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

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  1. scientific_writer/.claude/WRITER.md +748 -0
  2. scientific_writer/.claude/settings.local.json +30 -0
  3. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  4. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  5. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  6. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  7. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  8. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  9. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  10. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  16. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  17. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  18. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  19. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  31. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  39. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  47. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  48. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  49. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  50. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  98. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  106. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  118. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  174. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  177. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  182. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  183. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  184. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  188. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  189. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  192. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  193. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  194. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  195. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  196. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  197. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
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  281. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  283. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  287. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  288. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
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  292. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  294. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
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  296. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  297. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  298. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
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  300. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  301. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  302. scientific_writer/__init__.py +1 -1
  303. scientific_writer/api.py +9 -5
  304. scientific_writer/cli.py +9 -5
  305. scientific_writer/core.py +28 -5
  306. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/METADATA +1 -1
  307. scientific_writer-2.2.3.dist-info/RECORD +312 -0
  308. scientific_writer-2.2.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,456 @@
1
+ % Treatment Plan Standards and Best Practices
2
+ % Professional guidelines for treatment plan documentation
3
+ % Last updated: 2025
4
+
5
+ # Treatment Plan Standards
6
+
7
+ ## Overview
8
+
9
+ Treatment plans are comprehensive documents that outline systematic approaches to addressing patient health conditions through evidence-based interventions, measurable goals, and structured follow-up. This reference provides professional standards, documentation requirements, and legal considerations for creating high-quality treatment plans across all medical specialties.
10
+
11
+ ## Core Documentation Standards
12
+
13
+ ### 1. Essential Components
14
+
15
+ All treatment plans must include:
16
+
17
+ #### Patient Information (De-identified for Sharing)
18
+ - Unique patient identifier (not name or MRN)
19
+ - Age range (not exact birth date)
20
+ - Relevant demographics
21
+ - Date of plan creation
22
+ - Provider name and credentials
23
+ - HIPAA compliance statement
24
+
25
+ #### Diagnosis and Assessment
26
+ - Primary diagnosis with ICD-10 code
27
+ - Secondary diagnoses and comorbidities
28
+ - Severity classification or staging
29
+ - Functional assessment and baseline status
30
+ - Risk stratification
