scientific-writer 2.3.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
  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 +488 -0
  271. scientific_writer/.claude/skills/treatment-plans/SKILL.md +1536 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/STYLING_QUICK_REFERENCE.md +185 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +665 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +547 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/medical_treatment_plan.sty +222 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +774 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/one_page_treatment_plan.tex +193 -0
  278. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +799 -0
  279. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +753 -0
  280. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  281. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +756 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  283. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  284. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  285. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +655 -0
  286. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +485 -0
  287. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  288. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  289. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  290. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  291. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  294. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  295. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  296. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  297. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  298. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  299. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  300. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  301. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  302. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  303. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  304. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  305. scientific_writer/__init__.py +43 -0
  306. scientific_writer/api.py +393 -0
  307. scientific_writer/cli.py +326 -0
  308. scientific_writer/core.py +275 -0
  309. scientific_writer/models.py +76 -0
  310. scientific_writer/utils.py +289 -0
  311. scientific_writer-2.3.1.dist-info/METADATA +272 -0
  312. scientific_writer-2.3.1.dist-info/RECORD +315 -0
  313. scientific_writer-2.3.1.dist-info/WHEEL +4 -0
  314. scientific_writer-2.3.1.dist-info/entry_points.txt +2 -0
  315. scientific_writer-2.3.1.dist-info/licenses/LICENSE +22 -0
@@ -0,0 +1,663 @@
1
+ # ScholarEval Evaluation Framework
2
+
3
+ ## Overview
4
+
5
+ This document provides detailed evaluation criteria, rubrics, and quality indicators for each dimension of the ScholarEval framework. Use these standards when conducting systematic evaluations of scholarly work.
6
+
7
+ ---
8
+
9
+ ## Dimension 1: Problem Formulation & Research Questions
10
+
11
+ ### Quality Indicators
12
+
13
+ **Excellent (5):**
14
+ - Research question is specific, measurable, and clearly articulated
15
+ - Problem addresses significant gap in literature with high impact potential
16
+ - Scope is appropriate and feasible within constraints
17
+ - Novel contribution is clearly differentiated from existing work
18
+ - Theoretical or practical significance is compellingly justified
19
+
20
+ **Good (4):**
21
+ - Research question is clear with minor ambiguities
22
+ - Problem is relevant with moderate impact potential
23
+ - Scope is generally appropriate with minor feasibility concerns
24
+ - Contribution is identifiable though not groundbreaking
25
+ - Significance is adequately justified
26
+
27
+ **Adequate (3):**
28
+ - Research question is present but lacks specificity
29
+ - Problem relevance is unclear or incremental
30
+ - Scope may be too broad or narrow
31
+ - Contribution is unclear or overlaps heavily with existing work
32
+ - Significance justification is weak
33
+
34
+ **Needs Improvement (2):**
35
+ - Research question is vague or poorly defined
36
+ - Problem lacks clear relevance or significance
37
+ - Scope is inappropriate or infeasible
38
+ - Contribution is not articulated
39
+ - No clear justification for significance
40
+
41
+ **Poor (1):**
42
+ - No clear research question
43
+ - Problem is trivial or irrelevant
44
+ - Scope is fundamentally flawed
45
+ - No identifiable contribution
46
+ - No significance justification
47
+
48
+ ### Assessment Checklist
49
+
50
+ - [ ] Is the research question clearly stated?
51
+ - [ ] Can the question be answered with the proposed approach?
52
+ - [ ] Is the problem significant to the field?
53
+ - [ ] Is the scope feasible within resource constraints?
54
+ - [ ] Is the novelty/contribution clearly articulated?
55
+ - [ ] Are key assumptions explicitly stated?
56
+ - [ ] Are success criteria or expected outcomes defined?
