scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

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  1. scientific_writer/.claude/settings.local.json +30 -0
  2. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  3. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  4. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  5. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  6. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  7. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  8. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  9. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  10. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  16. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  17. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  18. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  19. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  31. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  39. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  47. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  48. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  49. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  50. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  98. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  106. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  118. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  174. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  177. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  182. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  183. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  184. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  188. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  189. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  192. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  193. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  194. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  195. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  196. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  197. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
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  286. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
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  304. scientific_writer/cli.py +12 -7
  305. scientific_writer/core.py +27 -5
  306. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
  307. scientific_writer-2.2.2.dist-info/RECORD +312 -0
  308. scientific_writer-2.1.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
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+ ---
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+ name: treatment-plans
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+ description: "Generate comprehensive medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions, regulatory compliance (HIPAA), and validation tools for complete patient-centered care planning."
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+ ---
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+
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+ # Treatment Plan Writing
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+
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+ ## Overview
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+
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+ Treatment plan writing is the systematic documentation of clinical care strategies designed to address patient health conditions through evidence-based interventions, measurable goals, and structured follow-up. This skill provides comprehensive LaTeX templates and validation tools for creating professional treatment plans across all medical specialties with full regulatory compliance.
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+
12
+ **Critical Principle: Treatment plans must be patient-centered, evidence-based, measurable, and compliant with healthcare regulations (HIPAA, documentation standards).** Every treatment plan should include clear goals, specific interventions, defined timelines, monitoring parameters, and expected outcomes that align with patient preferences and current clinical guidelines.
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+
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+ ## When to Use This Skill
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+
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+ This skill should be used when:
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+ - Creating individualized treatment plans for patient care
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+ - Documenting therapeutic interventions for chronic disease management
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+ - Developing rehabilitation programs (physical therapy, occupational therapy, cardiac rehab)
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+ - Writing mental health and psychiatric treatment plans
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+ - Planning perioperative and surgical care pathways
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+ - Establishing pain management protocols
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+ - Setting patient-centered goals using SMART criteria
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+ - Coordinating multidisciplinary care across specialties
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+ - Ensuring regulatory compliance in treatment documentation
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+ - Generating professional treatment plans for medical records
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+
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+ ## Core Capabilities
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+
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+ ### 1. General Medical Treatment Plans
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+
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+ General medical treatment plans address common chronic conditions and acute medical issues requiring structured therapeutic interventions.
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+
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+ #### Standard Components
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+
36
+ **Patient Information (De-identified)**
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+ - Demographics (age, sex, relevant medical background)
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+ - Active medical conditions and comorbidities
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+ - Current medications and allergies
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+ - Relevant social and family history
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+ - Functional status and baseline assessments
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+ - **HIPAA Compliance**: Remove all 18 identifiers per Safe Harbor method
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+
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+ **Diagnosis and Assessment Summary**
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+ - Primary diagnosis with ICD-10 code
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+ - Secondary diagnoses and comorbidities
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+ - Severity classification and staging
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+ - Functional limitations and quality of life impact
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+ - Risk stratification (e.g., cardiovascular risk, fall risk)
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+ - Prognostic indicators
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+
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+ **Treatment Goals (SMART Format)**
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+
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+ Short-term goals (1-3 months):
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+ - **Specific**: Clearly defined outcome (e.g., "Reduce HbA1c to <7%")
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+ - **Measurable**: Quantifiable metrics (e.g., "Decrease systolic BP by 10 mmHg")
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+ - **Achievable**: Realistic given patient capabilities
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+ - **Relevant**: Aligned with patient priorities and values
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+ - **Time-bound**: Specific timeframe (e.g., "within 8 weeks")
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+
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+ Long-term goals (6-12 months):
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+ - Disease control or remission targets
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+ - Functional improvement objectives
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+ - Quality of life enhancement
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+ - Prevention of complications
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+ - Maintenance of independence
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+
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+ **Interventions**
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+
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+ *Pharmacological*:
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+ - Medications with specific dosages, routes, frequencies
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+ - Titration schedules and target doses
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+ - Drug-drug interaction considerations
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+ - Monitoring for adverse effects
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+ - Medication reconciliation
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+
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+ *Non-pharmacological*:
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+ - Lifestyle modifications (diet, exercise, smoking cessation)
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+ - Behavioral interventions
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+ - Patient education and self-management
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+ - Monitoring and self-tracking (glucose, blood pressure, weight)
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+ - Assistive devices or adaptive equipment
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+
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+ *Procedural*:
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+ - Planned procedures or interventions
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+ - Referrals to specialists
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+ - Diagnostic testing schedule
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+ - Preventive care (vaccinations, screenings)
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+
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+ **Timeline and Schedule**
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+ - Treatment phases with specific timeframes
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+ - Appointment frequency (weekly, monthly, quarterly)
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+ - Milestone assessments and goal evaluations
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+ - Medication adjustments schedule
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+ - Expected duration of treatment
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+
97
+ **Monitoring Parameters**
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+ - Clinical outcomes to track (vital signs, lab values, symptoms)
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+ - Assessment tools and scales (e.g., PHQ-9, pain scales)
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+ - Frequency of monitoring
101
+ - Thresholds for intervention or escalation
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+ - Patient-reported outcomes
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+
104
+ **Expected Outcomes**
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+ - Primary outcome measures
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+ - Success criteria and benchmarks
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+ - Expected timeline for improvement
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+ - Criteria for treatment modification
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+ - Long-term prognosis
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+
111
+ **Follow-up Plan**
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+ - Scheduled appointments and reassessments
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+ - Communication plan (phone calls, secure messaging)
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+ - Emergency contact procedures
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+ - Criteria for urgent evaluation
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+ - Transition or discharge planning
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+
118
+ **Patient Education**
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+ - Understanding of condition and treatment rationale
120
+ - Self-management skills training
121
+ - Medication administration and adherence
122
+ - Warning signs and when to seek help
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+ - Resources and support services
124
+
125
+ **Risk Mitigation**
126
+ - Potential adverse effects and management
127
+ - Drug interactions and contraindications
128
+ - Fall prevention, infection prevention
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+ - Emergency action plans
130
+ - Safety monitoring
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+
132
+ #### Common Applications
133
+
134
+ - Diabetes mellitus management
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+ - Hypertension control
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+ - Heart failure treatment
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+ - COPD management
138
+ - Asthma care plans
139
+ - Hyperlipidemia treatment
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+ - Osteoarthritis management
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+ - Chronic kidney disease
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+
143
+ ### 2. Rehabilitation Treatment Plans
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+
145
+ Rehabilitation plans focus on restoring function, improving mobility, and enhancing quality of life through structured therapeutic programs.
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+
147
+ #### Core Components
148
+
149
+ **Functional Assessment**
150
+ - Baseline functional status (ADLs, IADLs)
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+ - Range of motion, strength, balance, endurance
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+ - Gait analysis and mobility assessment
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+ - Standardized measures (FIM, Barthel Index, Berg Balance Scale)
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+ - Environmental assessment (home safety, accessibility)
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+
156
+ **Rehabilitation Goals**
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+
158
+ *Impairment-level goals*:
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+ - Improve shoulder flexion to 140 degrees
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+ - Increase quadriceps strength by 2/5 MMT grades
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+ - Enhance balance (Berg Score >45/56)
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+
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+ *Activity-level goals*:
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+ - Independent ambulation 150 feet with assistive device
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+ - Climb 12 stairs with handrail supervision
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+ - Transfer bed-to-chair independently
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+
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+ *Participation-level goals*:
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+ - Return to work with modifications
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+ - Resume recreational activities
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+ - Independent community mobility
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+
173
+ **Therapeutic Interventions**
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+
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+ *Physical Therapy*:
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+ - Therapeutic exercises (strengthening, stretching, endurance)
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+ - Manual therapy techniques
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+ - Gait training and balance activities
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+ - Modalities (heat, ice, electrical stimulation, ultrasound)
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+ - Assistive device training
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+
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+ *Occupational Therapy*:
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+ - ADL training (bathing, dressing, grooming, feeding)
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+ - Upper extremity strengthening and coordination
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+ - Adaptive equipment and modifications
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+ - Energy conservation techniques
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+ - Cognitive rehabilitation
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+
189
+ *Speech-Language Pathology*:
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+ - Swallowing therapy and dysphagia management
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+ - Communication strategies and augmentative devices
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+ - Cognitive-linguistic therapy
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+ - Voice therapy
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+
195
+ *Other Services*:
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+ - Recreational therapy
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+ - Aquatic therapy
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+ - Cardiac rehabilitation
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+ - Pulmonary rehabilitation
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+ - Vestibular rehabilitation
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+
202
+ **Treatment Schedule**
