scientific-writer 2.3.1__py3-none-any.whl

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Files changed (315) hide show
  1. scientific_writer/.claude/WRITER.md +822 -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
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+ # Reporting Guidelines for Scientific Studies
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+
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+ ## Overview
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+
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+ Reporting guidelines are evidence-based recommendations for what information should be included when reporting specific types of research studies. They provide checklists and flow diagrams to ensure complete, accurate, and transparent reporting, which is essential for readers to assess study validity and for other researchers to replicate the work.
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+
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+ The EQUATOR Network (Enhancing the QUAlity and Transparency Of health Research) maintains a comprehensive library of reporting guidelines. Using appropriate reporting guidelines improves manuscript quality and increases the likelihood of publication acceptance.
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+
9
+ ## Why Use Reporting Guidelines?
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+
11
+ ### Benefits
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+
13
+ **For authors:**
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+ - Ensures nothing important is forgotten
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+ - Increases acceptance rates
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+ - Improves manuscript organization
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+ - Reduces reviewer requests for additional information
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+
19
+ **For readers and reviewers:**
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+ - Enables critical appraisal of study validity
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+ - Facilitates systematic reviews and meta-analyses
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+ - Improves understanding of what was actually done
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+
24
+ **For science:**
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+ - Enhances reproducibility
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+ - Reduces research waste
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+ - Improves transparency
28
+ - Enables better evidence synthesis
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+
30
+ ### When to Use
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+
32
+ - **During study design**: Many guidelines include protocol versions (e.g., SPIRIT for trial protocols)
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+ - **During manuscript drafting**: Use checklist to ensure all items are covered
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+ - **Before submission**: Verify adherence and often submit checklist with manuscript
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+ - **Many journals require**: Reporting guideline checklists as part of submission
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+
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+ ## Major Reporting Guidelines by Study Type
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+
39
+ ### CONSORT - Randomized Controlled Trials
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+
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+ **Full name:** Consolidated Standards of Reporting Trials
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+
43
+ **When to use:** Any randomized controlled trial (RCT), including pilot and feasibility trials
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+
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+ **Latest version:** CONSORT 2010 (updated statement)
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+
47
+ **Key components:**
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+ - **Checklist**: 25 items covering title, abstract, introduction, methods, results, discussion
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+ - **Flow diagram**: Participant flow through enrollment, allocation, follow-up, and analysis
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+
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+ **Main checklist items:**
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+ 1. Title identifies study as randomized trial