57
+
58
+ ---
59
+
60
+ ## Dimension 2: Literature Review
61
+
62
+ ### Quality Indicators
63
+
64
+ **Excellent (5):**
65
+ - Comprehensive coverage of relevant literature across key areas
66
+ - Critical synthesis identifying patterns, contradictions, and gaps
67
+ - Literature is current (majority from last 3-5 years for rapidly evolving fields)
68
+ - Sources are authoritative and peer-reviewed
69
+ - Clear positioning of current work within scholarly conversation
70
+ - Identifies genuine research gaps that the work addresses
71
+
72
+ **Good (4):**
73
+ - Good coverage with minor gaps in key areas
74
+ - Mostly synthesis with some description
75
+ - Literature is mostly current with some older foundational works
76
+ - Sources are generally authoritative
77
+ - Work positioning is present but could be stronger
78
+ - Research gaps are identified but may not be critical
79
+
80
+ **Adequate (3):**
81
+ - Partial coverage with notable gaps
82
+ - More descriptive summarization than synthesis
83
+ - Literature mix of current and dated sources
84
+ - Mix of authoritative and less rigorous sources
85
+ - Weak positioning within existing literature
86
+ - Research gaps are vague or questionable
87
+
88
+ **Needs Improvement (2):**
89
+ - Minimal coverage with major gaps
90
+ - Purely descriptive without synthesis
91
+ - Literature is largely outdated
92
+ - Sources lack authority or rigor
93
+ - Little to no positioning of current work
94
+ - No clear research gaps identified
95
+
96
+ **Poor (1):**
97
+ - Inadequate or absent literature review
98
+ - No synthesis
99
+ - Outdated or inappropriate sources
100
+ - No engagement with scholarly conversation
101
+ - No gap identification
102
+
103
+ ### Assessment Checklist
104
+
105
+ - [ ] Does review cover all major relevant areas?
106
+ - [ ] Is literature synthesized rather than just summarized?
107
+ - [ ] Are sources current and authoritative?
108
+ - [ ] Are contrasting viewpoints presented?
109
+ - [ ] Are research gaps clearly identified?
110
+ - [ ] Is the current work positioned within existing literature?
111
+ - [ ] Is citation balance appropriate (not over-relying on few authors)?
112
+ - [ ] Are seminal/foundational works included?
113
+
114
+ ### Common Issues
115
+
116
+ - **Insufficient coverage**: Missing key papers or research streams
117
+ - **Descriptive listing**: Summarizing papers sequentially without synthesis
118
+ - **Outdated sources**: Relying on literature more than 5-10 years old
119
+ - **Cherry-picking**: Only citing work that supports hypothesis
120
+ - **Poor organization**: Lack of thematic or conceptual structure
121
+ - **Weak gap identification**: Gaps are trivial or not actually gaps
122
+
123
+ ---
124
+
125
+ ## Dimension 3: Methodology & Research Design
126
+
127
+ ### Quality Indicators
128
+
129
+ **Excellent (5):**
130
+ - Research design perfectly aligned with research questions
131
+ - Methods are rigorous, valid, and reliable
132
+ - Procedures are detailed enough for replication
133
+ - Controls, randomization, or triangulation appropriate
134
+ - Potential biases acknowledged and mitigated
135
+ - Ethical considerations addressed comprehensively
136
+ - Limitations are explicitly discussed
137
+
138
+ **Good (4):**
139
+ - Design is appropriate with minor alignment issues
140
+ - Methods are sound with small validity concerns
141
+ - Procedures are mostly replicable
142
+ - Some controls or validation present
143
+ - Major biases addressed
144
+ - Ethical considerations mentioned
145
+ - Some limitations discussed
146
+
147
+ **Adequate (3):**
148
+ - Design partially appropriate for questions
149
+ - Methods have notable validity concerns
150
+ - Procedures lack detail for full replication
151
+ - Limited controls or validation
152
+ - Bias mitigation is minimal
153
+ - Ethics addressed superficially
154
+ - Limitations minimally discussed
155
+
156
+ **Needs Improvement (2):**
157
+ - Design poorly aligned with research questions
158
+ - Methods have serious validity issues
159
+ - Procedures too vague to replicate
160
+ - No controls or validation
161
+ - Biases not addressed
162
+ - Ethical concerns not addressed
163
+ - No limitation discussion
164
+
165
+ **Poor (1):**
166
+ - Inappropriate or absent methodology
167
+ - Methods fundamentally flawed
168
+ - Not replicable
169
+ - No validity considerations
170
+ - No ethical considerations
171
+ - No acknowledgment of limitations
172
+
173
+ ### Assessment Checklist
174
+
175
+ - [ ] Is methodology appropriate for research questions?
176
+ - [ ] Are procedures described in sufficient detail?
177
+ - [ ] Can the study be replicated from the description?
178
+ - [ ] Are validity and reliability addressed?
179
+ - [ ] Are potential biases identified and mitigated?
180
+ - [ ] Are ethical considerations discussed?
181
+ - [ ] Are limitations acknowledged?
182
+ - [ ] Is sample size justified (for quantitative work)?
183
+ - [ ] Are qualitative methods rigorous (if applicable)?