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+ - Frequency: 3x/week PT, 2x/week OT (example)
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+ - Session duration: 45-60 minutes
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+ - Treatment phase durations (acute, subacute, maintenance)
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+ - Expected total duration: 8-12 weeks
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+ - Reassessment intervals
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+
209
+ **Progress Monitoring**
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+ - Weekly functional assessments
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+ - Standardized outcome measures
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+ - Goal attainment scaling
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+ - Pain and symptom tracking
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+ - Patient satisfaction
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+
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+ **Home Exercise Program**
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+ - Specific exercises with repetitions/sets/frequency
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+ - Precautions and safety instructions
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+ - Progression criteria
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+ - Self-monitoring strategies
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+
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+ #### Specialty Rehabilitation
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+
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+ - Post-stroke rehabilitation
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+ - Orthopedic rehabilitation (joint replacement, fracture)
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+ - Cardiac rehabilitation (post-MI, post-surgery)
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+ - Pulmonary rehabilitation
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+ - Vestibular rehabilitation
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+ - Neurological rehabilitation
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+ - Sports injury rehabilitation
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+
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+ ### 3. Mental Health Treatment Plans
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+
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+ Mental health treatment plans address psychiatric conditions through integrated psychotherapeutic, pharmacological, and psychosocial interventions.
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+
236
+ #### Essential Components
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+
238
+ **Psychiatric Assessment**
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+ - Primary psychiatric diagnosis (DSM-5 criteria)
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+ - Symptom severity and functional impairment
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+ - Co-occurring mental health conditions
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+ - Substance use assessment
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+ - Suicide/homicide risk assessment
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+ - Trauma history and PTSD screening
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+ - Social determinants of mental health
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+
247
+ **Treatment Goals**
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+
249
+ *Symptom reduction*:
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+ - Decrease depression severity (PHQ-9 score from 18 to <10)
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+ - Reduce anxiety symptoms (GAD-7 score <5)
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+ - Improve sleep quality (Pittsburgh Sleep Quality Index)
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+ - Stabilize mood (reduced mood episodes)
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+
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+ *Functional improvement*:
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+ - Return to work or school
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+ - Improve social relationships and support
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+ - Enhance coping skills and emotional regulation
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+ - Increase engagement in meaningful activities
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+
261
+ *Recovery-oriented goals*:
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+ - Build resilience and self-efficacy
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+ - Develop crisis management skills
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+ - Establish sustainable wellness routines
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+ - Achieve personal recovery goals
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+
267
+ **Therapeutic Interventions**
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+
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+ *Psychotherapy*:
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+ - Evidence-based modality (CBT, DBT, ACT, psychodynamic, IPT)
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+ - Session frequency (weekly, biweekly)
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+ - Treatment duration (12-16 weeks, ongoing)
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+ - Specific techniques and targets
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+ - Group therapy participation
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+
276
+ *Psychopharmacology*:
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+ - Medication class and rationale
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+ - Starting dose and titration schedule
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+ - Target symptoms
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+ - Expected response timeline (2-4 weeks for antidepressants)
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+ - Side effect monitoring
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+ - Combination therapy considerations
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+
284
+ *Psychosocial Interventions*:
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+ - Case management services
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+ - Peer support programs
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+ - Family therapy or psychoeducation
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+ - Vocational rehabilitation
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+ - Supported housing or community integration
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+ - Substance abuse treatment
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+
292
+ **Safety Planning**
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+ - Crisis contacts and emergency services
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+ - Warning signs and triggers
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+ - Coping strategies and self-soothing techniques
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+ - Safe environment modifications
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+ - Means restriction (firearms, medications)
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+ - Support system activation
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+
300
+ **Monitoring and Assessment**
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+ - Symptom rating scales (weekly or biweekly)
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+ - Medication adherence and side effects
303
+ - Suicidal ideation screening
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+ - Functional status assessments
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+ - Treatment engagement and therapeutic alliance
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+
307
+ **Patient and Family Education**
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+ - Psychoeducation about diagnosis
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+ - Treatment rationale and expectations
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+ - Medication information
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+ - Relapse prevention strategies
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+ - Community resources
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+
314
+ #### Mental Health Conditions
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+
316
+ - Major depressive disorder
317
+ - Anxiety disorders (GAD, panic, social anxiety)
318
+ - Bipolar disorder
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+ - Schizophrenia and psychotic disorders
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+ - PTSD and trauma-related disorders
321
+ - Eating disorders
322
+ - Substance use disorders
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+ - Personality disorders
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+
325
+ ### 4. Chronic Disease Management Plans
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+
327
+ Comprehensive long-term care plans for chronic conditions requiring ongoing monitoring, treatment adjustments, and multidisciplinary coordination.