31
+ - Prognostic considerations
32
+
33
+ #### Treatment Goals (SMART Format)
34
+ - **Specific**: Clearly defined outcomes
35
+ - **Measurable**: Quantifiable metrics or observable criteria
36
+ - **Achievable**: Realistic given patient circumstances
37
+ - **Relevant**: Aligned with patient values and priorities
38
+ - **Time-bound**: Defined timeframe for achievement
39
+
40
+ Short-term goals (weeks to 3 months) and long-term goals (3-12+ months) should be distinguished.
41
+
42
+ #### Interventions
43
+ - **Pharmacological**: Specific medications, doses, frequencies, rationales
44
+ - **Non-pharmacological**: Lifestyle modifications, behavioral interventions, education
45
+ - **Procedural**: Planned procedures, specialist referrals, diagnostic testing
46
+
47
+ #### Timeline and Schedule
48
+ - Treatment phases with durations
49
+ - Appointment frequency
50
+ - Milestone assessments
51
+ - Expected treatment duration
52
+
53
+ #### Monitoring Parameters
54
+ - Clinical outcomes to track
55
+ - Assessment tools and scales
56
+ - Monitoring frequency
57
+ - Intervention thresholds
58
+
59
+ #### Expected Outcomes
60
+ - Primary outcome measures
61
+ - Success criteria
62
+ - Timeline for improvement
63
+ - Criteria for treatment modification
64
+
65
+ #### Follow-up Plan
66
+ - Scheduled appointments
67
+ - Communication protocols
68
+ - Emergency procedures
69
+ - Transition planning
70
+
71
+ #### Patient Education
72
+ - Condition understanding
73
+ - Self-management skills
74
+ - Warning signs
75
+ - Resources and support
76
+
77
+ #### Risk Mitigation
78
+ - Potential adverse effects
79
+ - Safety monitoring
80
+ - Emergency action plans
81
+ - Complication prevention
82
+
83
+ ### 2. Professional Documentation Standards
84
+
85
+ #### Clarity and Precision
86
+ - Use professional medical terminology appropriately
87
+ - Define abbreviations on first use
88
+ - Avoid ambiguous language
89
+ - Specific rather than vague descriptions
90
+
91
+ **Good Example**: "Reduce HbA1c from 8.5% to <7% within 3 months"
92
+ **Poor Example**: "Improve diabetes control"
93
+
94
+ #### Completeness
95
+ - Address all relevant aspects of condition
96
+ - Include rationale for treatment choices
97
+ - Document shared decision-making
98
+ - Address patient preferences and concerns
99
+
100
+ #### Accuracy
101
+ - Factually correct information
102
+ - Current evidence-based recommendations
103
+ - Appropriate dosing and frequencies
104
+ - Correct ICD-10 and CPT codes
105
+
106
+ #### Timeliness
107
+ - Plans created at diagnosis or treatment initiation
108
+ - Updated after significant clinical changes
109
+ - Regular scheduled updates (quarterly to annually)
110
+ - Dated and signed promptly
111
+
112
+ #### Legibility and Organization
113
+ - Professional formatting
114
+ - Logical flow and structure
115
+ - Consistent use of headings and sections
116
+ - Easy to locate key information
117
+
118
+ ### 3. Legal and Regulatory Requirements
119
+
120
+ #### Medical Necessity Documentation
121
+ Treatment plans must demonstrate:
122
+ - Appropriateness of interventions for diagnosis
123
+ - Evidence supporting treatment choices
124
+ - Expected outcomes justify costs and risks
125
+ - Frequency and duration are reasonable
126
+ - Less invasive options considered
127
+
128
+ #### Informed Consent Documentation
129
+ Record that patient:
130
+ - Understands diagnosis and prognosis
131
+ - Aware of treatment options, risks, and benefits
132
+ - Knows alternatives to proposed treatment
133
+ - Had opportunity to ask questions
134
+ - Voluntarily agrees to treatment plan
135
+
136
+ #### Privacy and Confidentiality (HIPAA)
137
+ - Protected Health Information (PHI) safeguarded
138
+ - De-identification for sharing:
139
+ - Remove 18 HIPAA identifiers per Safe Harbor method
140
+ - Names, dates (except year), geographic subdivisions smaller than state
141
+ - Contact information (phone, fax, email, addresses)
142
+ - Social Security numbers, medical record numbers, account numbers
143
+ - Biometric identifiers, photos, other unique identifiers
144
+ - Access limited to those with treatment, payment, or operations need
145
+ - Patient authorization for non-routine disclosures
146
+
147
+ #### Billing and Reimbursement Support
148
+ - ICD-10 diagnosis codes for all conditions
149
+ - CPT codes for procedures
150
+ - Documentation of medical necessity
151
+ - Justification for level of service
152
+ - Compliance with payer-specific requirements
153
+
154
+ #### Quality Measure Reporting
155
+ Enable extraction of quality metrics:
156
+ - HEDIS measures (diabetes HbA1c testing, BP control, etc.)
