., Feb., etc.)
346
+ - "vol." and "no." before volume and issue
347
+ - "pp." before page range
348
+
349
+ ## Additional Styles
350
+
351
+ ### ACS Style (American Chemical Society)
352
+
353
+ **In-Text**: Superscript numbers or numbers in parentheses
354
+ ```
355
+ This reaction has been well studied.¹
356
+ This reaction has been well studied (1).
357
+ ```
358
+
359
+ **Reference format:**
360
+ ```
361
+ (1) Smith, J. D.; Johnson, A. B.; Williams, C. D. Title of Article. J. Am. Chem. Soc. 2023, 145, 1234-1245.
362
+ ```
363
+
364
+ **Features:**
365
+ - Semicolons between authors
366
+ - Abbreviated journal names
367
+ - Year in bold
368
+ - No issue numbers
369
+
370
+ ### NLM Style (National Library of Medicine)
371
+
372
+ **Very similar to Vancouver**, used by PubMed/MEDLINE
373
+
374
+ **Key differences:**
375
+ - Uses PubMed journal abbreviations
376
+ - Specific format for electronic publications
377
+ - PMID or PMCID can be included
378
+
379
+ **Example:**
380
+ ```
381
+ Smith JD, Johnson AB, Williams CD. Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry. 2023 May;80(5):456-64. doi: 10.1001/jamapsychiatry.2023.0123. PMID: 12345678.
382
+ ```
383
+
384
+ ## General Citation Best Practices
385
+
386
+ ### Across All Styles
387
+
388
+ **When to cite:**
389
+ - Direct quotations
390
+ - Paraphrased ideas from others
391
+ - Statistics, data, or figures from other sources
392
+ - Theories, models, or frameworks developed by others
393
+ - Information that is not common knowledge
394
+
395
+ **Citation density:**
396
+ - Introduction: Cite liberally to establish context
397
+ - Methods: Cite when referencing established protocols or instruments
398
+ - Results: Rarely cite (focus on your own findings)
399
+ - Discussion: Cite frequently when comparing to prior work
400
+
401
+ **Source quality:**
402
+ - Prefer peer-reviewed journal articles
403
+ - Cite original sources when possible (not secondary citations)
404
+ - Use recent sources (within 5-10 years for active fields)
405
+ - Ensure sources are reputable and relevant
406
+
407
+ **Common mistakes to avoid:**
408
+ - Inconsistent formatting
409
+ - Missing required elements (DOI, page numbers, etc.)
410
+ - Citing sources not actually read (citation chaining)
411
+ - Over-reliance on review articles instead of primary sources
412
+ - Including uncited references or missing cited references
413
+ - Incorrect author names or initials
414
+ - Wrong year of publication
415
+ - Truncated titles
416
+
417
+ ### Managing Citations
418
+
419
+ **Reference Management Software:**
420
+ - **Zotero**: Free, open-source, browser integration
421
+ - **Mendeley**: Free, PDF annotation, social features
422
+ - **EndNote**: Commercial, powerful, institutional support
423
+ - **RefWorks**: Web-based, institutional subscriptions
424
+
425
+ **Software benefits:**
426
+ - Automatic formatting in multiple styles
427
+ - In-text citation insertion
428
+ - Reference list generation
429
+ - PDF organization
430
+ - Sharing capabilities
431
+
432
+ ### Verifying Citations
433
+
434
+ **Before submission, check:**
435
+ 1. Every in-text citation has a corresponding reference
436
+ 2. Every reference is cited in text
437
+ 3. Formatting is consistent throughout
438
+ 4. Author names and initials are correct
439
+ 5. Titles are accurate
440
+ 6. Journal names match required abbreviations
441
+ 7. Volume, issue, and page numbers are correct
442
+ 8. DOIs are included (when required)
443
+ 9. URLs are functional (for web sources)
444
+ 10. Citations appear in correct order (numerical styles)
445
+
446
+ ## DOI (Digital Object Identifier)
447
+
448
+ ### What is a DOI?
449
+ A unique alphanumeric string identifying digital content permanently.