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+ 2. Structured abstract
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+ 3. Scientific background and rationale
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+ 4. Specific objectives and hypotheses
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+ 5. Trial design description (parallel, crossover, factorial, etc.)
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+ 6. Eligibility criteria for participants
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+ 7. Settings and locations of data collection
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+ 8. Interventions described in sufficient detail for replication
60
+ 9. Primary and secondary outcomes defined
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+ 10. Sample size determination and power calculation
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+ 11. Randomization sequence generation
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+ 12. Allocation concealment mechanism
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+ 13. Blinding implementation
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+ 14. Statistical methods
66
+ 15. Participant flow with reasons for dropouts
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+ 16. Recruitment dates and follow-up dates
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+ 17. Baseline characteristics table
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+ 18. Analysis results for each outcome
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+ 19. Harms and adverse events
71
+ 20. Trial limitations
72
+ 21. Generalizability
73
+ 22. Interpretation consistent with results
74
+ 23. Trial registration number
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+ 24. Full protocol access
76
+ 25. Funding sources
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+
78
+ **Extensions for specific designs:**
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+ - CONSORT for cluster randomized trials
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+ - CONSORT for non-inferiority and equivalence trials
81
+ - CONSORT for pragmatic trials
82
+ - CONSORT for crossover trials
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+ - CONSORT for N-of-1 trials
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+ - CONSORT for stepped wedge designs
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+
86
+ **Where to access:** http://www.consort-statement.org/
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+
88
+ ### STROBE - Observational Studies
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+
90
+ **Full name:** Strengthening the Reporting of Observational Studies in Epidemiology
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+
92
+ **When to use:** Cohort studies, case-control studies, and cross-sectional studies
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+
94
+ **Latest version:** STROBE 2007 (widely adopted standard)
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+
96
+ **Key study designs covered:**
97
+ - **Cohort**: Follow exposed and unexposed groups forward in time
98
+ - **Case-control**: Compare exposure history between cases and controls
99
+ - **Cross-sectional**: Measure exposure and outcome simultaneously
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+
101
+ **Main checklist items (22 items):**
102
+ 1. Title and abstract indicate study design
103
+ 2. Background and rationale
104
+ 3. Objectives
105
+ 4. Study design with rationale
106
+ 5. Setting, locations, and dates
107
+ 6. Eligibility criteria and selection methods
108
+ 7. Variables clearly defined (outcomes, exposures, confounders)
109
+ 8. Data sources and measurement methods
110
+ 9. Bias management strategies
111
+ 10. Study size justification
112
+ 11. Handling of quantitative variables
113
+ 12. Statistical methods including confounding and interactions
114
+ 13. Sensitivity analyses
115
+ 14. Participant flow with reasons for non-participation
116
+ 15. Descriptive data including follow-up time
117
+ 16. Outcome data
118
+ 17. Main results with unadjusted and adjusted estimates
119
+ 18. Other analyses (subgroups, sensitivity analyses)
120
+ 19. Key results summary
121
+ 20. Limitations with potential bias discussion
122
+ 21. Interpretation and generalizability
123
+ 22. Funding sources and role
124
+
125
+ **Extensions:**
126
+ - STROBE-ME (Molecular Epidemiology)
127
+ - RECORD (Routinely collected health data)
128
+ - STROBE-RDS (Respondent-driven sampling)
129
+
130
