scientific-writer 2.3.1__py3-none-any.whl

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Files changed (315) hide show
  1. scientific_writer/.claude/WRITER.md +822 -0
  2. scientific_writer/.claude/settings.local.json +30 -0
  3. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  4. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  5. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  6. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  7. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  8. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  9. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  10. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  16. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  17. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  18. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  19. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  31. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  39. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  47. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  48. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  49. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  50. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  98. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  106. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  118. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  174. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  177. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  182. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  183. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  184. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  188. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  189. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  192. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  193. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  194. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  195. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  196. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  197. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  200. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  201. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
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@@ -0,0 +1,485 @@
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. Executive Summary Best Practices (Foundation Medicine Model)
14
+
15
+ **CRITICAL: All treatment plans MUST include a prominent "Treatment Plan Highlights" summary box on the first page.**
16
+
17
+ Following the Foundation Medicine model for genomic profiling reports, treatment plans should begin with a concise, bulletin-style summary that provides immediate access to key actionable information:
18
+
19
+ **Components of Treatment Plan Highlights Box:**
20
+ - **Key Diagnosis**: Primary condition with ICD-10 code, severity/stage (1 line)
21
+ - **Primary Treatment Goals**: 2-3 SMART goals in bullet format
22
+ - **Main Interventions**: 2-3 key interventions (pharmacological, non-pharmacological, monitoring)
23
+ - **Timeline Overview**: Brief treatment duration/phases (1 line)
24
+
25
+ **Format Requirements:**
26
+ - Use colored box (tcolorbox in LaTeX) to make it visually prominent
27
+ - Place immediately after title, before Patient Information section
28
+ - Summary must fit on first page with patient demographics
29
+ - Use concise, actionable language
30
+ - Focus on what clinicians need to know immediately
31
+
32
+ **Optimal Document Length:**
33
+ - **Preferred**: 1 page for most treatment plans (quick-reference format)
34
+ - **Standard**: 3-4 pages for moderate complexity cases
35
+ - **Extended**: 5-6 pages maximum for highly complex cases only
36
+ - Prioritize brevity, clarity, and actionability over comprehensive detail
37
+ - Think "clinical decision support card" not "comprehensive textbook"
38
+
39
+ **Design Philosophy:**
40
+ The highlights box enables efficient clinical decision-making by providing critical information upfront, following evidence-based practices from precision medicine reporting. This approach improves care coordination, reduces time to treatment initiation, and ensures key information is never overlooked.
41
+
42
+ ### 2. Essential Components
43
+
44
+ All treatment plans must include:
45
+
46
+ #### Patient Information (De-identified for Sharing)
47
+ - Unique patient identifier (not name or MRN)
48
+ - Age range (not exact birth date)
49
+ - Relevant demographics
50
+ - Date of plan creation
51
+ - Provider name and credentials
52
+ - HIPAA compliance statement
53
+
54
+ #### Diagnosis and Assessment
55
+ - Primary diagnosis with ICD-10 code
56
+ - Secondary diagnoses and comorbidities
57
+ - Severity classification or staging
58
+ - Functional assessment and baseline status
59
+ - Risk stratification
60
+ - Prognostic considerations
61
+
62
+ #### Treatment Goals (SMART Format)
63
+ - **Specific**: Clearly defined outcomes
64
+ - **Measurable**: Quantifiable metrics or observable criteria
65
+ - **Achievable**: Realistic given patient circumstances
66
+ - **Relevant**: Aligned with patient values and priorities
67
+ - **Time-bound**: Defined timeframe for achievement
68
+
69
+ Short-term goals (weeks to 3 months) and long-term goals (3-12+ months) should be distinguished.
