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SamuelBrand1SamuelBrand1
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Merge branch 'CDCgov:main' into main
2 parents ae737e7 + 4a98829 commit b57aaa1

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Lines changed: 97660 additions & 231 deletions

‎.github/workflows/actionlint.yaml‎

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name: "Lint GitHub Actions Workflows"
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on:
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pull_request:
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push:
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branches: [main]
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jobs:
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actionlint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- name: "Download actionlint"
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id: get_actionlint
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run: bash <(curl https://raw.githubusercontent.com/rhysd/actionlint/main/scripts/download-actionlint.bash)
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shell: bash
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- name: "Check Workflow Files"
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run: ${{ steps.get_actionlint.outputs.executable }} -color -ignore "SC2086" -ignore "timezone"
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shell: bash

‎.github/workflows/cache-hubval-deps.yaml‎

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paths:
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- '.github/workflows/cache-hubval-deps.yaml'
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schedule:
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- cron: "10 0 * * *" # run daily at 12:10 AM UTC (7:10 PM EST)
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- cron: "10 19 * * *" # run daily at 7:10 PM ET
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timezone: "America/New_York"
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jobs:
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build-deps-cache-on-main:

‎.github/workflows/create-baseline.yaml‎

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default: ""
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type: string
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schedule:
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- cron: "30 20 * * 3" # run every Wednesday at 8:30 PM UTC (3:30 PM EST)
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- cron: "30 15 * * 3" # run every Wednesday at 3:30 PM ET
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timezone: "America/New_York"
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jobs:
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generate-baseline-forecasts:

‎.github/workflows/create-ensemble.yaml‎

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default: ""
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type: string
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schedule:
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- cron: "30 13 * * 4" # run every Thursday at 1:30 PM UTC (8:30 AM EST)
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- cron: "45 9 * * 4" # run every Thursday at 9:45 AM ET
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timezone: "America/New_York"
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jobs:
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generate-ensemble-forecasts:

‎.github/workflows/hubverse-aws-upload.yaml‎

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jobs:
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upload:
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# Don't run on forked repositories
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# don't run on forked repositories
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if: github.event.repository.fork != true
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runs-on: ubuntu-latest
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steps:
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- name: "Checkout"
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uses: actions/checkout@v6
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- name: "Checkout"
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uses: actions/checkout@v6
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- name: "Get hub cloud config"
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# save cloud-related fields from admin config as environment variables
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# (jq json parser is installed on Github-hosted runners)
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run: |
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cloud_enabled=$(cat ./hub-config/admin.json | jq -r '.cloud.enabled') \
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&& echo "CLOUD_ENABLED=$cloud_enabled"
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cloud_storage_location=$(cat ./hub-config/admin.json | jq -r '.cloud.host.storage_location') \
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&& echo "CLOUD_STORAGE_LOCATION=$cloud_storage_location"
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echo "CLOUD_ENABLED=$cloud_enabled" >> $GITHUB_ENV
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echo "CLOUD_STORAGE_LOCATION=$cloud_storage_location" >> $GITHUB_ENV
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- name: "Get Hub Cloud Config"
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# save cloud-related fields from admin config as environment variables
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# (jq json parser is installed on Github-hosted runners)
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run: |
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cloud_enabled=$(jq -r '.cloud.enabled' ./hub-config/admin.json) \
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&& echo "CLOUD_ENABLED=$cloud_enabled"
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cloud_storage_location=$(jq -r '.cloud.host.storage_location' ./hub-config/admin.json) \
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&& echo "CLOUD_STORAGE_LOCATION=$cloud_storage_location"
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echo "CLOUD_ENABLED=$cloud_enabled" >> $GITHUB_ENV
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echo "CLOUD_STORAGE_LOCATION=$cloud_storage_location" >> $GITHUB_ENV
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- name: "Configure AWS credentials"
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# request credentials to assume the hub's AWS role via OpenID Connect
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if: env.CLOUD_ENABLED == 'true'
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uses: aws-actions/configure-aws-credentials@v6
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with:
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role-to-assume: arn:aws:iam::${{ env.AWS_ACCOUNT }}:role/${{ env.CLOUD_STORAGE_LOCATION }}
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aws-region: us-east-1
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- name: "Configure AWS Credentials"
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# request credentials to assume the hub's AWS role via OpenID Connect
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if: env.CLOUD_ENABLED == 'true'
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uses: aws-actions/configure-aws-credentials@v6
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with:
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role-to-assume: arn:aws:iam::${{ env.AWS_ACCOUNT }}:role/${{ env.CLOUD_STORAGE_LOCATION }}
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aws-region: us-east-1
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- name: "Install rclone"
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if: env.CLOUD_ENABLED == 'true'
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run: |
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# debian version of rclone is outdated and will result in config name errors
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# https://github.com/rclone/rclone/issues/6060
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curl https://rclone.org/install.sh | sudo bash
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rclone version
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- name: "Install rclone"
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if: env.CLOUD_ENABLED == 'true'
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run: |
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# debian version of rclone is outdated and will result in config name errors
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# https://github.com/rclone/rclone/issues/6060
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curl https://rclone.org/install.sh | sudo bash
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rclone version
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- name: "Sync files to cloud storage"
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# sync specified hub directories to S3
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# (to exclude a directory, remove it from the hub_directories list below)
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if: env.CLOUD_ENABLED == 'true'
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run: |
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hub_directories=(
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'auxiliary-data'
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'hub-config'
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'model-abstracts'
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'model-metadata'
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'target-data'
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)
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for DIRECTORY in "${hub_directories[@]}"
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do
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if [ -d "./$DIRECTORY" ]
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then
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rclone sync \
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"./$DIRECTORY/" \
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":s3,provider=AWS,env_auth:$BUCKET_NAME/$DIRECTORY" \
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--checksum --verbose --stats-one-line --config=/dev/null
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fi
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done
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# unlike other data, model-outputs are synced to a "raw" location
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# so we can transform it before presenting to users
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rclone sync ./model-output/ ":s3,provider=AWS,env_auth:$BUCKET_NAME/raw/model-output" \
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--checksum --verbose --stats-one-line --config=/dev/null
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shell: bash
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env:
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BUCKET_NAME: ${{ env.CLOUD_STORAGE_LOCATION }}
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- name: "Sync Files To Cloud Storage"
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# sync specified hub directories to S3
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# (to exclude a directory, remove it from the hub_directories list below)
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if: env.CLOUD_ENABLED == 'true'
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run: |
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hub_directories=(
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'auxiliary-data'
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'hub-config'
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'model-abstracts'
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'model-metadata'
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'target-data'
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)
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for DIRECTORY in "${hub_directories[@]}"
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do
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if [ -d "./$DIRECTORY" ]
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then
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rclone sync \
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"./$DIRECTORY/" \
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":s3,provider=AWS,env_auth:$BUCKET_NAME/$DIRECTORY" \
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--checksum --verbose --stats-one-line --config=/dev/null
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fi
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done
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# unlike other data, model-outputs are synced to a "raw" location
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# so we can transform it before presenting to users
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rclone sync ./model-output/ ":s3,provider=AWS,env_auth:$BUCKET_NAME/raw/model-output" \
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--checksum --verbose --stats-one-line --config=/dev/null
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shell: bash
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env:
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BUCKET_NAME: ${{ env.CLOUD_STORAGE_LOCATION }}

‎.github/workflows/update-target-data.yaml‎

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type: boolean
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default: true
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schedule:
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- cron: "00 17 * * 3" # run every Wednesday at 5:00 PM UTC (1:00 PM EST)
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- cron: "00 13 * * 3" # run every Wednesday at 1:00 PM ET
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timezone: "America/New_York"
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jobs:
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update-target-data:
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api_key_secret: ${{ secrets.NHSN_API_KEY_SECRET }}
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legacy_file: "true"
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nssp_update_local: ${{ inputs.nssp_update_local || 'true' }}
43+
# JSON array (e.g., '["VI", "GU"]') excludes from all targets.
44+
# JSON object (e.g., '{"all": ["VI"], "wk inc covid hosp": ["GU"]}')
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# supports target-specific exclusions.
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excluded_locations: '["VI", "GU", "AS", "MP", "UM"]'

‎auxiliary-data/nssp-raw-data/latest.parquet‎

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‎auxiliary-data/weekly-model-submissions/2026-03-28-models-submitted-to-hub.csv‎