+ **Where to access:** https://www.strobe-statement.org/
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+
132
+ ### PRISMA - Systematic Reviews and Meta-Analyses
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+
134
+ **Full name:** Preferred Reporting Items for Systematic Reviews and Meta-Analyses
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+
136
+ **When to use:** Systematic reviews with or without meta-analysis
137
+
138
+ **Latest version:** PRISMA 2020 (significant update)
139
+
140
+ **Key components:**
141
+ - **Checklist**: 27 items covering all sections
142
+ - **Flow diagram**: Study selection process
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+
144
+ **Main sections:**
145
+ 1. **Title**: Identify as systematic review/meta-analysis
146
+ 2. **Abstract**: Structured summary
147
+ 3. **Introduction**: Rationale and objectives
148
+ 4. **Methods**:
149
+ - Eligibility criteria
150
+ - Information sources (databases, dates)
151
+ - Search strategy (full strategy for at least one database)
152
+ - Selection process
153
+ - Data collection process
154
+ - Data items extracted
155
+ - Risk of bias assessment
156
+ - Effect measures
157
+ - Synthesis methods
158
+ - Reporting bias assessment
159
+ - Certainty assessment (e.g., GRADE)
160
+ 5. **Results**:
161
+ - Study selection flow diagram
162
+ - Study characteristics
163
+ - Risk of bias assessment results
164
+ - Synthesis results (meta-analysis if applicable)
165
+ - Reporting biases
166
+ - Certainty of evidence
167
+ 6. **Discussion**:
168
+ - Limitations
169
+ - Interpretation
170
+ - Implications
171
+
172
+ **Extensions:**
173
+ - PRISMA for Abstracts
174
+ - PRISMA for Protocols (PRISMA-P)
175
+ - PRISMA for Network Meta-Analyses
176
+ - PRISMA for Scoping Reviews (PRISMA-ScR)
177
+ - PRISMA for Individual Patient Data
178
+ - PRISMA for Diagnostic Test Accuracy
179
+ - PRISMA for Equity-focused reviews
180
+
181
+ **Where to access:** http://www.prisma-statement.org/
182
+
183
+ ### SPIRIT - Study Protocols for Clinical Trials
184
+
185
+ **Full name:** Standard Protocol Items: Recommendations for Interventional Trials
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+
187
+ **When to use:** Protocols for randomized trials and other planned intervention studies
188
+
189
+ **Latest version:** SPIRIT 2013
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+
191
+ **Purpose:** Ensure trial protocols contain complete descriptions before trial begins
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+
193
+ **Main checklist items (33 items):**
194
+ - Administrative information (title, trial registration, funding)
195
+ - Introduction (background, rationale, objectives)
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+ - Methods: Trial design
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+ - Study setting
198
+ - Eligibility criteria
199
+ - Interventions in detail
200
+ - Outcomes (primary and secondary)
201
+ - Participant timeline
202
+ - Sample size calculation
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+ - Recruitment strategy
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+ - Allocation and randomization
205
+ - Blinding
206
+ - Data collection methods
207
+ - Data management
208
+ - Statistical methods
209
+ - Monitoring (data monitoring committee)
210
+ - Harms reporting
211
+ - Auditing
212
+ - Ethics and dissemination
213
+ - Ethics approval
214
+ - Consent procedures
215
+ - Confidentiality
216
+ - Dissemination plans
217
+
218
+ **Where to access:** https://www.spirit-statement.org/
219
+
220
+ ### STARD - Diagnostic Accuracy Studies
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+
222
+ **Full name:** Standards for Reporting of Diagnostic Accuracy Studies
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+
224
+ **When to use:** Studies evaluating diagnostic test accuracy
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+
226
+ **Latest version:** STARD 2015
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+
228
+ **Main checklist items (30 items):**
229
+ 1. Study design identification
230
+ 2. Background information and objectives
231
+ 3. Study design description
232
+ 4. Participant selection criteria and recruitment
233
+ 5. Data collection methods
234
+ 6. Index test description and execution
235
+ 7. Reference standard description
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+ 8. Rationale for choosing reference standard
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+ 9. Test result definition and cutoffs
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+ 10. Flow of participants with timing