184
+
185
+ ### Design-Specific Considerations
186
+
187
+ **Quantitative Studies:**
188
+ - Sample size with power analysis
189
+ - Control groups and randomization
190
+ - Measurement validity and reliability
191
+ - Statistical assumptions checking
192
+
193
+ **Qualitative Studies:**
194
+ - Sampling strategy and saturation
195
+ - Data collection procedures
196
+ - Coding and analysis framework
197
+ - Trustworthiness criteria (credibility, transferability, etc.)
198
+
199
+ **Mixed Methods:**
200
+ - Integration rationale
201
+ - Sequencing justification
202
+ - Data convergence strategy
203
+
204
+ ---
205
+
206
+ ## Dimension 4: Data Collection & Sources
207
+
208
+ ### Quality Indicators
209
+
210
+ **Excellent (5):**
211
+ - Data sources are highly credible and appropriate
212
+ - Sample size is sufficient and well-justified
213
+ - Data collection procedures are rigorous and systematic
214
+ - Data quality controls are in place
215
+ - Sampling strategy ensures representativeness
216
+ - Missing data is minimal and handled appropriately
217
+
218
+ **Good (4):**
219
+ - Data sources are credible with minor concerns
220
+ - Sample size is adequate
221
+ - Collection procedures are systematic
222
+ - Some quality controls present
223
+ - Sampling is reasonable
224
+ - Missing data is addressed
225
+
226
+ **Adequate (3):**
227
+ - Data sources are acceptable but not optimal
228
+ - Sample size is marginal
229
+ - Collection procedures lack some rigor
230
+ - Limited quality controls
231
+ - Sampling may have bias concerns
232
+ - Missing data handling is basic
233
+
234
+ **Needs Improvement (2):**
235
+ - Data sources have credibility issues
236
+ - Sample size is insufficient
237
+ - Collection procedures are ad hoc
238
+ - No quality controls
239
+ - Sampling is clearly biased
240
+ - Missing data not addressed
241
+
242
+ **Poor (1):**
243
+ - Data sources are inappropriate or unreliable
244
+ - Sample size is inadequate
245
+ - Collection is unsystematic
246
+ - No quality considerations
247
+ - Sampling is fundamentally flawed
248
+ - Excessive missing data
249
+
250
+ ### Assessment Checklist
251
+
252
+ - [ ] Are data sources credible and appropriate?
253
+ - [ ] Is sample size sufficient for conclusions?
254
+ - [ ] Is sampling strategy clearly described?
255
+ - [ ] Is the sample representative of target population?
256
+ - [ ] Are data collection procedures systematic?
257
+ - [ ] Are data quality controls described?
258
+ - [ ] Is missing data addressed?
259
+ - [ ] Are any potential data biases discussed?
260
+
261
+ ---
262
+
263
+ ## Dimension 5: Analysis & Interpretation
264
+
265
+ ### Quality Indicators
266
+
267
+ **Excellent (5):**
268
+ - Analytical methods perfectly suited to data and questions
269
+ - Analysis is rigorous with appropriate techniques
270
+ - Results interpretation is logical and well-supported
271
+ - Alternative explanations are considered
272
+ - Claims are proportionate to evidence
273
+ - Assumptions are validated
274
+ - Analysis is transparent and reproducible
275
+
276
+ **Good (4):**
277
+ - Methods are appropriate with minor issues
278
+ - Analysis is sound
279
+ - Interpretation is mostly logical
280
+ - Some alternatives considered
281
+ - Claims generally match evidence
282
+ - Key assumptions checked
283
+ - Analysis is mostly transparent
284
+
285
+ **Adequate (3):**
286
+ - Methods are acceptable but not optimal
287
+ - Analysis has some technical issues
288
+ - Interpretation has logical gaps
289
+ - Alternatives not thoroughly explored
290
+ - Some claims exceed evidence
291
+ - Assumptions not fully validated
292
+ - Analysis transparency is limited
293
+
294
+ **Needs Improvement (2):**
295
+ - Methods are questionable for data/questions
296
+ - Analysis has significant technical flaws
297
+ - Interpretation is poorly supported
298
+ - No alternative explanations
299
+ - Claims significantly exceed evidence
300
+ - Assumptions not checked
301
+ - Analysis is not transparent
302
+
303
+ **Poor (1):**
304
+ - Methods are inappropriate
305
+ - Analysis is fundamentally flawed
306
+ - Interpretation is illogical
307
+ - No consideration of alternatives
308
+ - Claims unsupported by evidence
309
+ - No assumption validation
310
+ - Analysis is opaque
311
+
312
+ ### Assessment Checklist
313
+
314
+ - [ ] Are analytical methods appropriate?