157
+ - CMS quality reporting (MIPS, ACO measures)
158
+ - Disease-specific quality indicators
159
+ - Patient safety indicators
160
+
161
+ #### Liability Protection
162
+ Defensible documentation includes:
163
+ - Rationale for clinical decisions
164
+ - Consideration of differential diagnosis
165
+ - Risk-benefit analysis
166
+ - Patient education and warnings
167
+ - Follow-up plan for abnormal findings
168
+ - Addressing non-adherence or patient refusal
169
+
170
+ ## Professional Practice Standards
171
+
172
+ ### Joint Commission Standards
173
+
174
+ #### Patient-Centered Care
175
+ - Treatment plans developed with patient participation
176
+ - Goals reflect patient values and preferences
177
+ - Cultural and linguistic needs addressed
178
+ - Health literacy appropriate communication
179
+
180
+ #### Multidisciplinary Coordination
181
+ - Input from relevant disciplines
182
+ - Clear role delineation
183
+ - Communication among team members
184
+ - Coordinated interventions
185
+
186
+ #### Evidence-Based Practice
187
+ - Interventions based on current evidence
188
+ - Clinical practice guidelines followed
189
+ - Variation from guidelines documented and justified
190
+ - Literature supports treatment choices
191
+
192
+ ### Commission on Accreditation of Rehabilitation Facilities (CARF)
193
+
194
+ For rehabilitation treatment plans:
195
+ - Individualized based on comprehensive assessment
196
+ - Measurable, achievable, time-specific goals
197
+ - Regular team review and modification
198
+ - Patient and family involvement
199
+ - Transition and discharge planning
200
+
201
+ ### Centers for Medicare & Medicaid Services (CMS)
202
+
203
+ #### Conditions of Participation
204
+ - Physician orders for treatment
205
+ - Periodic review and revision
206
+ - Progress toward goals documented
207
+ - Care plan accessible to all team members
208
+
209
+ #### Documentation Requirements
210
+ - Legible (typed or clear handwriting)
211
+ - Dated and authenticated (signed)
212
+ - Amendments/corrections properly marked
213
+ - Retention per state law (typically 7-10 years, longer for minors)
214
+
215
+ ## Medical Specialty Standards
216
+
217
+ ### Primary Care
218
+ - Annual comprehensive assessment and plan update
219
+ - Chronic disease management protocols
220
+ - Preventive care integration
221
+ - Medication reconciliation
222
+ - Care coordination with specialists
223
+
224
+ ### Behavioral Health
225
+ - Mental status examination
226
+ - Psychiatric diagnoses per DSM-5 criteria
227
+ - Suicide/homicide risk assessment and safety planning
228
+ - Measurable behavioral outcomes
229
+ - Crisis intervention plan
230
+ - Substance use assessment
231
+ - 42 CFR Part 2 compliance for substance use treatment
232
+
233
+ ### Rehabilitation
234
+ - Functional assessments (FIM, Barthel Index, etc.)
235
+ - Activity limitations and participation restrictions
236
+ - Short-term and long-term functional goals
237
+ - Therapy frequency, intensity, duration
238
+ - Home exercise program
239
+ - Assistive devices and DME
240
+ - Discharge criteria
241
+
242
+ ### Surgical/Perioperative
243
+ - Indication for surgery documented
244
+ - Preoperative risk assessment (ASA, RCRI)
245
+ - Medical optimization plan
246
+ - Enhanced Recovery After Surgery (ERAS) protocols when applicable
247
+ - Postoperative milestones
248
+ - Discharge criteria and planning
249
+
250
+ ### Pain Management
251
+ - Comprehensive pain assessment (location, intensity, quality, temporal pattern, impact)
252
+ - Pain type (nociceptive, neuropathic, mixed)
253
+ - Multimodal analgesia approach
254
+ - Opioid risk assessment (ORT, SOAPP)
255
+ - If opioids: CDC guidelines compliance, treatment agreement, UDS, PDMP
256
+ - Functional goals (not just pain scores)
257
+ - Psychological screening and intervention