450
+
451
+ **Format:**
452
+ ```
453
+ doi:10.1001/jamapsychiatry.2023.0123
454
+ or
455
+ https://doi.org/10.1001/jamapsychiatry.2023.0123
456
+ ```
457
+
458
+ ### When to include:
459
+ - Required by most journals for recent publications
460
+ - Preferred over URLs because DOIs don't change
461
+ - Look up DOIs at https://www.crossref.org/ if not provided
462
+
463
+ ### Style-specific formatting:
464
+ - **AMA**: `doi:10.xxxx/xxxxx`
465
+ - **APA**: `https://doi.org/10.xxxx/xxxxx`
466
+ - **Vancouver**: Often omitted or added at journal's discretion
467
+ - **Chicago**: `https://doi.org/10.xxxx/xxxxx`
468
+
469
+ ## Quick Reference: Journal Article Format
470
+
471
+ | Style | Format |
472
+ |-------|--------|
473
+ | **AMA** | Author AA, Author BB. Title of article. *Journal*. Year;Vol(Iss):pp. doi:xx |
474
+ | **Vancouver** | Author AA, Author BB. Title of article. Journal. Year;Vol(Iss):pp. |
475
+ | **APA** | Author, A. A., & Author, B. B. (Year). Title of article. *Journal*, Vol(Iss), pp. https://doi.org/xx |
476
+ | **Chicago A-D** | Author, A. A., and B. B. Author. Year. "Title." *Journal* Vol (Iss): pp. |
477
+ | **IEEE** | A. A. Author and B. B. Author, "Title," *Journal*, vol. X, no. X, pp. XX-XX, Mon. Year. |
478
+
479
+ ## Common Abbreviations
480
+
481
+ ### Journal Abbreviations
482
+ Follow the journal's specified system (usually Index Medicus or ISO):
483
+ - *The Journal of Biological Chemistry* → *J Biol Chem*
484
+ - *Proceedings of the National Academy of Sciences* → *Proc Natl Acad Sci USA*
485
+ - *Nature Medicine* → *Nat Med*
486
+
487
+ ### Month Abbreviations
488
+ - Jan., Feb., Mar., Apr., May, June, July, Aug., Sept., Oct., Nov., Dec.
489
+ - Some styles use three-letter abbreviations without periods
490
+
491
+ ### Edition Abbreviations
492
+ - 1st ed., 2nd ed., 3rd ed., etc.
493
+ - Or: 1st edition, 2nd edition
494
+
495
+ ## Special Publication Types
496
+
497
+ ### Preprints
498
+ ```
499
+ APA: Author, A. A. (Year). Title [Preprint]. Repository Name. https://doi.org/xx.xxxx
500
+ ```
501
+
502
+ ### Theses and Dissertations
503
+ ```
504
+ APA: Author, A. A. (Year). Title [Doctoral dissertation, University Name]. Repository Name. URL
505
+ ```
506
+
507
+ ### Conference Proceedings
508
+ ```
509
+ IEEE: A. A. Author, "Title," in Proc. Conf. Name, City, Year, pp. XX-XX.
510
+ ```
511
+
512
+ ### Software/Code
513
+ ```
514
+ APA: Author, A. A. (Year). Title (Version X.X) [Computer software]. Publisher. URL
515
+ ```
516
+
517
+ ### Datasets
518
+ ```
519
+ APA: Author, A. A. (Year). Title of dataset (Version X) [Data set]. Repository. https://doi.org/xx.xxxx
520
+ ```
521
+
522
+ ## Transitioning Between Styles
523
+
524
+ When converting between citation styles:
525
+
526
+ 1. **Use reference management software** for automatic conversion
527
+ 2. **Check these elements** that vary by style:
528
+ - In-text citation format (numbered vs. author-date)
529
+ - Author name format (initials vs. full names)
530
+ - Title capitalization (sentence case vs. title case)
531
+ - Journal name formatting (abbreviated vs. full)
532
+ - Punctuation (periods, commas, semicolons)
533
+ - Use of italics and bold
534
+ - Order of elements
535
+ 3. **Manually verify** after automatic conversion
536
+ 4. **Check journal guidelines** for specific requirements
537
+
538
+ ## Journal-Specific Citation Styles and Requirements
539
+
540
+ ### How to Identify a Journal's Citation Style
541
+
542
+ **Step 1: Check Author Guidelines**
543
+ - Every journal provides author instructions (usually "Instructions for Authors" or "Author Guidelines")
544
+ - Citation style is typically specified in "References" or "Citations" section
545
+ - Look for example references formatted in the journal's style
546
+
547
+ **Step 2: Review Recent Publications**
548
+ - Examine 3-5 recent articles from your target journal
549
+ - Note the in-text citation format (numbered vs. author-date)
550
+ - Compare reference list formatting
551
+ - Check for journal-specific variations
552
+
553
+ **Step 3: Verify Journal-Specific Variations**
554
+ Some journals use modified versions of standard styles:
555
+ - Abbreviated vs. full journal names
556
+ - DOI inclusion requirements
557
+ - Article titles in title case vs. sentence case
558
+ - Maximum number of authors before "et al."