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+ 11. Baseline demographic and clinical characteristics
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+ 12. Cross-tabulation of index test results by reference standard
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+ 13. Estimates of diagnostic accuracy with confidence intervals
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+ 14. Handling of indeterminate results
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+ 15. Adverse events from testing
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+
245
+ **Flow diagram:** Shows participant flow and test results
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+
247
+ **Where to access:** https://www.equator-network.org/reporting-guidelines/stard/
248
+
249
+ ### TRIPOD - Prediction Model Studies
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+
251
+ **Full name:** Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis
252
+
253
+ **When to use:** Studies developing, validating, or updating prediction models
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+
255
+ **Latest version:** TRIPOD 2015
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+
257
+ **Types of studies:**
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+ - Model development only
259
+ - Model development with validation
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+ - External validation of existing model
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+ - Model update
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+
263
+ **Main checklist items (22 items):**
264
+ 1. Title identifies study as prediction model study
265
+ 2. Abstract summarizes key elements
266
+ 3. Background and objectives
267
+ 4. Data source and participants
268
+ 5. Outcome definition
269
+ 6. Predictors (candidate and selected)
270
+ 7. Sample size justification
271
+ 8. Missing data handling
272
+ 9. Model building procedure
273
+ 10. Model specification (equation or algorithm)
274
+ 11. Model performance measures
275
+ 12. Risk groups if used
276
+ 13. Participant flow diagram
277
+ 14. Model development results
278
+ 15. Model performance
279
+ 16. Model updating if applicable
280
+
281
+ **Where to access:** https://www.tripod-statement.org/
282
+
283
+ ### ARRIVE - Animal Research
284
+
285
+ **Full name:** Animal Research: Reporting of In Vivo Experiments
286
+
287
+ **When to use:** All in vivo animal studies
288
+
289
+ **Latest version:** ARRIVE 2.0 (2020 update)
290
+
291
+ **Two sets of items:**
292
+
293
+ **ARRIVE Essential 10** (minimum requirements):
294
+ 1. Study design
295
+ 2. Sample size calculation
296
+ 3. Inclusion and exclusion criteria
297
+ 4. Randomization
298
+ 5. Blinding
299
+ 6. Outcome measures
300
+ 7. Statistical methods
301
+ 8. Experimental animals (species, strain, sex, age)
302
+ 9. Experimental procedures
303
+ 10. Results and interpretation
304
+
305
+ **ARRIVE Recommended Set** (additional items for full reporting):
306
+ - Abstract, background, objectives
307
+ - Ethics statement
308
+ - Housing and husbandry
309
+ - Animal care and monitoring
310
+ - Interpretation and generalizability
311
+ - Protocol registration
312
+ - Data access
313
+
314
+ **Where to access:** https://arriveguidelines.org/
315
+
316
+ ### CARE - Case Reports
317
+
318
+ **Full name:** CAse REport Guidelines
319
+
320
+ **When to use:** Case reports and case series
321
+
322
+ **Latest version:** CARE 2013
323
+
324
+ **Main checklist items (13 items):**
325
+ 1. Title with "case report"
326
+ 2. Abstract summarizing case
327
+ 3. Introduction with case background
328
+ 4. Patient information (demographics, primary concern)
329
+ 5. Clinical findings
330
+ 6. Timeline of events
331
+ 7. Diagnostic assessment
332
+ 8. Therapeutic intervention
333
+ 9. Follow-up and outcomes
334
+ 10. Discussion with strengths and limitations
335
+ 11. Patient perspective
336
+ 12. Informed consent
337
+
338
+ **Where to access:** https://www.care-statement.org/
339
+
340
+ ### SQUIRE - Quality Improvement Studies
341
+
342
+ **Full name:** Standards for QUality Improvement Reporting Excellence
343
+
344
+ **When to use:** Healthcare quality improvement reports
345
+
346
+ **Latest version:** SQUIRE 2.0 (2015)
347
+
348
+ **Main sections (18 items):**
349
+ 1. Title and abstract
350
+ 2. Introduction (problem description, available knowledge, rationale, objectives)
351
+ 3. Methods (context, intervention, study design, measures, analysis, ethical review)
352
+ 4. Results (intervention, outcomes)
353