70
+
71
+ #### Interventions
72
+ - **Pharmacological**: Specific medications, doses, frequencies, rationales
73
+ - **Non-pharmacological**: Lifestyle modifications, behavioral interventions, education
74
+ - **Procedural**: Planned procedures, specialist referrals, diagnostic testing
75
+
76
+ #### Timeline and Schedule
77
+ - Treatment phases with durations
78
+ - Appointment frequency
79
+ - Milestone assessments
80
+ - Expected treatment duration
81
+
82
+ #### Monitoring Parameters
83
+ - Clinical outcomes to track
84
+ - Assessment tools and scales
85
+ - Monitoring frequency
86
+ - Intervention thresholds
87
+
88
+ #### Expected Outcomes
89
+ - Primary outcome measures
90
+ - Success criteria
91
+ - Timeline for improvement
92
+ - Criteria for treatment modification
93
+
94
+ #### Follow-up Plan
95
+ - Scheduled appointments
96
+ - Communication protocols
97
+ - Emergency procedures
98
+ - Transition planning
99
+
100
+ #### Patient Education
101
+ - Condition understanding
102
+ - Self-management skills
103
+ - Warning signs
104
+ - Resources and support
105
+
106
+ #### Risk Mitigation
107
+ - Potential adverse effects
108
+ - Safety monitoring
109
+ - Emergency action plans
110
+ - Complication prevention
111
+
112
+ ### 2. Professional Documentation Standards
113
+
114
+ #### Clarity and Precision
115
+ - Use professional medical terminology appropriately
116
+ - Define abbreviations on first use
117
+ - Avoid ambiguous language
118
+ - Specific rather than vague descriptions
119
+
120
+ **Good Example**: "Reduce HbA1c from 8.5% to <7% within 3 months"
121
+ **Poor Example**: "Improve diabetes control"
122
+
123
+ #### Completeness
124
+ - Address all relevant aspects of condition
125
+ - Include rationale for treatment choices
126
+ - Document shared decision-making
127
+ - Address patient preferences and concerns
128
+
129
+ #### Accuracy
130
+ - Factually correct information
131
+ - Current evidence-based recommendations
132
+ - Appropriate dosing and frequencies
133
+ - Correct ICD-10 and CPT codes
134
+
135
+ #### Timeliness
136
+ - Plans created at diagnosis or treatment initiation
137
+ - Updated after significant clinical changes
138
+ - Regular scheduled updates (quarterly to annually)
139
+ - Dated and signed promptly
140
+
141
+ #### Legibility and Organization
142
+ - Professional formatting
143
+ - Logical flow and structure
144
+ - Consistent use of headings and sections
145
+ - Easy to locate key information
146
+
147
+ ### 3. Legal and Regulatory Requirements
148
+
149
+ #### Medical Necessity Documentation
150
+ Treatment plans must demonstrate:
151
+ - Appropriateness of interventions for diagnosis
152
+ - Evidence supporting treatment choices
153
+ - Expected outcomes justify costs and risks
154
+ - Frequency and duration are reasonable
155
+ - Less invasive options considered
156
+
157
+ #### Informed Consent Documentation
158
+ Record that patient:
159
+ - Understands diagnosis and prognosis
160
+ - Aware of treatment options, risks, and benefits
161
+ - Knows alternatives to proposed treatment
162
+ - Had opportunity to ask questions
163
+ - Voluntarily agrees to treatment plan
164
+
165
+ #### Privacy and Confidentiality (HIPAA)
166
+ - Protected Health Information (PHI) safeguarded
167
+ - De-identification for sharing:
168
+ - Remove 18 HIPAA identifiers per Safe Harbor method
169
+ - Names, dates (except year), geographic subdivisions smaller than state
170
+ - Contact information (phone, fax, email, addresses)
171
+ - Social Security numbers, medical record numbers, account numbers
172
+ - Biometric identifiers, photos, other unique identifiers
173
+ - Access limited to those with treatment, payment, or operations need
174
+ - Patient authorization for non-routine disclosures
175
+
176
+ #### Billing and Reimbursement Support
177
+ - ICD-10 diagnosis codes for all conditions
178
+ - CPT codes for procedures
179
+ - Documentation of medical necessity
180
+ - Justification for level of service
181
+ - Compliance with payer-specific requirements
182
+
183
+ #### Quality Measure Reporting
184
+ Enable extraction of quality metrics:
185
+ - HEDIS measures (diabetes HbA1c testing, BP control, etc.)
