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479 make the input messages format json ld (#495)
* Sandbox generator and input messages examples are made json-ld. pipeline updated to be able to consime new json-ld formatted inpu files. Minor bug fix related to preferences setup in batch-csv command line interface. Readme updated * context file added * sandbox json input files updated using the context file
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‎context/1.0/context.jsonld‎

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{
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"@id": "https://display-lab.github.io/scaffold/context.jsonld",
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"@context": {
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"dc": "http://purl.org/dc/elements/1.1/",
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"dcterms": "http://purl.org/dc/terms/",
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"schema": "http://schema.org/",
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"scaffold": "http://displaylab.com/scaffold#",
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"psdo": "http://purl.obolibrary.org/obo/",
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"fhir": "http://hl7.org/fhir/",
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"message_template": {
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"@id": "psdo:PSDO_0000002"
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},
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"measure": {
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"@id": "psdo:PSDO_0000102"
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},
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"performance_summary_document": {
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"@id": "psdo:PSDO_0000098"
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},
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"performance_measure_report": {
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"@id": "psdo:PSDO_0000107"
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},
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"performance_month": {
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"@id": "scaffold:performance_month"
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},
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"History": {
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"@id": "scaffold:History"
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},
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"Preferences": {
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"@id": "scaffold:Preferences"
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},
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"comparator_measure_report": {
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"@id": "scaffold:comparator_measure_report"
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},
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"PractitionerRole": {
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"@id": "scaffold:PractitionerRole"
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},
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"subject": {
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"@id": "scaffold:subject"
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},
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"PractitionerRole.identifier": {
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"@id": "scaffold:PractitionerRole.identifier"
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},
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"PractitionerRole.practitioner": {
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"@id": "scaffold:PractitionerRole.practitioner"
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},
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"PractitionerRole.organization": {
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"@id": "scaffold:PractitionerRole.organization"
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},
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"PractitionerRole.code": {
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"@id": "scaffold:PractitionerRole.code"
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},
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"identifier": {
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"@id": "scaffold:identifier"
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},
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"period.start": {
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"@id": "scaffold:period.start"
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},
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"period.end": {
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"@id": "scaffold:period.end"
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},
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"measureScore.rate": {
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"@id": "scaffold:measureScore.rate"
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},
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"measureScore.denominator": {
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"@id": "scaffold:measureScore.denominator"
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},
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"measureScore.range": {
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"@id": "scaffold:measureScore.range"