+ 5. Discussion (summary, interpretation, limitations, conclusions)
354
+ 6. Other information (funding)
355
+
356
+ **Where to access:** http://www.squire-statement.org/
357
+
358
+ ### CHEERS - Economic Evaluations
359
+
360
+ **Full name:** Consolidated Health Economic Evaluation Reporting Standards
361
+
362
+ **When to use:** Health economic evaluations
363
+
364
+ **Latest version:** CHEERS 2022 (major update from 2013)
365
+
366
+ **Main checklist items (28 items):**
367
+ 1. Title identification as economic evaluation
368
+ 2. Abstract
369
+ 3. Background and objectives
370
+ 4. Target population and subgroups
371
+ 5. Setting and location
372
+ 6. Study perspective
373
+ 7. Comparators
374
+ 8. Time horizon
375
+ 9. Discount rate
376
+ 10. Selection of outcomes
377
+ 11. Measurement of effectiveness
378
+ 12. Measurement and valuation of costs
379
+ 13. Currency and price adjustments
380
+ 14. Choice of model
381
+ 15. Assumptions
382
+ 16. Analytical methods
383
+
384
+ **Where to access:** https://www.equator-network.org/reporting-guidelines/cheers/
385
+
386
+ ### SRQR - Qualitative Research
387
+
388
+ **Full name:** Standards for Reporting Qualitative Research
389
+
390
+ **When to use:** Qualitative and mixed methods research
391
+
392
+ **Latest version:** SRQR 2014
393
+
394
+ **Main sections:**
395
+ - Title and abstract
396
+ - Introduction (problem formulation, purpose)
397
+ - Methods (qualitative approach, researcher characteristics, context, sampling strategy, ethical issues, data collection, data analysis, trustworthiness)
398
+ - Results (synthesis and interpretation, links to empirical data)
399
+ - Discussion (limitations, implications)
400
+
401
+ **Alternative:** COREQ (Consolidated criteria for reporting qualitative research) for interviews and focus groups
402
+
403
+ **Where to access:** https://www.equator-network.org/reporting-guidelines/srqr/
404
+
405
+ ## How to Use Reporting Guidelines
406
+
407
+ ### During Study Planning
408
+
409
+ 1. **Identify relevant guideline** based on study design
410
+ 2. **Review checklist items** that require planning (e.g., randomization, blinding)
411
+ 3. **Design study** to ensure all required elements will be captured
412
+ 4. **Consider protocol guidelines** (e.g., SPIRIT for trials)
413
+
414
+ ### During Manuscript Drafting
415
+
416
+ 1. **Download checklist** from guideline website
417
+ 2. **Work through each item** systematically
418
+ 3. **Note where each item is addressed** in manuscript (page/line numbers)
419
+ 4. **Revise manuscript** to include missing items
420
+ 5. **Use flow diagrams** as appropriate
421
+
422
+ ### Before Submission
423
+
424
+ 1. **Complete formal checklist** with page numbers
425
+ 2. **Review all items** are adequately addressed
426
+ 3. **Include checklist** with submission if journal requires
427
+ 4. **Note guideline adherence** in cover letter or methods
428
+
429
+ ### Example Checklist Entry
430
+
431
+ ```
432
+ Item 7: Eligibility criteria for participants, and the settings and locations where the data were collected
433
+ Page 6, lines 112-125: "Participants were community-dwelling adults aged 60-85 years with mild cognitive impairment (MCI) as defined by Petersen criteria. Exclusion criteria included dementia diagnosis, major psychiatric disorders, or unstable medical conditions. Recruitment occurred from three memory clinics in Boston, MA, between January 2022 and December 2023."
434
+ ```
435
+
436
+ ## Finding the Right Guideline
437
+
438
+ ### EQUATOR Network Search
439
+
440
+ **Website:** https://www.equator-network.org/
441
+
442
+ **How to use:**
443
+ 1. Select your study design from the wizard
444
+ 2. Browse by health research category
445
+ 3. Search for specific keywords
446
+ 4. Filter by guideline status (development stage)
447
+
448
+ ### By Study Design
449
+
450
+ | If your study is a... | Use this guideline |
451
+ |----------------------|-------------------|
452
+ | Randomized controlled trial | CONSORT |
453
+ | Cohort, case-control, or cross-sectional study | STROBE |
454
+ | Systematic review or meta-analysis | PRISMA |
455
+ | Protocol for a trial | SPIRIT |
456
+ | Diagnostic accuracy study | STARD |
457
+ | Prediction model study | TRIPOD |
458
+ | Animal study | ARRIVE |
459
+ | Case report | CARE |
460
+ | Quality improvement study | SQUIRE |
461
+ | Economic evaluation | CHEERS |
462
+ | Qualitative research | SRQR or COREQ |
463
+
464
+ ### Multiple Guidelines
465
+
466
+ **Some studies may require multiple guidelines:**
467
+
468
+ **Example 1:** Pilot RCT with qualitative component
469
+ - CONSORT for quantitative arm
470
