CADPH-CATaLog.yml

# Required fields
team_name: "California Department of Public Health"  # No more than 50 characters
team_abbr: "CADPH"  # Up to 16 alphanumeric characters or underscores

model_name: "Clade Assessment Tool, a Logistic Growth Function"  # No more than 50 characters
model_abbr: "CATaLog"  # Up to 16 alphanumeric characters or underscores

model_contributors:
  [
    {
      "name": "Brent Siegel",
      "affiliation": "California Department of Public Health, Center for Infectious Diseases, Modeling and Advanced Analytics Section",
      "email": "brent.siegel@cdph.ca.gov",
      "orcid": "0000-0002-4695-9474"
    },
    {
      "name": "Mugdha Thakur",
      "affiliation": "California Department of Public Health, Center for Infectious Diseases, Modeling and Advanced Analytics Section",
      "email": "mugdha.thakur@cdph.ca.gov",
       "orcid": "0000-0002-3883-8656"
    },
    {
      "name": "Natalie Linton",
      "affiliation": "California Department of Public Health, Center for Infectious Diseases, Modeling and Advanced Analytics Section",
      "email": "natalie.linton@cdph.ca.gov",
      "orcid": "0000-0002-5464-0076"
    },
    {
      "name": "Chris Hoover",
      "affiliation": "Formerly: California Department of Public Health, Center for Infectious Diseases, Modeling and Advanced Analytics Section",
      "email": "chris.hoover@cdph.ca.gov"
    },
    {
      "name": "Rahil Ryder",
      "affiliation": "California Department of Public Health, Center for Laboratory Sciences, Viral and Rickettsial Disease Laboratory",
      "email": "rahil.ryder@cdph.ca.gov"
    },
    {
      "name": "Jesse Elder",
      "affiliation": "California Department of Public Health, Center for Laboratory Sciences, Viral and Rickettsial Disease Laboratory",
      "email": "jesse.elder@cdph.ca.gov"
    },
    {
      "name": "Tomas Leon",
      "affiliation": "California Department of Public Health, Center for Infectious Diseases, Modeling and Advanced Analytics Section",
      "email": "tomas.leon@cdph.ca.gov"
    }
  ]

license: "CC-BY-4.0"  # Choose from accepted licenses

team_funding:
  - "The content is solely the responsibility of the authors and does not necessarily represent the official views of the California Department of Public Health or the California Health and Human Services Agency."

methods: "Fits a logistic growth function to data. Based on Althaus, Christian L., et al. ''A Tale of Two Variants: Spread of SARS-CoV-2 Variants Alpha in Geneva, Switzerland, and Beta in South Africa. 1.1 Adds filtering criteria/ GISAID data addition"

methods_url: "https://calcat.cdph.ca.gov"

data_sources:
  - "Theiagen Genomics manages the viral sequence data."

ensemble_of_models: false  # Set to true if it is an ensemble of separate models

ensemble_of_hub_models: false  # Set to true if it is an ensemble of hub-submitted models

# Optional fields
model_version: "1.2"  # Optional version identifier

repo_url: "https://github.com/breesie/variant-nowcast-hub" # Optional repository URL

citation:
- "Wadford et al. Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance. Front Public Health. 2023 Oct 23;11:1249614. doi: 10.3389/fpubh.2023.1249614. PMID: 37937074; PMCID: PMC10627185."