315
+ - [ ] Are statistical tests/qualitative methods properly applied?
316
+ - [ ] Are assumptions tested?
317
+ - [ ] Is interpretation logical and well-supported?
318
+ - [ ] Are alternative explanations considered?
319
+ - [ ] Do claims align with evidence strength?
320
+ - [ ] Is analysis reproducible from description?
321
+ - [ ] Are uncertainties acknowledged?
322
+
323
+ ### Quantitative Analysis
324
+
325
+ - Appropriate statistical tests
326
+ - Assumptions checked (normality, homogeneity, etc.)
327
+ - Effect sizes reported
328
+ - Confidence intervals provided
329
+ - Multiple testing corrections (if applicable)
330
+ - Model diagnostics performed
331
+
332
+ ### Qualitative Analysis
333
+
334
+ - Coding framework is clear
335
+ - Inter-rater reliability (if applicable)
336
+ - Saturation discussed
337
+ - Negative cases examined
338
+ - Member checking or validation
339
+ - Clear audit trail
340
+
341
+ ---
342
+
343
+ ## Dimension 6: Results & Findings
344
+
345
+ ### Quality Indicators
346
+
347
+ **Excellent (5):**
348
+ - Results are clearly and comprehensively presented
349
+ - Visualizations are effective and appropriate
350
+ - Statistical or qualitative rigor is evident
351
+ - Key findings are highlighted effectively
352
+ - Results directly address research questions
353
+ - Patterns and relationships are clearly shown
354
+ - Negative and null results are reported
355
+
356
+ **Good (4):**
357
+ - Results are clear with minor presentation issues
358
+ - Visualizations are generally effective
359
+ - Rigor is present
360
+ - Main findings are identifiable
361
+ - Results mostly address questions
362
+ - Patterns are shown
363
+ - Some negative results included
364
+
365
+ **Adequate (3):**
366
+ - Results presentation is adequate but could be clearer
367
+ - Visualizations are basic or have issues
368
+ - Rigor is questionable in places
369
+ - Findings are present but not emphasized
370
+ - Partial alignment with questions
371
+ - Patterns are unclear
372
+ - Negative results may be omitted
373
+
374
+ **Needs Improvement (2):**
375
+ - Results presentation is unclear or confusing
376
+ - Visualizations are poor or misleading
377
+ - Lack of rigor
378
+ - Findings are difficult to identify
379
+ - Weak alignment with questions
380
+ - No clear patterns
381
+ - Only positive results shown
382
+
383
+ **Poor (1):**
384
+ - Results are poorly presented or absent
385
+ - Visualizations are inappropriate or missing
386
+ - No evidence of rigor
387
+ - Findings are unclear
388
+ - Results don't address questions
389
+ - No identifiable patterns
390
+ - Results appear selective
391
+
392
+ ### Assessment Checklist
393
+
394
+ - [ ] Are results clearly presented?
395
+ - [ ] Do results directly address research questions?
396
+ - [ ] Are visualizations appropriate and effective?
397
+ - [ ] Are key findings highlighted?
398
+ - [ ] Are negative/null results reported?
399
+ - [ ] Is appropriate precision reported (p-values, CIs, effect sizes)?
400
+ - [ ] Are qualitative findings supported by data excerpts?
401
+ - [ ] Is there evidence of selective reporting?