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},
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"group.subject": {
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"@id": "scaffold:group.subject"
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},
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"group.code": {
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"@id": "scaffold:group.code"
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},
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"message_template_name": {
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"@id": "scaffold:message_template_name"
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},
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"message_generated_datetime": {
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"@id": "scaffold:message_generated_datetime:"
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},
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"acceptable_by": {
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"@id": "scaffold:acceptable_by"
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},
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"Utilities": {
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"@id": "scaffold:Utilities"
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},
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"Message_Format": {
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"@id": "scaffold:Message_Format"
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},
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"Display_Format": {
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"@id": "scaffold:Display_Format"
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},
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"Social gain": {
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"@id": "scaffold:Social_gain"
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},
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"Worsening": {
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"@id": "scaffold:Worsening"
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},
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"Bar chart": {
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"@id": "scaffold:Bar_chart"
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},
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"Line chart": {
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"@id": "scaffold:Line_chart"
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}
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}
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}

‎data ingestion model/README.md‎

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Here is an example of the output from SCAFFOLD after processing the sandbox example data:
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Successful: 100, Failed: 0
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| # | causal_pathway | count | % |
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| -- | --------------- | ----- | ---- |
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| 0 | Goal Approach | 10 | 10.0 |
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| 1 | Goal Gain | 3 | 3.0 |
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| 2 | Goal Loss | 7 | 7.0 |
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| 3 | Goal Worse | 1 | 1.0 |
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| 4 | Improving | 14 | 14.0 |
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| 5 | Social Approach | 20 | 20.0 |
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| 6 | Social Better | 1 | 1.0 |
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| 7 | Social Gain | 6 | 6.0 |
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| 8 | Social Loss | 13 | 13.0 |
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| 9 | Social Worse | 15 | 15.0 |
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| 10 | Worsening | 10 | 10.0 |
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| # | causal_pathway | acceptable | % acceptable | acceptable_score | selected | % selected | selected_score | % of acceptable selected |
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| -- | --------------- | ---------- | ------------ | ---------------- | -------- | ---------- | -------------- | ------------------------ |
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| 0 | Goal Approach | 36 | 1.0 | 2.82 | 10 | 10.0 | 2.98 | 27.8 |
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| 1 | Goal Gain | 53 | 1.4 | 2.44 | 3 | 3.0 | 2.78 | 5.7 |
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| 2 | Goal Loss | 129 | 3.5 | 2.34 | 7 | 7.0 | 2.89 | 5.4 |
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| 3 | Goal Worse | 563 | 15.2 | 2.21 | 1 | 1.0 | 2.89 | 0.2 |
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| 4 | Improving | 159 | 4.3 | 2.69 | 14 | 14.0 | 2.88 | 8.8 |
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| 5 | Social Approach | 104 | 2.8 | 2.80 | 20 | 20.0 | 2.96 | 19.2 |
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| 6 | Social Better | 352 | 9.5 | 2.27 | 1 | 1.0 | 2.65 | 0.3 |
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| 7 | Social Gain | 137 | 3.7 | 2.41 | 6 | 6.0 | 2.94 | 4.4 |
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| 8 | Social Loss | 229 | 6.2 | 2.39 | 13 | 13.0 | 2.93 | 5.7 |
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| 9 | Social Worse | 1696 | 45.8 | 2.20 | 15 | 15.0 | 2.83 | 0.9 |