+ - SRQR for qualitative component
471
+
472
+ **Example 2:** Systematic review of diagnostic tests
473
+ - PRISMA for review methods
474
+ - STARD considerations for included studies
475
+
476
+ ## Extensions and Adaptations
477
+
478
+ Many reporting guidelines have extensions for specific contexts:
479
+
480
+ ### CONSORT Extensions (examples)
481
+
482
+ - **CONSORT for Abstracts**: Structured abstracts for RCT reports
483
+ - **CONSORT for Harms**: Reporting adverse events
484
+ - **CONSORT-EHEALTH**: eHealth interventions
485
+ - **CONSORT-SPI**: Social and psychological interventions
486
+
487
+ ### PRISMA Extensions (examples)
488
+
489
+ - **PRISMA-P**: Protocols for systematic reviews
490
+ - **PRISMA for Abstracts**: Conference abstracts
491
+ - **PRISMA-NMA**: Network meta-analyses
492
+ - **PRISMA-IPD**: Individual patient data reviews
493
+ - **PRISMA-S**: Search strategies
494
+ - **PRISMA-DTA**: Diagnostic test accuracy reviews
495
+
496
+ ### STROBE Extensions (examples)
497
+
498
+ - **STROBE-ME**: Molecular epidemiology
499
+ - **RECORD**: Routinely collected health data
500
+
501
+ ## Creating Flow Diagrams
502
+
503
+ ### CONSORT Flow Diagram
504
+
505
+ **Four stages:**
506
+ 1. **Enrollment**: Assessed for eligibility
507
+ 2. **Allocation**: Randomly assigned to groups
508
+ 3. **Follow-up**: Received intervention, lost to follow-up
509
+ 4. **Analysis**: Included in analysis
510
+
511
+ **Example:**
512
+ ```
513
+ Assessed for eligibility (n=250)
514
+
515
+ Excluded (n=50)
516
+ • Did not meet criteria (n=30)
517
+ • Declined to participate (n=15)
518
+ • Other reasons (n=5)
519
+
520
+ Randomized (n=200)
521
+ ├─────────────────┬─────────────────┐
522
+ ↓ ↓ ↓
523
+ Allocated to Allocated to Allocated to
524
+ Intervention A Intervention B Control
525
+ (n=67) (n=66) (n=67)
526
+ ↓ ↓ ↓
527
+ Lost to follow-up Lost to follow-up Lost to follow-up
528
+ (n=3) (n=5) (n=2)
529
+ ↓ ↓ ↓
530
+ Analyzed Analyzed Analyzed
531
+ (n=64) (n=61) (n=65)
532
+ ```
533
+
534
+ ### PRISMA Flow Diagram
535
+
536
+ **Stages:**
537
+ 1. **Identification**: Records from databases and registers
538
+ 2. **Screening**: Records screened, excluded
539
+ 3. **Included**: Studies included in review and synthesis
540
+
541
+ **New features in PRISMA 2020:**
542
+ - Separate tracking for database and register searches
543
+ - Tracking of duplicate removal
544
+ - Clear distinction between reports and studies
545
+
546
+ ## Common Mistakes and How to Avoid Them
547
+
548
+ ### Mistake 1: Not Using Guidelines at All
549
+
550
+ **Impact:** Missing critical information, lower chance of acceptance
551
+
552
+ **Solution:** Identify and use appropriate guideline from study planning stage
553
+
554
+ ### Mistake 2: Using Guidelines Only After Manuscript is Complete
555
+
556
+ **Impact:** May realize key data were not collected or documented
557
+
558
+ **Solution:** Review guidelines during study design and data collection
559
+
560
+ ### Mistake 3: Incomplete Checklist Completion
561
+
562
+ **Impact:** Missed items remain unreported
563
+
564
+ **Solution:** Systematically address every single checklist item
565
+
566
+ ### Mistake 4: Using Outdated Guidelines
567
+
568
+ **Impact:** Missing recent improvements in reporting standards
569
+
570
+ **Solution:** Always check for latest version on official guideline website
571
+
572
+ ### Mistake 5: Using Wrong Guideline for Study Design
573
+
574
+ **Impact:** Important design-specific elements not reported
575
+
576
+ **Solution:** Carefully match study design to appropriate guideline
577
+
578
+ ### Mistake 6: Not Submitting Checklist When Required
579
+
580
+ **Impact:** Editorial desk rejection or delays
581
+
582
+ **Solution:** Check journal submission guidelines and include checklist
583
+
584
+ ### Mistake 7: Generic Reporting Without Specificity
585
+
586
+ **Impact:** Insufficient detail for replication or appraisal
587
+
588
+ **Solution:** Provide specific, detailed information for each item
589
+
590
+ ## Journal Requirements
591
+
592
+ ### Many Journals Now Require:
593
+
594
+ 1. **Statement of adherence** to reporting guidelines in Methods
595
+ 2. **Completed checklist** uploaded as supplementary file
596
+ 3. **Page/line numbers** on checklist indicating where items are addressed
597
+ 4. **Flow diagrams** as figures in manuscript
598
+
599
+ ### Example Methods Statement:
600
+
601
+ ```
602
+ "This study is reported in accordance with the Strengthening the Reporting of
603
+ Observational Studies in Epidemiology (STROBE) statement. A completed STROBE
604
+ checklist is provided as Supplementary File 1."