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+
329
+ #### Key Features
330
+
331
+ **Disease-Specific Targets**
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+ - Evidence-based treatment goals per guidelines
333
+ - Stage-appropriate interventions
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+ - Complication prevention strategies
335
+ - Disease progression monitoring
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+
337
+ **Self-Management Support**
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+ - Patient activation and engagement
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+ - Shared decision-making
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+ - Action plans for symptom changes
341
+ - Technology-enabled monitoring (apps, remote monitoring)
342
+
343
+ **Care Coordination**
344
+ - Primary care physician oversight
345
+ - Specialist consultations and co-management
346
+ - Care transitions (hospital to home)
347
+ - Medication management across providers
348
+ - Communication protocols
349
+
350
+ **Population Health Integration**
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+ - Registry tracking and outreach
352
+ - Preventive care and screening schedules
353
+ - Quality measure reporting
354
+ - Care gaps identification
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+
356
+ #### Applicable Conditions
357
+
358
+ - Type 1 and Type 2 diabetes
359
+ - Cardiovascular disease (CHF, CAD)
360
+ - Chronic respiratory diseases (COPD, asthma)
361
+ - Chronic kidney disease
362
+ - Inflammatory bowel disease
363
+ - Rheumatoid arthritis and autoimmune conditions
364
+ - HIV/AIDS
365
+ - Cancer survivorship care
366
+
367
+ ### 5. Perioperative Care Plans
368
+
369
+ Structured plans for surgical and procedural patients covering preoperative preparation, intraoperative management, and postoperative recovery.
370
+
371
+ #### Components
372
+
373
+ **Preoperative Assessment**
374
+ - Surgical indication and planned procedure
375
+ - Preoperative risk stratification (ASA class, cardiac risk)
376
+ - Optimization of medical conditions
377
+ - Medication management (continuation, discontinuation)
378
+ - Preoperative testing and clearances
379
+ - Informed consent and patient education
380
+
381
+ **Perioperative Interventions**
382
+ - Enhanced recovery after surgery (ERAS) protocols
383
+ - Venous thromboembolism prophylaxis
384
+ - Antibiotic prophylaxis
385
+ - Glycemic control strategies
386
+ - Pain management plan (multimodal analgesia)
387
+
388
+ **Postoperative Care**
389
+ - Immediate recovery goals (24-48 hours)
390
+ - Early mobilization protocols
391
+ - Diet advancement
392
+ - Wound care and drain management
393
+ - Pain control regimen
394
+ - Complication monitoring
395
+
396
+ **Discharge Planning**
397
+ - Activity restrictions and progression
398
+ - Medication reconciliation
399
+ - Follow-up appointments
400
+ - Home health or rehabilitation services
401
+ - Return-to-work timeline
402
+
403
+ ### 6. Pain Management Plans
404
+
405
+ Multimodal approaches to acute and chronic pain using evidence-based interventions and opioid-sparing strategies.