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| 10 | Worsening | 246 | 6.6 | 2.63 | 10 | 10.0 | 2.83 | 4.1 |
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| # | message | acceptable | % acceptable | acceptable_score | selected | % selected | selected_score | % of acceptable selected |
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| -- | -------------------------------------------- | ---------- | ------------ | ---------------- | -------- | ---------- | -------------- | ------------------------ |
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| 0 | Achieved Peer Average | 61 | 1.6 | 2.39 | 1 | 1.0 | 2.76 | 1.6 |
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| 1 | Achieved Top 10 Peer Benchmark | 76 | 2.1 | 2.42 | 5 | 5.0 | 2.98 | 6.6 |
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| 2 | Approach Goal | 36 | 1.0 | 2.82 | 10 | 10.0 | 2.98 | 27.8 |
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| 3 | Approach Peer Average | 21 | 0.6 | 2.79 | 1 | 1.0 | 3.39 | 4.8 |
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| 4 | Approach Top 10 Peer Benchmark | 83 | 2.2 | 2.81 | 19 | 19.0 | 2.94 | 22.9 |
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| 5 | Drop Below Goal | 129 | 3.5 | 2.34 | 7 | 7.0 | 2.89 | 5.4 |
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| 6 | Drop Below Peer Average | 136 | 3.7 | 2.36 | 4 | 4.0 | 2.94 | 2.9 |
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| 7 | Getting Worse | 246 | 6.6 | 2.63 | 10 | 10.0 | 2.83 | 4.1 |
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| 8 | No Longer Top Performer | 93 | 2.5 | 2.55 | 9 | 9.0 | 2.93 | 9.7 |
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| 9 | Not Top Performer | 848 | 22.9 | 2.20 | 7 | 7.0 | 2.82 | 0.8 |
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| 10 | Opportunity to Improve Goal | 563 | 15.2 | 2.21 | 1 | 1.0 | 2.89 | 0.2 |
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| 11 | Opportunity to Improve Top 10 Peer Benchmark | 848 | 22.9 | 2.20 | 8 | 8.0 | 2.85 | 0.9 |
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| 12 | Performance Improving | 159 | 4.3 | 2.69 | 14 | 14.0 | 2.88 | 8.8 |
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| 13 | Reached Goal | 53 | 1.4 | 2.44 | 3 | 3.0 | 2.78 | 5.7 |
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| 14 | Top Performer | 352 | 9.5 | 2.27 | 1 | 1.0 | 2.65 | 0.3 |
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| # | measure | acceptable | % acceptable | acceptable_score | selected | % selected | selected_score | % of acceptable selected |
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| -- | --------------------- | ---------- | ------------ | ---------------- | -------- | ---------- | -------------- | ------------------------ |
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| 0 | Care-Rating-01 | 338 | 9.1 | 2.34 | 7 | 7.0 | 2.85 | 2.1 |
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| 1 | Clean-Rating-01 | 330 | 8.9 | 2.28 | 12 | 12.0 | 2.93 | 3.6 |
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| 2 | Discharge-01 | 299 | 8.1 | 2.27 | 10 | 10.0 | 2.91 | 3.3 |
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| 3 | Hand-01 | 287 | 7.7 | 2.33 | 5 | 5.0 | 2.88 | 1.7 |
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| 4 | Nurse-informed-01 | 270 | 7.3 | 2.34 | 7 | 7.0 | 2.90 | 2.6 |
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| 5 | Nurse-language-01 | 286 | 7.7 | 2.38 | 11 | 11.0 | 2.86 | 3.8 |
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| 6 | Patient-Concern-01 | 288 | 7.8 | 2.34 | 3 | 3.0 | 2.94 | 1.0 |
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| 7 | Physician-informed-01 | 295 | 8.0 | 2.24 | 9 | 9.0 | 2.85 | 3.1 |
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| 8 | Physician-language-01 | 299 | 8.1 | 2.30 | 5 | 5.0 | 2.92 | 1.7 |
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| 9 | Provider-Rating-01 | 264 | 7.1 | 2.32 | 6 | 6.0 | 2.87 | 2.3 |
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| 10 | Quiet-Rating-01 | 361 | 9.7 | 2.28 | 12 | 12.0 | 2.90 | 3.3 |
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| 11 | Transfer-01 | 387 | 10.4 | 2.24 | 13 | 13.0 | 2.97 | 3.4 |
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| causal_pathway | count | % |
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|-----------------|-------|------|
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| Goal Approach | 11 | 11.0 |
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| Goal Gain | 3 | 3.0 |
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| Goal Loss | 7 | 7.0 |
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| Goal Worse | 1 | 1.0 |
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| Improving | 14 | 14.0 |
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| Social Approach | 18 | 18.0 |
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| Social Better | 1 | 1.0 |
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| Social Gain | 6 | 6.0 |
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| Social Loss | 13 | 13.0 |
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| Social Worse | 16 | 16.0 |
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| Worsening | 10 | 10.0 |
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| causal_pathway | acceptable | % acceptable | acceptable_score | selected | % selected | selected_score | % of acceptable selected |
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|-----------------|------------|--------------|-----------------|----------|------------|----------------|---------------------------|