559
+
560
+ ### Common Journals and Their Citation Styles
561
+
562
+ | Journal | Citation Style | Key Features |
563
+ |---------|---------------|--------------|
564
+ | **JAMA, JAMA Network journals** | AMA | Superscript numbers, abbreviated journal names, no issue numbers |
565
+ | **New England Journal of Medicine** | Modified Vancouver | Numbered brackets, abbreviated journals, limited authors (3 then et al) |
566
+ | **The Lancet** | Vancouver | Numbered brackets, PubMed abbreviations |
567
+ | **BMJ** | Vancouver | Numbered in-text, DOIs required when available |
568
+ | **Nature, Nature journals** | Nature style (numbered) | Numbered superscripts, abbreviated journals, no article titles in some journals |
569
+ | **Science** | Science style (numbered) | Numbered in-text, abbreviated format |
570
+ | **Cell, Cell Press journals** | Cell style (author-year) | Author-date, specific formatting for multiple citations |
571
+ | **PLOS journals** | Vancouver | Numbered brackets, full journal names in some PLOS journals |
572
+ | **Journal of Biological Chemistry** | JBC style (numbered) | Numbered in-text, specific abbreviation rules |
573
+ | **Psychological journals** | APA | Author-date, DOIs required |
574
+ | **IEEE journals** | IEEE | Numbered brackets, specific format for conference papers |
575
+ | **ACS journals** | ACS | Superscript or numbered, semicolons between authors |
576
+
577
+ ### Journal Family Consistency
578
+
579
+ **Journals from the same publisher often share citation styles:**
580
+
581
+ **Elsevier journals:**
582
+ - Vary widely; check specific journal
583
+ - Many use numbered Vancouver-style
584
+ - Some allow author-date
585
+
586
+ **Springer Nature journals:**
587
+ - Nature journals: Nature style (numbered, abbreviated)
588
+ - Springer journals: Often numbered or author-date depending on field
589
+ - BMC journals: Vancouver with full journal names
590
+
591
+ **Wiley journals:**
592
+ - Varies by field
593
+ - Many biomedical journals use Vancouver
594
+ - Psychology/social science journals often use APA
595
+
596
+ **American Chemical Society (ACS):**
597
+ - All ACS journals use ACS style
598
+ - Consistent across Journal of American Chemical Society, Analytical Chemistry, etc.
599
+
600
+ ### High-Impact Journal and Conference Preferences
601
+
602
+ | Venue | Field | Citation Preference | Key Features |
603
+ |-------|-------|-------------------|--------------|
604
+ | **Nature/Science** | Multidisciplinary | Numbered, abbreviated | Space-saving, broad readability |
605
+ | **Cell family** | Life sciences | Author-date or numbered | Attribution visibility |
606
+ | **NEJM/Lancet/JAMA** | Medicine | Vancouver/AMA numbered | Medical standard |
607
+ | **NeurIPS/ICML/ICLR** | Machine Learning | Numbered [1] or (Author, Year) | Varies by conference, check template |
608
+ | **CVPR/ICCV/ECCV** | Computer Vision | Numbered [1], IEEE-like | Compact format |
609
+ | **ACL/EMNLP** | NLP | Author-year (ACL style) | Attribution-focused |
610
+
611
+ ### Adapting Citations for Different Target Journals
612
+
613
+ **When switching journals after desk rejection or withdrawal:**
614
+
615
+ **Use reference management software:**
616
+ 1. Import references into Zotero, Mendeley, or EndNote
617
+ 2. Select target journal's citation style from software library
618
+ 3. Regenerate citations and reference list automatically
619
+ 4. Manually verify formatting matches journal examples
620
+
621
+ **Key elements to check when converting:**
622
+ - In-text format (switch numbered ↔ author-date)
623
+ - Journal name abbreviation style
624
+ - Article title capitalization
625
+ - Author name format (initials vs. full names)
626
+ - DOI format and inclusion
627
+ - Issue number inclusion/exclusion
628
+ - Page number format
629
+
630
+ **Manual verification essential for:**
631
+ - Preprints and non-standard sources
632
+ - Software/datasets citations
633
+ - Conference proceedings
634