406
+
407
+ #### Comprehensive Components
408
+
409
+ **Pain Assessment**
410
+ - Pain location, quality, intensity (0-10 scale)
411
+ - Temporal pattern (constant, intermittent, breakthrough)
412
+ - Aggravating and alleviating factors
413
+ - Functional impact (sleep, activities, mood)
414
+ - Previous treatments and responses
415
+ - Psychosocial contributors
416
+
417
+ **Multimodal Interventions**
418
+
419
+ *Pharmacological*:
420
+ - Non-opioid analgesics (acetaminophen, NSAIDs)
421
+ - Adjuvant medications (antidepressants, anticonvulsants, muscle relaxants)
422
+ - Topical agents (lidocaine, capsaicin, diclofenac)
423
+ - Opioid therapy (when appropriate, with risk mitigation)
424
+ - Titration and rotation strategies
425
+
426
+ *Interventional Procedures*:
427
+ - Nerve blocks and injections
428
+ - Radiofrequency ablation
429
+ - Spinal cord stimulation
430
+ - Intrathecal drug delivery
431
+
432
+ *Non-pharmacological*:
433
+ - Physical therapy and exercise
434
+ - Cognitive-behavioral therapy for pain
435
+ - Mindfulness and relaxation techniques
436
+ - Acupuncture
437
+ - TENS units
438
+
439
+ **Opioid Safety (when prescribed)**
440
+ - Indication and planned duration
441
+ - Prescription drug monitoring program (PDMP) check
442
+ - Opioid risk assessment tools
443
+ - Naloxone prescription
444
+ - Treatment agreements
445
+ - Random urine drug screening
446
+ - Frequent follow-up and reassessment
447
+
448
+ **Functional Goals**
449
+ - Specific activity improvements
450
+ - Sleep quality enhancement
451
+ - Reduced pain interference
452
+ - Improved quality of life
453
+ - Return to work or meaningful activities
454
+
455
+ ## Best Practices
456
+
457
+ ### SMART Goal Setting
458
+
459
+ All treatment goals should meet SMART criteria:
460
+
461
+ - **Specific**: "Improve HbA1c to <7%" not "Better diabetes control"
462
+ - **Measurable**: Use quantifiable metrics, validated scales, objective measures
463
+ - **Achievable**: Consider patient capabilities, resources, social support
464
+ - **Relevant**: Align with patient values, priorities, and life circumstances
465
+ - **Time-bound**: Define clear timeframes for goal achievement and reassessment
466
+
467
+ ### Patient-Centered Care
468
+
469
+ ✓ **Shared Decision-Making**: Involve patients in goal-setting and treatment choices
470
+ ✓ **Cultural Competence**: Respect cultural beliefs, language preferences, health literacy
471
+ ✓ **Patient Preferences**: Honor treatment preferences and personal values
472
+ ✓ **Individualization**: Tailor plans to patient's unique circumstances
473
+ ✓ **Empowerment**: Support patient activation and self-management
474
+
475
+ ### Evidence-Based Practice
476
+
477
+ ✓ **Clinical Guidelines**: Follow current specialty society recommendations
478
+ ✓ **Quality Measures**: Incorporate HEDIS, CMS quality measures
479
+ ✓ **Comparative Effectiveness**: Use treatments with proven efficacy
480
+ ✓ **Avoid Low-Value Care**: Eliminate unnecessary tests and interventions
481
+ ✓ **Stay Current**: Update plans based on emerging evidence
482
+
483
+ ### Documentation Standards
484
+
485
+ ✓ **Completeness**: Include all required elements
486
+ ✓ **Clarity**: Use clear, professional medical language
487
+ ✓ **Accuracy**: Ensure factual correctness and current information
488
+ ✓ **Timeliness**: Document plans promptly
489
+ ✓ **Legibility**: Professional formatting and organization
490
+ ✓ **Signature and Date**: Authenticate all treatment plans
491
+
492
+ ### Regulatory Compliance
493
+
494
+ ✓ **HIPAA Privacy**: De-identify all protected health information
495
+ ✓ **Informed Consent**: Document patient understanding and agreement
496
+ ✓ **Billing Support**: Include documentation to support medical necessity
497
+ ✓ **Quality Reporting**: Enable extraction of quality metrics
498
+ ✓ **Legal Protection**: Maintain defensible clinical documentation
499