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| Goal Approach | 36 | 1.0 | 2.78 | 11 | 11.0 | 2.90 | 30.6 |
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| Goal Gain | 53 | 1.4 | 2.43 | 3 | 3.0 | 2.78 | 5.7 |
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| Goal Loss | 129 | 3.5 | 2.32 | 7 | 7.0 | 2.89 | 5.4 |
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| Goal Worse | 563 | 15.2 | 2.19 | 1 | 1.0 | 2.89 | 0.2 |
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| Improving | 159 | 4.3 | 2.69 | 14 | 14.0 | 2.88 | 8.8 |
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| Social Approach | 104 | 2.8 | 2.77 | 18 | 18.0 | 2.86 | 17.3 |
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| Social Better | 352 | 9.5 | 2.30 | 1 | 1.0 | 2.65 | 0.3 |
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| Social Gain | 137 | 3.7 | 2.41 | 6 | 6.0 | 2.94 | 4.4 |
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| Social Loss | 229 | 6.2 | 2.37 | 13 | 13.0 | 2.93 | 5.7 |
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| Social Worse | 1696 | 45.8 | 2.18 | 16 | 16.0 | 2.81 | 0.9 |
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| Worsening | 246 | 6.6 | 2.63 | 10 | 10.0 | 2.83 | 4.1 |
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| message | acceptable | % acceptable | acceptable_score | selected | % selected | selected_score | % of acceptable selected |
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|----------------------------------------|------------|--------------|-----------------|----------|------------|----------------|---------------------------|
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| Achieved Peer Average | 61 | 1.6 | 2.38 | 1 | 1.0 | 2.78 | 1.6 |
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| Achieved Top 10 Peer Benchmark | 76 | 2.1 | 2.42 | 5 | 5.0 | 2.98 | 6.6 |
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| Approach Goal | 36 | 1.0 | 2.78 | 11 | 11.0 | 2.90 | 30.6 |
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| Approach Peer Average | 21 | 0.6 | 2.76 | 0 | 0.0 | NaN | 0.0 |
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| Approach Top 10 Peer Benchmark | 83 | 2.2 | 2.77 | 18 | 18.0 | 2.86 | 21.7 |
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| Drop Below Goal | 129 | 3.5 | 2.32 | 7 | 7.0 | 2.89 | 5.4 |
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| Drop Below Peer Average | 136 | 3.7 | 2.34 | 4 | 4.0 | 2.94 | 2.9 |
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| Getting Worse | 246 | 6.6 | 2.63 | 10 | 10.0 | 2.83 | 4.1 |
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| No Longer Top Performer | 93 | 2.5 | 2.51 | 9 | 9.0 | 2.93 | 9.7 |
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| Not Top Performer | 848 | 22.9 | 2.18 | 7 | 7.0 | 2.76 | 0.8 |
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| Opportunity to Improve Goal | 563 | 15.2 | 2.19 | 1 | 1.0 | 2.89 | 0.2 |
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| Opportunity to Improve Top 10 Peer Benchmark | 848 | 22.9 | 2.18 | 9 | 9.0 | 2.84 | 1.1 |
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| Performance Improving | 159 | 4.3 | 2.69 | 14 | 14.0 | 2.88 | 8.8 |
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| Reached Goal | 53 | 1.4 | 2.43 | 3 | 3.0 | 2.78 | 5.7 |
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| Top Performer | 352 | 9.5 | 2.30 | 1 | 1.0 | 2.65 | 0.3 |
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| measure | acceptable | % acceptable | acceptable_score | selected | % selected | selected_score | % of acceptable selected |
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|------------------------|-------------|---------------|------------------|-----------|-------------|----------------|---------------------------|
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| Care-Rating-01 | 338 | 9.1 | 2.33 | 8 | 8.0 | 2.84 | 2.4 |
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| Clean-Rating-01 | 330 | 8.9 | 2.26 | 12 | 12.0 | 2.88 | 3.6 |
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| Discharge-01 | 299 | 8.1 | 2.25 | 10 | 10.0 | 2.85 | 3.3 |
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| Hand-01 | 287 | 7.7 | 2.34 | 5 | 5.0 | 2.88 | 1.7 |
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| Nurse-informed-01 | 270 | 7.3 | 2.33 | 6 | 6.0 | 2.86 | 2.2 |
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| Nurse-language-01 | 286 | 7.7 | 2.37 | 11 | 11.0 | 2.82 | 3.8 |
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| Patient-Concern-01 | 288 | 7.8 | 2.34 | 3 | 3.0 | 2.94 | 1.0 |
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| Physician-informed-01 | 295 | 8.0 | 2.23 | 9 | 9.0 | 2.85 | 3.1 |
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| Physician-language-01 | 299 | 8.1 | 2.28 | 5 | 5.0 | 2.92 | 1.7 |
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| Provider-Rating-01 | 264 | 7.1 | 2.31 | 6 | 6.0 | 2.87 | 2.3 |
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| Quiet-Rating-01 | 361 | 9.7 | 2.25 | 12 | 12.0 | 2.84 | 3.3 |
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| Transfer-01 | 387 | 10.4 | 2.22 | 13 | 13.0 | 2.92 | 3.4 |
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SCAFFOLD also creates a `messages` folder, which contains a summary of the generated candidates (`candidates.csv`) and a detailed JSON file for each generated message. Each JSON file includes information about the selected message, all created candidates with their scoring details, and any generated images.

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