scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl
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- scientific_writer/.claude/settings.local.json +30 -0
- scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
- scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
- scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
- scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
- scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
- scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
- scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
- scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
- scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
- scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
- scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
- scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
- scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
- scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
- scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
- scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
- scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
- scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
- scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
- scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
- scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
- scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
- scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
- scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
- scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
- scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
- scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
- scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
- scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
- scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
- scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
- scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
- scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
- scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
- scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
- scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
- scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
- scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
- scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
- scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
- scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
- scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
- scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
- scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
- scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
- scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
- scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
- scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
- scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
- scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
- scientific_writer/.claude/skills/latex-posters/README.md +417 -0
- scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
- scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
- scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
- scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
- scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
- scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
- scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
- scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
- scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
- scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
- scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
- scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
- scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
- scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
- scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
- scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
- scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
- scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
- scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
- scientific_writer/.claude/skills/markitdown/README.md +184 -0
- scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
- scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
- scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
- scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
- scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
- scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
- scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
- scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
- scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
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- scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
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- scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
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- scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
- scientific_writer/.claude/skills/research-grants/README.md +285 -0
- scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
- scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
- scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
- scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
- scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
- scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
- scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
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- scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
- scientific_writer/.claude/skills/research-lookup/README.md +116 -0
- scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
- scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
- scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
- scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
- scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
- scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
- scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
- scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
- scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
- scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
- scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
- scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
- scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
- scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
- scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
- scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
- scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
- scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
- scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
- scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
- scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
- scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
- scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
- scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
- scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
- scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
- scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
- scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
- scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
- scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
- scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
- scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
- scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
- scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
- scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
- scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
- scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
- scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
- scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
- scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
- scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
- scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
- scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
- scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
- scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
- scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
- scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
- scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
- scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
- scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
- scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
- scientific_writer/CLAUDE.md +748 -0
- scientific_writer/__init__.py +2 -2
- scientific_writer/api.py +14 -7
- scientific_writer/cli.py +12 -7
- scientific_writer/core.py +27 -5
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
- scientific_writer-2.2.2.dist-info/RECORD +312 -0
- scientific_writer-2.1.1.dist-info/RECORD +0 -11
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
- {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
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# SOAP Note Template
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## Patient Information
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**Patient Name:** [Last, First] or [Patient ID for teaching/research contexts]
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**Date of Birth:** [MM/DD/YYYY]
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**Medical Record Number:** [MRN]
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**Date of Visit:** [MM/DD/YYYY]
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**Time:** [HH:MM]
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**Location:** [Clinic, Hospital Floor, ED, etc.]
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**Provider:** [Your name and credentials]
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---
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## S - SUBJECTIVE
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### Chief Complaint (CC)
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"[Patient's chief complaint in their own words]"
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### History of Present Illness (HPI)
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[Patient Name] is a [age]-year-old [sex] with a history of [relevant PMHx] who presents with [chief complaint].
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**Onset:** [When did symptoms start? Sudden or gradual?]
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**Location:** [Where is the symptom? Does it radiate?]
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**Duration:** [How long has this been going on?]
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**Characterization:** [Describe the quality - sharp, dull, burning, etc.]
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**Aggravating factors:** [What makes it worse?]
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**Relieving factors:** [What makes it better?]
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**Timing:** [Constant or intermittent? Frequency?]
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**Severity:** [How bad is it? 0-10 scale if pain]
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**Associated symptoms:** [Other symptoms occurring with this?]
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**Prior treatment and response:** [What has patient tried? Did it help?]
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**Functional impact:** [How does this affect daily activities?]
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**Review of Systems (pertinent to visit):**
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- Constitutional: [fever, chills, weight change, fatigue, night sweats]
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- [Other relevant systems based on chief complaint]
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- **Pertinent negatives:** [Important symptoms patient denies]