258
+
259
+ ## Quality Indicators for Treatment Plans
260
+
261
+ ### Completeness Metrics
262
+ - All required sections present (100%)
263
+ - Goals meet SMART criteria ($\geq$90%)
264
+ - Interventions have clear rationales ($\geq$95%)
265
+ - Monitoring plan includes frequency ($\geq$95%)
266
+ - Patient education documented (100%)
267
+
268
+ ### Clinical Quality Metrics
269
+ - Evidence-based interventions ($\geq$90%)
270
+ - Guideline-concordant care ($\geq$85%)
271
+ - Avoidance of low-value care (100%)
272
+ - Appropriate preventive care included ($\geq$95%)
273
+
274
+ ### Patient-Centered Metrics
275
+ - Patient preferences documented ($\geq$90%)
276
+ - Shared decision-making noted ($\geq$85%)
277
+ - Culturally appropriate care (100%)
278
+ - Health literacy addressed ($\geq$90%)
279
+
280
+ ### Safety Metrics
281
+ - Risk mitigation strategies present (100%)
282
+ - Medication safety addressed (100%)
283
+ - Emergency procedures documented (100%)
284
+ - Red flags/warning signs communicated (100%)
285
+
286
+ ## Common Documentation Deficiencies and Solutions
287
+
288
+ ### Problem: Vague Goals
289
+ **Deficiency**: "Improve diabetes"
290
+ **Solution**: "Reduce HbA1c from 8.5% to <7% within 3 months through medication intensification and lifestyle modification"
291
+
292
+ ### Problem: Missing Rationales
293
+ **Deficiency**: Lists medications without explanation
294
+ **Solution**: "Metformin 1000mg BID - first-line therapy for T2DM, reduces hepatic glucose production, target dose for HbA1c reduction"
295
+
296
+ ### Problem: No Timeline
297
+ **Deficiency**: Goals without timeframes
298
+ **Solution**: "Short-term (3 months): HbA1c <7.5%; Long-term (6 months): HbA1c <7%"
299
+
300
+ ### Problem: Incomplete Monitoring
301
+ **Deficiency**: "Monitor labs"
302
+ **Solution**: "HbA1c every 3 months until at goal, then every 6 months; CMP every 6 months to monitor renal function on metformin and ACE inhibitor"
303
+
304
+ ### Problem: Absent Patient Education
305
+ **Deficiency**: No documentation of education provided
306
+ **Solution**: Dedicated section documenting: condition education, self-management skills taught, warning signs communicated, resources provided
307
+
308
+ ### Problem: Missing Safety Planning
309
+ **Deficiency**: No risk mitigation
310
+ **Solution**: Specific safety concerns addressed (e.g., hypoglycemia risk with insulin, monitoring plan, patient taught recognition and treatment)
311
+
312
+ ## Electronic Health Record (EHR) Integration
313
+
314
+ ### Structured Data Entry
315
+ - Use templates for consistency
316
+ - Coded diagnoses (ICD-10), procedures (CPT)
317
+ - Structured goals enable outcome tracking
318
+ - Discrete medication fields (name, dose, route, frequency)
319
+
320
+ ### Clinical Decision Support
321
+ - Evidence-based order sets
322
+ - Drug-drug interaction alerts
323
+ - Guideline reminders
324
+ - Quality measure tracking
325
+
326
+ ### Care Plan Sharing
327
+ - Patient portal access (patient-friendly version)
328
+ - Interoperability standards (C-CDA)
329
+ - Shared with care team
330
+ - Transitions of care summary
331
+
332
+ ## Audit and Peer Review
333
+
334
+ ### Internal Quality Review
335
+ - Random sample chart audits (e.g., 5% quarterly)
336
+ - Checklist-based review (completeness, quality)
337
+ - Feedback to providers
338
+ - Continuous quality improvement
339
+
340
+ ### External Review
341
+ - Payer audits (documentation supports billing)
342
+ - Regulatory surveys (Joint Commission, CMS)
343
+ - Malpractice case review
344
+ - Peer review for privileging/credentialing
345
+
346
+ ### Audit Criteria
347
+ - Documentation completeness
348
+ - Clinical appropriateness
349
+ - Regulatory compliance
350
+ - Billing integrity
351
+ - Patient safety
352
+
353
+ ## Treatment Plan Revision and Updates