186
+ - CMS quality reporting (MIPS, ACO measures)
187
+ - Disease-specific quality indicators
188
+ - Patient safety indicators
189
+
190
+ #### Liability Protection
191
+ Defensible documentation includes:
192
+ - Rationale for clinical decisions
193
+ - Consideration of differential diagnosis
194
+ - Risk-benefit analysis
195
+ - Patient education and warnings
196
+ - Follow-up plan for abnormal findings
197
+ - Addressing non-adherence or patient refusal
198
+
199
+ ## Professional Practice Standards
200
+
201
+ ### Joint Commission Standards
202
+
203
+ #### Patient-Centered Care
204
+ - Treatment plans developed with patient participation
205
+ - Goals reflect patient values and preferences
206
+ - Cultural and linguistic needs addressed
207
+ - Health literacy appropriate communication
208
+
209
+ #### Multidisciplinary Coordination
210
+ - Input from relevant disciplines
211
+ - Clear role delineation
212
+ - Communication among team members
213
+ - Coordinated interventions
214
+
215
+ #### Evidence-Based Practice
216
+ - Interventions based on current evidence
217
+ - Clinical practice guidelines followed
218
+ - Variation from guidelines documented and justified
219
+ - Literature supports treatment choices
220
+
221
+ ### Commission on Accreditation of Rehabilitation Facilities (CARF)
222
+
223
+ For rehabilitation treatment plans:
224
+ - Individualized based on comprehensive assessment
225
+ - Measurable, achievable, time-specific goals
226
+ - Regular team review and modification
227
+ - Patient and family involvement
228
+ - Transition and discharge planning
229
+
230
+ ### Centers for Medicare & Medicaid Services (CMS)
231
+
232
+ #### Conditions of Participation
233
+ - Physician orders for treatment
234
+ - Periodic review and revision
235
+ - Progress toward goals documented
236
+ - Care plan accessible to all team members
237
+
238
+ #### Documentation Requirements
239
+ - Legible (typed or clear handwriting)
240
+ - Dated and authenticated (signed)
241
+ - Amendments/corrections properly marked
242
+ - Retention per state law (typically 7-10 years, longer for minors)
243
+
244
+ ## Medical Specialty Standards
245
+
246
+ ### Primary Care
247
+ - Annual comprehensive assessment and plan update
248
+ - Chronic disease management protocols
249
+ - Preventive care integration
250
+ - Medication reconciliation
251
+ - Care coordination with specialists
252
+
253
+ ### Behavioral Health
254
+ - Mental status examination
255
+ - Psychiatric diagnoses per DSM-5 criteria
256
+ - Suicide/homicide risk assessment and safety planning
257
+ - Measurable behavioral outcomes
258
+ - Crisis intervention plan
259
+ - Substance use assessment
260
+ - 42 CFR Part 2 compliance for substance use treatment
261
+
262
+ ### Rehabilitation
263
+ - Functional assessments (FIM, Barthel Index, etc.)