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---
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## O - OBJECTIVE
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### Vital Signs
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- Temperature: \_\_\_\_\_ °F (oral/axillary/tympanic)
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- Blood Pressure: \_\_\_\_\_/\_\_\_\_\_ mmHg
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- Heart Rate: \_\_\_\_\_ bpm
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- Respiratory Rate: \_\_\_\_\_ breaths/min
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- Oxygen Saturation: \_\_\_\_\_% on [room air / O2 at \_\_ L/min]
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- Height: \_\_\_\_\_ cm / inches
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- Weight: \_\_\_\_\_ kg / lbs
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- BMI: \_\_\_\_\_ kg/m²
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- Pain Score: \_\_\_/10
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### Physical Examination
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**General Appearance:**
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[Well-appearing, no distress / ill-appearing / mild/moderate/severe distress]
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**HEENT:**
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- Head: [Normocephalic, atraumatic]
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- Eyes: [PERRLA, EOMI, conjunctiva, sclera]
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- Ears: [TMs clear bilaterally, canals patent]
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- Nose: [Nares patent, no discharge]
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- Throat: [Oropharynx clear, no erythema or exudate, mucosa moist]
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**Neck:**
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[Supple, no lymphadenopathy, no thyromegaly, no JVD, carotids 2+ without bruits]
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**Cardiovascular:**
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[RRR, normal S1/S2, no murmurs/rubs/gallops] OR [describe abnormalities]
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[Peripheral pulses: radial 2+/2+ bilaterally, dorsalis pedis 2+/2+ bilaterally]
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[Lungs clear to auscultation bilaterally, no wheezes/rales/rhonchi, normal work of breathing] OR [describe abnormalities]
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**Abdomen:**
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**Extremities:**
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[No edema, no cyanosis, no clubbing, full range of motion, no joint swelling or tenderness]
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**Skin:**
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[Warm and dry, no rashes, no lesions, normal turgor, capillary refill <2 sec]
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**Neurological:**
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- Mental status: [Alert and oriented to person, place, time]
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- Cranial nerves: [II-XII intact] OR [specify abnormalities]
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- Motor: [5/5 strength all extremities, normal tone]
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- Sensory: [Intact to light touch and pinprick]
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- Reflexes: [2+ symmetric, downgoing Babinski]
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- Gait: [Normal / not assessed]
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- Coordination: [Finger-to-nose intact, rapid alternating movements normal]
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**Psychiatric:**
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[Normal mood and affect, thought process logical and goal-directed, no SI/HI]
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### Laboratory Results (if applicable)
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| Test | Result | Reference Range | Flag |
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|------|--------|----------------|------|
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| [Test name] | [Value] [unit] | [Range] | [H/L/-] |
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### Imaging Results (if applicable)
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[Modality] ([Date]): [Key findings]
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### Other Diagnostic Tests
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[ECG, etc.]: [Results]
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---
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## A - ASSESSMENT
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### Problem List with Assessment
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**1. [Primary Problem/Diagnosis] ([ICD-10 code])**
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- [Brief assessment: severity, stability, progress toward goals]
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- [Relevant exam and lab findings supporting diagnosis]
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- [Differential diagnosis if uncertain]
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**2. [Secondary Problem/Diagnosis] ([ICD-10 code])**
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- [Assessment]
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**3. [Additional problems as needed]**
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### Overall Assessment
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[Summary statement about patient's overall status, response to treatment, trajectory]
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---
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## P - PLAN
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### Problem-Based Plan
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**1. [Primary Problem]**
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**Diagnostics:**
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- [Further tests, labs, imaging, consultations needed]
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- [Rationale for testing]
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**Therapeutics:**
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- [Medications:]
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- [Drug name] [dose] [route] [frequency] x [duration]
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- Indication: [Why prescribed]
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- [Procedures or interventions]
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- [Non-pharmacological interventions]
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**Monitoring:**
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- [What to monitor, how often]
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- [Parameters for follow-up labs or imaging]
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**Education:**
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- [Topics discussed with patient]
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- [Patient understanding verified]
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- [Written materials provided]
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**Follow-up:**
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- [When and where]
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- [Specific goals for follow-up visit]
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**Return Precautions:**
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- [When to seek urgent/emergency care]
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- [Warning signs discussed]
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**2. [Secondary Problem]**
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**Diagnostics:**
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- [Tests or studies]
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**Therapeutics:**
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- [Medications or interventions]
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**Monitoring:**
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- [Parameters to follow]
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**3. [Additional Problems]**
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[Plan for each problem]
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### Overall Plan Summary
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- Total new prescriptions: [number]
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- Referrals placed: [specialty, reason]
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- Follow-up appointment: [date/timeframe and with whom]
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- Patient verbalized understanding of plan: [Yes/No, questions answered]
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- Time spent: [Total time and time spent on counseling/coordination if relevant for billing]
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---
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## Billing Information (if applicable)
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**CPT Code:** [E/M code - 99201-99215 for office visits]
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**Level of Service Justification:**
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- History: [Problem focused / Expanded / Detailed / Comprehensive]
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- Exam: [Problem focused / Expanded / Detailed / Comprehensive]
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- Medical Decision Making: [Straightforward / Low / Moderate / High complexity]
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- Number of diagnoses/management options: [Minimal / Limited / Multiple / Extensive]
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- Amount of data to review: [Minimal / Limited / Moderate / Extensive]
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- Risk: [Minimal / Low / Moderate / High]
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[OR if time-based:]
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+
- Total time: [minutes]
|
|
212
|
+
- Time spent on counseling/coordination: [minutes] (>50% of visit)
|
|
213
|
+
|
|
214
|
+
---
|
|
215
|
+
|
|
216
|
+
## Signature
|
|
217
|
+
|
|
218
|
+
[Provider name, credentials]
|
|
219
|
+
[Electronic signature or handwritten signature]
|
|
220
|
+
[Date and time of documentation]
|
|
221
|
+
|
|
222
|
+
---
|
|
223
|
+
|
|
224
|
+
## Notes for Using This Template
|
|
225
|
+
|
|
226
|
+
**Best Practices:**
|
|
227
|
+
- Document as soon as possible after encounter
|
|
228
|
+
- Be specific and objective in observations
|
|
229
|
+
- Avoid copy-forward errors
|
|
230
|
+
- Review and update problem list
|
|
231
|
+
- Sign and date all entries
|
|
232
|
+
- Use standard abbreviations only
|
|
233
|
+
|
|
234
|
+
**Billing Considerations:**
|
|
235
|
+
- Document medical necessity
|
|
236
|
+
- Match documentation level to billing code
|
|
237
|
+
- For time-based billing, document total time and counseling time
|
|
238
|
+
- Include relevant history, exam, and MDM elements
|
|
239
|
+
|
|
240
|
+
**Legal Considerations:**
|
|
241
|
+
- Document facts, not opinions
|
|
242
|
+
- Quote patient when relevant
|
|
243
|
+
- Document non-compliance objectively
|
|
244
|
+
- Never alter records - use addendum for corrections
|
|
245
|
+
- Ensure legibility
|
|
246
|
+
|
|
247
|
+
**Customization:**
|
|
248
|
+
- Adapt level of detail to setting (quick outpatient visit vs. complex hospital consultation)
|
|
249
|
+
- Include or exclude sections as relevant
|
|
250
|
+
- Follow institutional templates if required
|
|
251
|
+
- Use problem-oriented approach consistently
|
|
252
|
+
|
|
253
|
+
|