354
+
355
+ ### When to Update Treatment Plans
356
+
357
+ **Scheduled Updates**:
358
+ - Chronic disease management: Every 3-6 months minimum
359
+ - Behavioral health: Every 30-90 days depending on acuity
360
+ - Rehabilitation: Weekly to biweekly during active therapy
361
+ - Annual comprehensive update for all chronic conditions
362
+
363
+ **Triggered Updates**:
364
+ - Significant change in clinical status
365
+ - New diagnosis
366
+ - Treatment goals achieved or not progressing
367
+ - Patient request or preference change
368
+ - Hospitalization or emergency department visit
369
+ - Medication changes or adverse events
370
+
371
+ ### Documentation of Changes
372
+ - Date of revision
373
+ - Reason for update
374
+ - What changed (goals, interventions, timeline)
375
+ - Provider signature
376
+ - Maintain prior versions for record
377
+
378
+ ## Specialty-Specific Requirements
379
+
380
+ ### Diabetes Management Plans
381
+ - HbA1c targets individualized
382
+ - Complication screening schedule (eyes, feet, kidneys)
383
+ - Self-monitoring blood glucose frequency
384
+ - Hypoglycemia recognition and treatment
385
+ - Sick day management
386
+
387
+ ### Heart Failure Plans
388
+ - GDMT (guideline-directed medical therapy) checklist
389
+ - Volume management (daily weights, fluid/sodium restriction)
390
+ - NYHA functional class documentation
391
+ - Device therapy consideration
392
+ - Hospitalization triggers
393
+
394
+ ### Mental Health Treatment Plans
395
+ - DSM-5 diagnostic criteria met
396
+ - Suicide/violence risk assessment
397
+ - Safety planning
398
+ - Psychotherapy modality and frequency
399
+ - Medication trials and responses
400
+ - Functional goals (return to work, relationships)
401
+
402
+ ### Chronic Pain Plans
403
+ - Comprehensive pain assessment
404
+ - Functional goals (not just pain scores)
405
+ - Multimodal analgesia
406
+ - Opioid risk assessment if prescribing
407
+ - Physical and psychological interventions
408
+ - Activity modification and pacing
409
+
410
+ ## Cultural Competence and Health Equity
411
+
412
+ ### Culturally Appropriate Care
413
+ - Recognize cultural health beliefs and practices
414
+ - Address language barriers (interpreter services)
415
+ - Respect religious and cultural preferences in treatment
416
+ - Consider social determinants of health (housing, food security, transportation)
417
+ - Avoid assumptions based on stereotypes
418
+
419
+ ### Health Literacy
420
+ - Assess patient understanding (teach-back method)
421
+ - Use plain language, avoid medical jargon
422
+ - Visual aids and written materials at appropriate reading level
423
+ - Tailor education to patient's learning style
424
+
425
+ ### Addressing Disparities
426
+ - Screen for social needs and barriers
427
+ - Connect to community resources
428
+ - Culturally tailored interventions when evidence supports
429
+ - Track outcomes by demographic groups, address disparities
430
+
431
+ ## References and Guidelines
432
+
433
+ ### General Standards
434
+ - Joint Commission Standards Manual
435
+ - CMS Conditions of Participation
436
+ - State medical board documentation requirements
437
+
438
+ ### Specialty Guidelines
439
+ - American College of Physicians (ACP)
440
+ - American Academy of Family Physicians (AAFP)
441
+ - American Psychiatric Association (APA)
442
+ - American Physical Therapy Association (APTA)
443
+ - Disease-specific societies (ADA, AHA, ACC, etc.)
444
+
445
+ ### Regulatory
446
+ - HIPAA Privacy Rule (45 CFR Part 160, 164)
447
+ - 42 CFR Part 2 (Substance Use Disorder Confidentiality)
448
+ - 21 CFR Part 11 (Electronic Records, applicable for research/trials)
449
+ - State scope of practice laws
450
+
451
+ ---
452
+
453
+ **Document Version**: 1.0
454
+ **Last Updated**: January 2025
455
+ **Next Review**: January 2026
456
+