264
+ - Activity limitations and participation restrictions
265
+ - Short-term and long-term functional goals
266
+ - Therapy frequency, intensity, duration
267
+ - Home exercise program
268
+ - Assistive devices and DME
269
+ - Discharge criteria
270
+
271
+ ### Surgical/Perioperative
272
+ - Indication for surgery documented
273
+ - Preoperative risk assessment (ASA, RCRI)
274
+ - Medical optimization plan
275
+ - Enhanced Recovery After Surgery (ERAS) protocols when applicable
276
+ - Postoperative milestones
277
+ - Discharge criteria and planning
278
+
279
+ ### Pain Management
280
+ - Comprehensive pain assessment (location, intensity, quality, temporal pattern, impact)
281
+ - Pain type (nociceptive, neuropathic, mixed)
282
+ - Multimodal analgesia approach
283
+ - Opioid risk assessment (ORT, SOAPP)
284
+ - If opioids: CDC guidelines compliance, treatment agreement, UDS, PDMP
285
+ - Functional goals (not just pain scores)
286
+ - Psychological screening and intervention
287
+
288
+ ## Quality Indicators for Treatment Plans
289
+
290
+ ### Completeness Metrics
291
+ - All required sections present (100%)
292
+ - Goals meet SMART criteria ($\geq$90%)
293
+ - Interventions have clear rationales ($\geq$95%)
294
+ - Monitoring plan includes frequency ($\geq$95%)
295
+ - Patient education documented (100%)
296
+
297
+ ### Clinical Quality Metrics
298
+ - Evidence-based interventions ($\geq$90%)
299
+ - Guideline-concordant care ($\geq$85%)
300
+ - Avoidance of low-value care (100%)
301
+ - Appropriate preventive care included ($\geq$95%)
302
+
303
+ ### Patient-Centered Metrics
304
+ - Patient preferences documented ($\geq$90%)
305
+ - Shared decision-making noted ($\geq$85%)
306
+ - Culturally appropriate care (100%)
307
+ - Health literacy addressed ($\geq$90%)
308
+
309
+ ### Safety Metrics
310
+ - Risk mitigation strategies present (100%)
311
+ - Medication safety addressed (100%)
312
+ - Emergency procedures documented (100%)
313
+ - Red flags/warning signs communicated (100%)
314
+
315
+ ## Common Documentation Deficiencies and Solutions
316
+
317
+ ### Problem: Vague Goals
318
+ **Deficiency**: "Improve diabetes"
319
+ **Solution**: "Reduce HbA1c from 8.5% to <7% within 3 months through medication intensification and lifestyle modification"
320
+
321
+ ### Problem: Missing Rationales
322
+ **Deficiency**: Lists medications without explanation
323
+ **Solution**: "Metformin 1000mg BID - first-line therapy for T2DM, reduces hepatic glucose production, target dose for HbA1c reduction"
324
+
325
+ ### Problem: No Timeline
326
+ **Deficiency**: Goals without timeframes
327
+ **Solution**: "Short-term (3 months): HbA1c <7.5%; Long-term (6 months): HbA1c <7%"
328
+
329
+ ### Problem: Incomplete Monitoring
330
+ **Deficiency**: "Monitor labs"
331
+ **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"
332
+
333
+ ### Problem: Absent Patient Education
334
+ **Deficiency**: No documentation of education provided
335
+ **Solution**: Dedicated section documenting: condition education, self-management skills taught, warning signs communicated, resources provided
336
+
337
+ ### Problem: Missing Safety Planning
338
+ **Deficiency**: No risk mitigation
339
+ **Solution**: Specific safety concerns addressed (e.g., hypoglycemia risk with insulin, monitoring plan, patient taught recognition and treatment)
340
+
341
+ ## Electronic Health Record (EHR) Integration
342
+
343
+ ### Structured Data Entry
344
+ - Use templates for consistency
345
+ - Coded diagnoses (ICD-10), procedures (CPT)
346
+ - Structured goals enable outcome tracking
347
+ - Discrete medication fields (name, dose, route, frequency)
348
+
349
+ ### Clinical Decision Support
350
+ - Evidence-based order sets
351
+ - Drug-drug interaction alerts
352
+ - Guideline reminders
353
+ - Quality measure tracking
354
+
355
+ ### Care Plan Sharing
356
+ - Patient portal access (patient-friendly version)
357
+ - Interoperability standards (C-CDA)
358
+ - Shared with care team
359
+ - Transitions of care summary
360
+
361
+ ## Audit and Peer Review
362
+
363
+ ### Internal Quality Review
364
+ - Random sample chart audits (e.g., 5% quarterly)
365
+ - Checklist-based review (completeness, quality)
366
+ - Feedback to providers
367
+ - Continuous quality improvement