605
+ ```
606
+
607
+ ### Journals with Strong Requirements:
608
+
609
+ - PLOS journals (require checklists for specific designs)
610
+ - BMJ (requires CONSORT, PRISMA, and others)
611
+ - The Lancet (requires adherence statements)
612
+ - JAMA and JAMA Network journals (require checklists)
613
+ - Nature portfolio journals (encourage guidelines)
614
+
615
+ ## Resources
616
+
617
+ ### Official Guideline Websites
618
+
619
+ - **EQUATOR Network**: https://www.equator-network.org/
620
+ - **CONSORT**: http://www.consort-statement.org/
621
+ - **STROBE**: https://www.strobe-statement.org/
622
+ - **PRISMA**: http://www.prisma-statement.org/
623
+ - **SPIRIT**: https://www.spirit-statement.org/
624
+ - **ARRIVE**: https://arriveguidelines.org/
625
+ - **CARE**: https://www.care-statement.org/
626
+
627
+ ### Training Materials
628
+
629
+ - EQUATOR Network provides webinars and training resources
630
+ - Many guidelines have explanatory papers published in medical journals
631
+ - Universities often provide workshops on reporting guidelines
632
+
633
+ ### Software Tools
634
+
635
+ - **Some reference managers** can insert reporting guideline citations
636
+ - **Covidence, RevMan** for systematic review reporting
637
+ - **PRISMA flow diagram generator**: http://prisma.thetacollaborative.ca/
638
+
639
+ ## Checklist: Using Reporting Guidelines
640
+
641
+ **Before starting your study:**
642
+ - [ ] Identified appropriate reporting guideline(s)
643
+ - [ ] Reviewed checklist items requiring prospective planning
644
+ - [ ] Designed study to capture all required elements
645
+ - [ ] Registered protocol if applicable
646
+
647
+ **During manuscript drafting:**
648
+ - [ ] Downloaded latest version of guideline checklist
649
+ - [ ] Systematically addressed each checklist item
650
+ - [ ] Created required flow diagram
651
+ - [ ] Noted where each item is addressed (page/line)
652
+
653
+ **Before submission:**
654
+ - [ ] Completed formal checklist with page numbers
655
+ - [ ] Verified all items adequately addressed
656
+ - [ ] Included adherence statement in Methods
657
+ - [ ] Prepared checklist as supplementary file if required
658
+ - [ ] Checked journal-specific requirements
659
+ - [ ] Mentioned guideline adherence in cover letter
660
+
661
+ ## Venue-Specific Reporting Requirements
662
+
663
+ ### Reporting Standards by Venue Type
664
+
665
+ | Venue Type | Guideline Use | Transparency Requirements |
666
+ |-----------|--------------|---------------------------|
667
+ | **Medical journals** | Mandatory (CONSORT, STROBE, etc.) | Checklist required at submission |
668
+ | **PLOS/BMC** | Mandatory for study types | Checklist uploaded as supplement |
669
+ | **Nature/Science** | Recommended | Methods completeness emphasized |
670
+ | **ML conferences** | No formal guidelines | Reproducibility details required |
671
+
672
+ ### ML Conference Reporting Standards
673
+
674
+ **NeurIPS/ICML/ICLR reproducibility requirements:**
675
+ - **Datasets**: Names, versions, access methods, preprocessing
676
+ - **Code**: Availability statement; GitHub common
677
+ - **Hyperparameters**: All settings reported (learning rate, batch size, etc.)