+
500
+ ### Multidisciplinary Coordination
501
+
502
+ ✓ **Team Communication**: Share plans across care team
503
+ ✓ **Role Clarity**: Define responsibilities for each team member
504
+ ✓ **Care Transitions**: Ensure continuity across settings
505
+ ✓ **Specialist Integration**: Coordinate with subspecialty care
506
+ ✓ **Patient-Centered Medical Home**: Align with PCMH principles
507
+
508
+ ## LaTeX Template Usage
509
+
510
+ ### Template Selection
511
+
512
+ Choose the appropriate template based on clinical context:
513
+
514
+ 1. **general_medical_treatment_plan.tex** - Primary care, chronic disease, general medicine
515
+ 2. **rehabilitation_treatment_plan.tex** - PT/OT, post-surgery, injury recovery
516
+ 3. **mental_health_treatment_plan.tex** - Psychiatric conditions, behavioral health
517
+ 4. **chronic_disease_management_plan.tex** - Complex chronic diseases, multiple conditions
518
+ 5. **perioperative_care_plan.tex** - Surgical patients, procedural care
519
+ 6. **pain_management_plan.tex** - Acute or chronic pain conditions
520
+
521
+ ### Template Structure
522
+
523
+ All LaTeX templates include:
524
+ - Professional formatting with appropriate margins and fonts
525
+ - Structured sections for all required components
526
+ - Tables for medications, interventions, timelines
527
+ - Goal-tracking sections with SMART criteria
528
+ - Space for provider signatures and dates
529
+ - HIPAA-compliant de-identification guidance
530
+ - Comments with detailed instructions
531
+
532
+ ### Generating PDFs
533
+
534
+ ```bash
535
+ # Compile LaTeX template to PDF
536
+ pdflatex general_medical_treatment_plan.tex
537
+
538
+ # For templates with references
539
+ pdflatex treatment_plan.tex
540
+ bibtex treatment_plan
541
+ pdflatex treatment_plan.tex
542
+ pdflatex treatment_plan.tex
543
+ ```
544
+
545
+ ## Validation and Quality Assurance
546
+
547
+ ### Completeness Checking
548
+
549
+ Use validation scripts to ensure all required sections are present:
550
+
551
+ ```bash
552
+ python check_completeness.py my_treatment_plan.tex
553
+ ```
554
+
555
+ The script checks for:
556
+ - Patient information section
557
+ - Diagnosis and assessment
558
+ - SMART goals (short-term and long-term)
559
+ - Interventions (pharmacological, non-pharmacological)
560
+ - Timeline and schedule
561
+ - Monitoring parameters
562
+ - Expected outcomes
563
+ - Follow-up plan
564
+ - Patient education
565
+ - Risk mitigation
566
+
567
+ ### Treatment Plan Validation
568
+
569
+ Comprehensive validation of treatment plan quality:
570
+
571
+ ```bash
572
+ python validate_treatment_plan.py my_treatment_plan.tex
573
+ ```
574
+
575
+ Validation includes:
576
+ - SMART goal criteria assessment
577
+ - Evidence-based intervention verification
578
+ - Timeline feasibility check
579
+ - Monitoring parameter adequacy
580
+ - Safety and risk mitigation review
581
+ - Regulatory compliance check
582
+
583
+ ### Quality Checklist
584
+
585
+ Review treatment plans against the quality checklist (`quality_checklist.md`):
586
+
587
+ **Clinical Quality**
588
+ - [ ] Diagnosis is accurate and properly coded (ICD-10)
589
+ - [ ] Goals are SMART and patient-centered
590
+ - [ ] Interventions are evidence-based and guideline-concordant
591
+ - [ ] Timeline is realistic and clearly defined
592
+ - [ ] Monitoring plan is comprehensive
593
+ - [ ] Safety considerations are addressed
594
+
595
+ **Patient-Centered Care**
596
+ - [ ] Patient preferences and values incorporated
597
+ - [ ] Shared decision-making documented
598
+ - [ ] Health literacy appropriate language
599
+ - [ ] Cultural considerations addressed
600
+ - [ ] Patient education plan included
601
+
602
+ **Regulatory Compliance**
603
+ - [ ] HIPAA-compliant de-identification
604
+ - [ ] Medical necessity documented
605
+ - [ ] Informed consent noted
606
+ - [ ] Provider signature and credentials
607