+ - Dissertations and theses
635
+
636
+ ### Venue-Specific Evaluation Criteria
637
+
638
+ **Content expectations:**
639
+ - **High-impact journals**: >50% citations from last 5 years; primary sources preferred
640
+ - **Medical journals**: Recent clinical evidence; systematic reviews valued
641
+ - **ML conferences**: Recent papers (last 2-3 years); preprints (arXiv) acceptable
642
+ - **Self-citation**: Keep <20% across all venues
643
+
644
+ **Format compliance (often automated):**
645
+ - Match venue citation style exactly
646
+ - All in-text citations have corresponding references
647
+ - Include DOIs when required (journals) or arXiv IDs (ML conferences)
648
+ - Use correct abbreviations (PubMed for medical, standard for ML)
649
+
650
+ **ML conference specifics:**
651
+ - **NeurIPS/ICML/ICLR**: ArXiv preprints widely cited; recent work heavily valued
652
+ - **Page limits strict**: Citation formatting affects space
653
+ - **Supplementary material**: Can include extended bibliography
654
+ - **Double-blind review**: Avoid obvious self-citation patterns during review
655
+
656
+ ### Citation Density by Venue Type
657
+
658
+ | Venue Type | Expected Citations | Key Notes |
659
+ |-----------|-------------------|-----------|
660
+ | **Nature/Science research** | 30-50 | Selective, high-impact citations |
661
+ | **Medical journals (RCT)** | 25-40 | Recent clinical evidence |
662
+ | **Field-specific journals** | 30-60 | Comprehensive field coverage |
663
+ | **ML conferences (8-page)** | 20-40 | Space-limited, recent work |
664
+ | **Review articles** | 100-300+ | Comprehensive coverage |
665
+
666
+ **ML conference citation practices:**
667
+ - **NeurIPS/ICML**: 25-40 references typical for 8-page papers
668
+ - **Workshop papers**: 15-25 references
669
+ - **ArXiv preprints**: Widely accepted and cited
670
+ - **Related work**: Concise but comprehensive; often moved to appendix
671
+ - **Recency critical**: Cite work from last 1-2 years when relevant
672
+
673
+ ### Pre-Submission Citation Checklist
674
+
675
+ **Content:**
676
+ - [ ] ≥50% citations from last 5-10 years (or 2-3 years for ML conferences)
677
+ - [ ] <20% self-citations; balanced perspectives
678
+ - [ ] Primary sources cited (not citation chains)
679
+ - [ ] All claims supported by appropriate citations
680
+
681
+ **Format:**
682
+ - [ ] Style matches venue exactly (check template)
683
+ - [ ] All in-text citations in reference list and vice versa
684
+ - [ ] DOIs/arXiv IDs included as required
685
+ - [ ] Abbreviations match venue style
686
+
687
+ **ML conferences additional:**
688
+ - [ ] ArXiv preprints properly formatted
689
+ - [ ] Self-citations anonymized if double-blind review
690
+ - [ ] References fit within page limits
691
+
692
+ ## Resources for Citation Styles
693
+
694
+ ### Official Manuals
695
+ - AMA: https://www.amamanualofstyle.com/
696
+ - Vancouver/ICMJE: http://www.icmje.org/
697
+ - APA: https://apastyle.apa.org/
698
+ - Chicago: https://www.chicagomanualofstyle.org/
699
+ - IEEE: https://ieeeauthorcenter.ieee.org/
700
+
701
+ ### Journal-Specific Style Guides
702
+ - Nature: https://www.nature.com/nature/for-authors/formatting-guide
703
+ - Science: https://www.science.org/content/page/instructions-authors
704
+ - Cell: https://www.cell.com/cell/authors
705
+ - JAMA: https://jamanetwork.com/journals/jama/pages/instructions-for-authors
706
+
707
+ ### Quick Reference Guides
708
+ - Purdue OWL: https://owl.purdue.edu/
709
+ - Citation Machine: https://www.citationmachine.net/
710
+ - EasyBib: https://www.easybib.com/
711
+
712
+ ### Reference Management
713
+ - Zotero: https://www.zotero.org/
714
+ - Mendeley: https://www.mendeley.com/
715
+ - EndNote: https://endnote.com/
716
+
717
+ ### Journal Citation Style Databases
718
+ - Journal Citation Reports (Clarivate): Lists journal citation styles
719
+ - EndNote style repository: >7000 journal-specific styles
720
+ - Zotero Style Repository: https://www.zotero.org/styles