368
+
369
+ ### External Review
370
+ - Payer audits (documentation supports billing)
371
+ - Regulatory surveys (Joint Commission, CMS)
372
+ - Malpractice case review
373
+ - Peer review for privileging/credentialing
374
+
375
+ ### Audit Criteria
376
+ - Documentation completeness
377
+ - Clinical appropriateness
378
+ - Regulatory compliance
379
+ - Billing integrity
380
+ - Patient safety
381
+
382
+ ## Treatment Plan Revision and Updates
383
+
384
+ ### When to Update Treatment Plans
385
+
386
+ **Scheduled Updates**:
387
+ - Chronic disease management: Every 3-6 months minimum
388
+ - Behavioral health: Every 30-90 days depending on acuity
389
+ - Rehabilitation: Weekly to biweekly during active therapy
390
+ - Annual comprehensive update for all chronic conditions
391
+
392
+ **Triggered Updates**:
393
+ - Significant change in clinical status
394
+ - New diagnosis
395
+ - Treatment goals achieved or not progressing
396
+ - Patient request or preference change
397
+ - Hospitalization or emergency department visit
398
+ - Medication changes or adverse events
399
+
400
+ ### Documentation of Changes
401
+ - Date of revision
402
+ - Reason for update
403
+ - What changed (goals, interventions, timeline)
404
+ - Provider signature
405
+ - Maintain prior versions for record
406
+
407
+ ## Specialty-Specific Requirements
408
+
409
+ ### Diabetes Management Plans
410
+ - HbA1c targets individualized
411
+ - Complication screening schedule (eyes, feet, kidneys)
412
+ - Self-monitoring blood glucose frequency
413
+ - Hypoglycemia recognition and treatment
414
+ - Sick day management
415
+
416
+ ### Heart Failure Plans
417
+ - GDMT (guideline-directed medical therapy) checklist
418
+ - Volume management (daily weights, fluid/sodium restriction)
419
+ - NYHA functional class documentation
420
+ - Device therapy consideration
421
+ - Hospitalization triggers
422
+
423
+ ### Mental Health Treatment Plans
424
+ - DSM-5 diagnostic criteria met
425
+ - Suicide/violence risk assessment
426
+ - Safety planning
427
+ - Psychotherapy modality and frequency
428
+ - Medication trials and responses
429
+ - Functional goals (return to work, relationships)
430
+
431
+ ### Chronic Pain Plans
432
+ - Comprehensive pain assessment
433
+ - Functional goals (not just pain scores)
434
+ - Multimodal analgesia
435
+ - Opioid risk assessment if prescribing
436
+ - Physical and psychological interventions
437
+ - Activity modification and pacing
438
+
439
+ ## Cultural Competence and Health Equity
440
+
441
+ ### Culturally Appropriate Care
442
+ - Recognize cultural health beliefs and practices
443
+ - Address language barriers (interpreter services)
444
+ - Respect religious and cultural preferences in treatment
445
+ - Consider social determinants of health (housing, food security, transportation)
446
+ - Avoid assumptions based on stereotypes
447
+
448
+ ### Health Literacy
449
+ - Assess patient understanding (teach-back method)
450
+ - Use plain language, avoid medical jargon
451
+ - Visual aids and written materials at appropriate reading level
452
+ - Tailor education to patient's learning style
453
+
454
+ ### Addressing Disparities
455
+ - Screen for social needs and barriers
456
+ - Connect to community resources
457
+ - Culturally tailored interventions when evidence supports
458
+ - Track outcomes by demographic groups, address disparities
459
+
460
+ ## References and Guidelines
461
+
462
+ ### General Standards
463
+ - Joint Commission Standards Manual
464
+ - CMS Conditions of Participation
465
+ - State medical board documentation requirements
466
+
467
+ ### Specialty Guidelines
468
+ - American College of Physicians (ACP)
469
+ - American Academy of Family Physicians (AAFP)
470
+ - American Psychiatric Association (APA)
471
+ - American Physical Therapy Association (APTA)
472
+ - Disease-specific societies (ADA, AHA, ACC, etc.)
473
+
474
+ ### Regulatory
475
+ - HIPAA Privacy Rule (45 CFR Part 160, 164)
476
+ - 42 CFR Part 2 (Substance Use Disorder Confidentiality)
477
+ - 21 CFR Part 11 (Electronic Records, applicable for research/trials)
478
+ - State scope of practice laws
479
+
480
+ ---
481
+
482
+ **Document Version**: 1.0
483
+ **Last Updated**: January 2025
484
+ **Next Review**: January 2026
485
+