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model_id,designated_model,target
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CADPH-CovidCAT_Ensemble,TRUE,wk inc covid hosp
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CEPH-Rtrend_covid,TRUE,wk inc covid hosp
4+
CFA-EpiAutoGP,TRUE,wk inc covid hosp
5+
CFA_Pyrenew-Pyrenew_HE_COVID,TRUE,wk inc covid hosp
6+
CFA_Pyrenew-Pyrenew_H_COVID,FALSE,wk inc covid hosp
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CMU-TimeSeries,TRUE,wk inc covid hosp
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CovidHub-baseline,FALSE,wk inc covid hosp
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Google_SAI-Ensemble,TRUE,wk inc covid hosp
10+
NEU_ISI-AdaptiveEnsemble,TRUE,wk inc covid hosp
11+
OHT_JHU-nbxd,TRUE,wk inc covid hosp
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UGA_flucast-INFLAenza,TRUE,wk inc covid hosp
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UM-DeepOutbreak,TRUE,wk inc covid hosp
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UMass-ar6_pooled,TRUE,wk inc covid hosp
15+
UMass-gbqr,TRUE,wk inc covid hosp
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CFA_Pyrenew-Pyrenew_E_COVID,FALSE,wk inc covid prop ed visits
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CFA_Pyrenew-Pyrenew_HE_COVID,TRUE,wk inc covid prop ed visits
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CMU-TimeSeries,TRUE,wk inc covid prop ed visits
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CovidHub-baseline,FALSE,wk inc covid prop ed visits
20+
UGA_flucast-INFLAenza,TRUE,wk inc covid prop ed visits

‎model-output/CADPH-CovidCAT_Ensemble/2026-04-04-CADPH-CovidCAT_Ensemble.csv‎

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"reference_date","target","horizon","target_end_date","location","output_type","output_type_id","value"
2+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.01,71.1129078111157
3+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.025,74.736567793583
4+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.05,78.23633360302
5+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.1,82.3247127163511
6+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.15,85.2756689226037
7+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.2,87.6969272396646
8+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.25,89.8289770797168
9+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.3,91.7437913472933
10+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.35,93.5321515095574
11+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.4,95.2765622215838
12+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.45,96.990214426584
13+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.5,98.812580929932
14+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.55,100.551866111295
15+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.6,102.35841887818
16+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.65,104.279136232323
17+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.7,106.317947493455
18+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.75,108.603523524445
19+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.8,111.272183923983
20+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.85,114.407914484415
21+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.9,118.468749024362
22+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.95,124.727951191312
23+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.975,130.181553199048
24+
2026-04-04,"wk inc covid hosp",0,2026-04-04,"06","quantile",0.99,136.956551943212
25+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.01,50.1105124472673
26+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.025,53.7882942648696
27+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.05,57.6452483930072
28+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.1,62.336459115263
29+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.15,65.8210624195844
30+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.2,68.7927402548316
31+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.25,71.4294754895045
32+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.3,73.9994217558229
33+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.35,76.3085913670353
34+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.4,78.7778184931867
35+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.45,81.1223964026666
36+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.5,83.5232831417435
37+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.55,85.9920367828532
38+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.6,88.5215888632877
39+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.65,91.2069748726711
40+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.7,94.2032055435601
41+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.75,97.5059423609345
42+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.8,101.268511182957
43+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.85,105.900799551889
44+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.9,111.884574760719
45+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.95,121.630356360632
46+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.975,130.310762056168
47+
2026-04-04,"wk inc covid hosp",1,2026-04-11,"06","quantile",0.99,141.199013871096
48+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.01,36.8380156747834
49+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.025,40.0283479136355
50+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.05,43.3638513660655
51+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.1,48.0148535967993
52+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.15,51.5024465909321
53+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.2,54.5583776998348
54+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.25,57.4177530532217
55+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.3,60.0813580646942
56+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.35,62.6493684896497
57+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.4,65.2508721894755
58+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.45,67.9362977739911
59+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.5,70.5312681602777
60+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.55,73.4720836279795
61+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.6,76.3778910476035
62+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.65,79.5035249854776
63+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.7,82.9973954751612
64+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.75,86.9435095688471
65+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.8,91.4512388521501
66+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.85,96.9848304379833
67+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.9,104.58282497684
68+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.95,116.630976715807
69+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.975,127.759163356159
70+
2026-04-04,"wk inc covid hosp",2,2026-04-18,"06","quantile",0.99,142.853555970721
71+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.01,29.6926911207556
72+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.025,32.6176711022205
73+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.05,35.4900153864744
74+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.1,39.6861646559083
75+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.15,43.0195559285366
76+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.2,46.1300506323518
77+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.25,48.9661585397726
78+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.3,51.7057813211915
79+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.35,54.4541777914449
80+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.4,57.2497768980894
81+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.45,60.0512304091141
82+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.5,62.9067217266092
83+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.55,66.0717751139374
84+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.6,69.2879526575499
85+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.65,72.8589479543789
86+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.7,76.8295732184075
87+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.75,81.3967151374679
88+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.8,86.6629914659948
89+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.85,93.2190119811787
90+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.9,102.111499689969
91+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.95,116.793010908382
92+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.975,130.660815876919
93+
2026-04-04,"wk inc covid hosp",3,2026-04-25,"06","quantile",0.99,148.900066031035

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