678
+ - **Seeds**: Random seeds for reproducibility
679
+ - **Computational resources**: GPUs used, training time
680
+ - **Statistical significance**: Error bars, confidence intervals, multiple runs
681
+ - **Broader Impact** statement (NeurIPS): Societal implications
682
+
683
+ **What to include (typically in appendix):**
684
+ - Complete hyperparameter settings
685
+ - Training details and convergence criteria
686
+ - Hardware specifications
687
+ - Software versions (PyTorch 2.0, etc.)
688
+ - Dataset splits and any preprocessing
689
+ - Evaluation metrics and protocols
690
+
691
+ ### Enforcement and Evaluation
692
+
693
+ **What gets checked:**
694
+ - **Medical journals**: Checklist uploaded; adherence statement in Methods; systematic completeness
695
+ - **PLOS/BMC**: Mandatory checklists for certain designs; reproducibility emphasized
696
+ - **High-impact**: Methods sufficiency for replication (checklist often not required)
697
+ - **ML conferences**: Reproducibility checklist (NeurIPS); code availability increasingly expected
698
+
699
+ **Common issues leading to rejection:**
700
+ - Missing required checklists (medical journals)
701
+ - Insufficient methods detail for reproduction
702
+ - Missing key information (randomization, blinding, power calculation)
703
+ - No data/code availability statement when required
704
+
705
+ **Methods statement examples:**
706
+
707
+ **Journal (STROBE):**
708
+ ```
709
+ This study followed STROBE reporting guidelines. Checklist provided in Supplement 1.
710
+ ```
711
+
712
+ **ML conference (reproducibility):**
713
+ ```
714
+ Code available at github.com/user/project. All hyperparameters in Appendix A.
715
+ Training used 4×A100 GPUs (~20 hours). Seeds: {42, 123, 456}.
716
+ ```
717
+
718
+ ### Pre-Submission Reporting Checklist
719
+
720
+ **For clinical trials (medical journals):**
721
+ - [ ] CONSORT checklist complete with page numbers
722
+ - [ ] Trial registration number in abstract and methods
723
+ - [ ] CONSORT flow diagram included
724
+ - [ ] Statistical analysis plan described
725
+ - [ ] Adherence statement in Methods
726
+
727
+ **For observational studies (medical/epidemiology):**
728
+ - [ ] STROBE checklist complete
729
+ - [ ] Study design clearly stated
730
+ - [ ] Statistical methods detailed
731
+ - [ ] Confounders addressed
732
+ - [ ] Adherence statement in Methods
733
+
734
+ **For systematic reviews:**
735
+ - [ ] PRISMA checklist complete
736
+ - [ ] PRISMA flow diagram included
737
+ - [ ] Protocol registered (PROSPERO)
738
+ - [ ] Search strategy documented
739
+ - [ ] Risk of bias assessment included
740
+
741
+ **For ML conference papers:**
742
+ - [ ] All datasets named with versions
743
+ - [ ] Code availability stated (GitHub link if available)
744
+ - [ ] Hyperparameters listed (appendix acceptable)
745
+ - [ ] Random seeds reported
746
+ - [ ] Computational resources specified
747
+ - [ ] Error bars/confidence intervals shown
748
+ - [ ] Broader Impact statement (if required)