402
+
403
+ ### Presentation Quality
404
+
405
+ **Tables:**
406
+ - Clear labels and captions
407
+ - Appropriate precision
408
+ - Organized logically
409
+ - Not overly complex
410
+
411
+ **Figures:**
412
+ - Clear axes and legends
413
+ - Appropriate chart type
414
+ - Professional appearance
415
+ - Accessible (color-blind friendly)
416
+
417
+ **Text:**
418
+ - Highlights key findings
419
+ - Avoids redundancy with tables/figures
420
+ - Uses appropriate statistical language
421
+
422
+ ---
423
+
424
+ ## Dimension 7: Scholarly Writing & Presentation
425
+
426
+ ### Quality Indicators
427
+
428
+ **Excellent (5):**
429
+ - Writing is clear, concise, and precise
430
+ - Organization is logical with excellent flow
431
+ - Academic tone is appropriate and consistent
432
+ - Grammar and mechanics are flawless
433
+ - Technical terms are used correctly
434
+ - Accessible to target audience
435
+ - Abstract/summary is comprehensive and accurate
436
+
437
+ **Good (4):**
438
+ - Writing is clear with minor awkwardness
439
+ - Organization is logical with good flow
440
+ - Tone is mostly appropriate
441
+ - Few grammar/mechanical errors
442
+ - Technical terms mostly correct
443
+ - Generally accessible
444
+ - Abstract is adequate
445
+
446
+ **Adequate (3):**
447
+ - Writing is understandable but has clarity issues
448
+ - Organization has some logical gaps
449
+ - Tone inconsistencies
450
+ - Noticeable grammar/mechanical errors
451
+ - Some technical term misuse
452
+ - Accessibility issues for target audience
453
+ - Abstract is incomplete or vague
454
+
455
+ **Needs Improvement (2):**
456
+ - Writing is often unclear or verbose
457
+ - Poor organization and flow
458
+ - Tone is inappropriate
459
+ - Frequent grammar/mechanical errors
460
+ - Technical terminology problems
461
+ - Not accessible to target audience
462
+ - Abstract is poor or missing
463
+
464
+ **Poor (1):**
465
+ - Writing is unclear and difficult to follow
466
+ - No clear organization
467
+ - Tone is inappropriate
468
+ - Pervasive grammar/mechanical errors
469
+ - Incorrect technical terminology
470
+ - Inaccessible
471
+ - No adequate abstract
472
+
473
+ ### Assessment Checklist
474
+
475
+ - [ ] Is writing clear and concise?
476
+ - [ ] Is organization logical?
477
+ - [ ] Is tone appropriate for academic writing?
478
+ - [ ] Are grammar and mechanics correct?
479
+ - [ ] Are technical terms used appropriately?
480
+ - [ ] Is jargon explained when necessary?
481
+ - [ ] Does abstract accurately summarize the work?
482
+ - [ ] Are transitions between sections smooth?
483
+ - [ ] Is the target audience clear?
484
+
485
+ ### Common Writing Issues
486
+
487
+ - **Wordiness**: Unnecessarily complex or lengthy prose
488
+ - **Passive voice overuse**: Reduces clarity and directness
489
+ - **Paragraph structure**: Lack of topic sentences or coherence
490
+ - **Redundancy**: Repeating information unnecessarily
491
+ - **Logical flow**: Poor transitions between ideas
492
+ - **Precision**: Vague or ambiguous language
493
+ - **Accessibility**: Too technical or not technical enough
494
+
495
+ ---
496
+
497
+ ## Dimension 8: Citations & References
498
+
499
+ ### Quality Indicators
500
+
501
+ **Excellent (5):**
502
+ - All claims are appropriately cited
503
+ - Sources are authoritative and current
504
+ - Citations are accurate and complete
505
+ - Diverse perspectives are represented
506
+ - Citation format is consistent and correct
507
+ - Balance between self-citation and others
508
+ - Primary sources used appropriately
509
+
510
+ **Good (4):**
511
+ - Most claims are cited
512
+ - Sources are generally authoritative
513
+ - Few citation errors
514
+ - Reasonable diversity of sources
515
+ - Format is mostly consistent
516
+ - Citation balance is good
517
+ - Mix of primary and secondary sources
518
+
519
+ **Adequate (3):**
520
+ - Some claims lack citations
521
+ - Source quality is mixed
522
+ - Several citation errors
523
+ - Limited source diversity
524
+ - Format inconsistencies
525
+ - Citation balance issues
526
+ - Over-reliance on secondary sources
527
+
528
+ **Needs Improvement (2):**
529
+ - Many claims uncited
530
+ - Sources are questionable
531
+ - Numerous citation errors
532
+ - Narrow source base
533
+ - Format is inconsistent
534
+ - Excessive self-citation or narrow citing
535
+ - Inappropriate sources (e.g., only secondary)
536
+
537
+ **Poor (1):**
538
+ - Inadequate citations
539
+ - Unreliable sources
540
+ - Pervasive citation errors
541
+ - Minimal source diversity
542
+ - No consistent format
543
+ - Severe citation imbalance
544
+ - Inappropriate source types
545
+
546
+ ### Assessment Checklist
547
+
548
+ - [ ] Are all factual claims cited?
549
+ - [ ] Are citations to primary sources when appropriate?
550
+ - [ ] Are sources authoritative and peer-reviewed?