+ - [ ] Date of plan creation/revision
608
+
609
+ **Coordination and Communication**
610
+ - [ ] Specialist referrals documented
611
+ - [ ] Care team roles defined
612
+ - [ ] Follow-up schedule clear
613
+ - [ ] Emergency contacts provided
614
+ - [ ] Transition planning addressed
615
+
616
+ ## Integration with Other Skills
617
+
618
+ ### Clinical Reports Integration
619
+
620
+ Treatment plans often accompany other clinical documentation:
621
+
622
+ - **SOAP Notes** (`clinical-reports` skill): Document ongoing implementation
623
+ - **H&P** (`clinical-reports` skill): Initial assessment informs treatment plan
624
+ - **Discharge Summaries** (`clinical-reports` skill): Summarize treatment plan execution
625
+ - **Progress Notes**: Track goal achievement and plan modifications
626
+
627
+ ### Scientific Writing Integration
628
+
629
+ Evidence-based treatment planning requires literature support:
630
+
631
+ - **Citation Management** (`citation-management` skill): Reference clinical guidelines
632
+ - **Literature Review** (`literature-review` skill): Understand treatment evidence base
633
+ - **Research Lookup** (`research-lookup` skill): Find current best practices
634
+
635
+ ### Research Integration
636
+
637
+ Treatment plans may be developed for clinical trials or research studies:
638
+
639
+ - **Research Grants** (`research-grants` skill): Treatment protocols for funded studies
640
+ - **Clinical Trial Reports** (`clinical-reports` skill): Intervention documentation
641
+
642
+ ## Common Use Cases
643
+
644
+ ### Example 1: Type 2 Diabetes Management
645
+
646
+ **Scenario**: 58-year-old patient with newly diagnosed Type 2 diabetes, HbA1c 8.5%, BMI 32
647
+
648
+ **Template**: `general_medical_treatment_plan.tex`
649
+
650
+ **Goals**:
651
+ - Short-term: Reduce HbA1c to <7.5% in 3 months
652
+ - Long-term: Achieve HbA1c <7%, lose 15 pounds in 6 months
653
+
654
+ **Interventions**:
655
+ - Pharmacological: Metformin 500mg BID, titrate to 1000mg BID
656
+ - Lifestyle: Mediterranean diet, 150 min/week moderate exercise
657
+ - Education: Diabetes self-management education, glucose monitoring
658
+
659
+ ### Example 2: Post-Stroke Rehabilitation
660
+
661
+ **Scenario**: 70-year-old patient s/p left MCA stroke with right hemiparesis
662
+
663
+ **Template**: `rehabilitation_treatment_plan.tex`
664
+
665
+ **Goals**:
666
+ - Short-term: Improve right arm strength 2/5 to 3/5 in 4 weeks
667
+ - Long-term: Independent ambulation 150 feet with cane in 12 weeks
668
+
669
+ **Interventions**:
670
+ - PT 3x/week: Gait training, balance, strengthening
671
+ - OT 3x/week: ADL training, upper extremity function
672
+ - SLP 2x/week: Dysphagia therapy
673
+
674
+ ### Example 3: Major Depressive Disorder
675
+
676
+ **Scenario**: 35-year-old with moderate depression, PHQ-9 score 16
677
+
678
+ **Template**: `mental_health_treatment_plan.tex`
679
+
680
+ **Goals**:
681
+ - Short-term: Reduce PHQ-9 to <10 in 8 weeks
682
+ - Long-term: Achieve remission (PHQ-9 <5), return to work
683
+
684
+ **Interventions**:
685
+ - Psychotherapy: CBT weekly sessions
686
+ - Medication: Sertraline 50mg daily, titrate to 100mg
687
+ - Lifestyle: Sleep hygiene, exercise 30 min 5x/week
688
+
689
+ ### Example 4: Total Knee Arthroplasty
690
+
691
+ **Scenario**: 68-year-old scheduled for right TKA for osteoarthritis
692
+
693
+ **Template**: `perioperative_care_plan.tex`
694
+
695
+ **Preoperative Goals**:
696
+ - Optimize diabetes control (glucose <180)
697
+ - Discontinue anticoagulation per protocol
698
+ - Complete medical clearance
699
+
700
+ **Postoperative Goals**:
701
+ - Ambulate 50 feet by POD 1
702
+ - 90-degree knee flexion by POD 3
703
+ - Discharge home with PT services by POD 2-3
704
+
705
+ ### Example 5: Chronic Low Back Pain
706
+
707
+ **Scenario**: 45-year-old with chronic non-specific low back pain, pain 7/10
708
+
709
+ **Template**: `pain_management_plan.tex`