551
+ - [ ] Is there balance in perspectives cited?
552
+ - [ ] Are citations accurate (authors, dates, pages)?
553
+ - [ ] Is citation format consistent?
554
+ - [ ] Are self-citations appropriate (typically <20%)?
555
+ - [ ] Are sources current (for time-sensitive topics)?
556
+ - [ ] Are classic/seminal works included where relevant?
557
+
558
+ ### Citation Quality Assessment
559
+
560
+ **Source Types (in order of preference for most academic work):**
561
+ 1. Peer-reviewed journal articles
562
+ 2. Academic books from reputable publishers
563
+ 3. Conference proceedings (field-dependent)
564
+ 4. Technical reports from reputable institutions
565
+ 5. Dissertations/theses
566
+ 6. Preprints (with caution, field-dependent)
567
+ 7. Grey literature (limited use)
568
+ 8. Websites (rarely appropriate, except for factual data)
569
+
570
+ **Red Flags:**
571
+ - Wikipedia as a primary source
572
+ - Excessive self-citation (>30%)
573
+ - Only citing papers that support hypothesis
574
+ - Outdated sources when current ones exist
575
+ - Missing key papers in the field
576
+ - Citing abstracts only when full papers are available
577
+ - Inconsistent or incorrect citation format
578
+
579
+ ---
580
+
581
+ ## Cross-Cutting Considerations
582
+
583
+ ### Reproducibility
584
+
585
+ Assess across dimensions:
586
+ - Are methods detailed enough to replicate?
587
+ - Are data and code available (or availability explained)?
588
+ - Are analysis steps transparent?
589
+ - Are materials/instruments specified?
590
+
591
+ ### Ethics
592
+
593
+ Consider:
594
+ - IRB approval (for human subjects)
595
+ - Informed consent
596
+ - Privacy and confidentiality
597
+ - Conflicts of interest
598
+ - Research integrity
599
+ - Data sharing ethics
600
+
601
+ ### Bias and Limitations
602
+
603
+ Evaluate whether:
604
+ - Potential biases are acknowledged
605
+ - Limitations are discussed honestly
606
+ - Boundary conditions are specified
607
+ - Generalizability is appropriately claimed
608
+
609
+ ### Impact and Significance
610
+
611
+ Consider:
612
+ - Theoretical contribution
613
+ - Practical implications
614
+ - Policy relevance
615
+ - Methodological innovation
616
+ - Field advancement
617
+
618
+ ---
619
+
620
+ ## Scoring Guidelines
621
+
622
+ ### Dimension Weighting (Suggested, Adjust by Context)
623
+
624
+ - Problem Formulation: 15%
625
+ - Literature Review: 15%
626
+ - Methodology: 20%
627
+ - Data Collection: 10%
628
+ - Analysis: 15%
629
+ - Results: 10%
630
+ - Writing: 10%
631
+ - Citations: 5%
632
+
633
+ ### Overall Assessment Thresholds
634
+
635
+ - **Exceptional (4.5-5.0)**: Ready for top-tier publication
636
+ - **Strong (4.0-4.4)**: Publication-ready with minor revisions
637
+ - **Good (3.5-3.9)**: Major revisions required, promising work
638
+ - **Acceptable (3.0-3.4)**: Significant revisions needed
639
+ - **Weak (2.0-2.9)**: Fundamental issues, major rework required
640
+ - **Poor (<2.0)**: Not suitable for publication without complete revision
641
+
642
+ ### Contextual Adjustments
643
+
644
+ Adjust standards based on:
645
+ - **Stage**: Proposal < Draft < Final submission
646
+ - **Venue**: Student thesis < Conference < Journal < Top-tier journal
647
+ - **Type**: Theoretical < Empirical < Meta-analysis
648
+ - **Field**: Standards vary by discipline
649
+ - **Purpose**: Educational < Professional < Publication
650
+
651
+ ---
652
+
653
+ ## Using This Framework
654
+
655
+ 1. **Read the work thoroughly** before beginning evaluation
656
+ 2. **Score each dimension** using the 5-point scale
657
+ 3. **Document evidence** for each score with specific examples
658
+ 4. **Consider context** and adjust expectations appropriately
659
+ 5. **Synthesize findings** across dimensions
660
+ 6. **Provide actionable feedback** prioritized by impact
661
+ 7. **Balance criticism with recognition** of strengths
662
+
663
+ This framework is a guide, not a rigid checklist. Professional judgment should always be applied in context.