710
+
711
+ **Goals**:
712
+ - Short-term: Reduce pain to 4/10 in 6 weeks
713
+ - Long-term: Return to work full-time, pain 2-3/10
714
+
715
+ **Interventions**:
716
+ - Pharmacological: Gabapentin 300mg TID, duloxetine 60mg daily
717
+ - PT: Core strengthening, McKenzie exercises 2x/week x 8 weeks
718
+ - Behavioral: CBT for pain, mindfulness meditation
719
+ - Interventional: Consider lumbar ESI if inadequate response
720
+
721
+ ## Professional Standards and Guidelines
722
+
723
+ Treatment plans should align with:
724
+
725
+ ### General Medicine
726
+ - American Diabetes Association (ADA) Standards of Care
727
+ - ACC/AHA Cardiovascular Guidelines
728
+ - GOLD COPD Guidelines
729
+ - JNC-8 Hypertension Guidelines
730
+ - KDIGO Chronic Kidney Disease Guidelines
731
+
732
+ ### Rehabilitation
733
+ - APTA Clinical Practice Guidelines
734
+ - AOTA Practice Guidelines
735
+ - Cardiac Rehabilitation Guidelines (AHA/AACVPR)
736
+ - Stroke Rehabilitation Guidelines
737
+
738
+ ### Mental Health
739
+ - APA Practice Guidelines
740
+ - VA/DoD Clinical Practice Guidelines
741
+ - NICE Guidelines (National Institute for Health and Care Excellence)
742
+ - Cochrane Reviews for psychiatric interventions
743
+
744
+ ### Pain Management
745
+ - CDC Opioid Prescribing Guidelines
746
+ - AAPM/APS Chronic Pain Guidelines
747
+ - WHO Pain Ladder
748
+ - Multimodal Analgesia Best Practices
749
+
750
+ ## Timeline Generation
751
+
752
+ Use the timeline generator script to create visual treatment timelines:
753
+
754
+ ```bash
755
+ python timeline_generator.py --plan my_treatment_plan.tex --output timeline.pdf
756
+ ```
757
+
758
+ Generates:
759
+ - Gantt chart of treatment phases
760
+ - Milestone markers for goal assessments
761
+ - Medication titration schedules
762
+ - Follow-up appointment calendar
763
+ - Intervention intensity over time
764
+
765
+ ## Support and Resources
766
+
767
+ ### Template Generation
768
+
769
+ Interactive template selection:
770
+
771
+ ```bash
772
+ cd .claude/skills/treatment-plans/scripts
773
+ python generate_template.py
774
+
775
+ # Or specify type directly
776
+ python generate_template.py --type mental_health --output depression_treatment_plan.tex
777
+ ```
778
+
779
+ ### Validation Workflow
780
+
781
+ 1. **Create treatment plan** using appropriate LaTeX template
782
+ 2. **Check completeness**: `python check_completeness.py plan.tex`
783
+ 3. **Validate quality**: `python validate_treatment_plan.py plan.tex`
784
+ 4. **Review checklist**: Compare against `quality_checklist.md`
785
+ 5. **Generate PDF**: `pdflatex plan.tex`
786
+ 6. **Review with patient**: Ensure understanding and agreement
787
+ 7. **Implement and document**: Track progress in clinical notes
788
+
789
+ ### Additional Resources
790
+
791
+ - Clinical practice guidelines from specialty societies
792
+ - AHRQ Effective Health Care Program
793
+ - Cochrane Library for intervention evidence
794
+ - UpToDate and DynaMed for treatment recommendations
795
+ - CMS Quality Measures and HEDIS specifications
796
+
797
+ ## Ethical Considerations
798
+
799
+ ### Informed Consent
800
+ All treatment plans should involve patient understanding and voluntary agreement to proposed interventions.
801
+
802
+ ### Cultural Sensitivity
803
+ Treatment plans must respect diverse cultural beliefs, health practices, and communication styles.
804
+
805
+ ### Health Equity
806
+ Consider social determinants of health, access barriers, and health disparities when developing plans.
807
+
808
+ ### Privacy Protection
809
+ Maintain strict HIPAA compliance; de-identify all protected health information in shared documents.
810
+
811
+ ### Autonomy and Beneficence
812
+ Balance medical recommendations with patient autonomy and values while promoting patient welfare.
813
+
814
+ ## License
815
+
816
+ Part of the Claude Scientific Writer project. See main LICENSE file.
817
+