SIR model

Name: SIR

Description: The SIR model

Compartments

Compartment: Susceptible

  • Code name: sus
  • Value can be used for calibration
  • Appears in the databook
  • Databook values will be used for model initialization
  • Description:
  • Data entry guidance:

Compartment: Infected

  • Code name: inf
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Compartment: Recovered

  • Code name: rec
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Compartment: Dead

  • Code name: dead
  • Is sink
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Characteristics

Characteristic: Total number of entities

  • Code name: ch_all
  • Value can be used for calibration
  • Includes:
    • Susceptible
    • Infected
    • Recovered
  • Appears in the databook
  • Databook values will be used for model initialization
  • Description:
  • Data entry guidance:

Characteristic: Prevalence

  • Code name: ch_prev
  • Value can be used for calibration
  • Includes:
    • Infected
  • Denominator: Total number of entities
  • Appears in the databook
  • Databook values will be used for model initialization
  • Description:
  • Data entry guidance:

Characteristic: Number ever infected

  • Code name: ch_infrec
  • Includes:
    • Infected
    • Recovered
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Characteristic: Number infected or susceptible

  • Code name: ch_infsus
  • Includes:
    • Infected
    • Susceptible
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Characteristic: Number not at risk of death

  • Code name: ch_newinf
  • Includes:
    • Susceptible
    • Recovered
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Characteristic: Proportion ever infected

  • Code name: ch_propinfrec
  • Includes:
    • Number ever infected
  • Denominator: Total number of entities
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Characteristic: Proportion infected or susceptible

  • Code name: ch_propinfsus
  • Includes:
    • Number infected or susceptible
  • Denominator: Total number of entities
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Characteristic: Proportion not at risk of death

  • Code name: ch_propnewinf
  • Includes:
    • Number not at risk of death
  • Denominator: Total number of entities
  • Does not appear in the databook
  • Description:
  • Data entry guidance:

Parameters

Parameter: Transmission probability per contact

  • Code name: transpercontact
  • Value can be used for calibration
  • Units/format: probability
  • Default value: 0.0008
  • Appears in the databook
  • Used to compute:
    • “Force of infection”
  • Description:
  • Data entry guidance:

Parameter: Number of contacts annually

  • Code name: contacts
  • Value can be used for calibration
  • Units/format: None
  • Default value: 80
  • Appears in the databook
  • Used to compute:
    • “Force of infection”
  • Description:
  • Data entry guidance:

Parameter: Average duration of infections (years)

  • Code name: recrate
  • Value can be used for calibration
  • Units/format: duration
  • Contributes to transitions from:
    • “Infected” to “Recovered”
  • Default value: 0.5
  • Appears in the databook
  • Description:
  • Data entry guidance:

Parameter: Death rate for infected people

  • Code name: infdeath
  • Value can be used for calibration
  • Units/format: probability
  • Contributes to transitions from:
    • “Infected” to “Dead”
  • Default value: 0.016
  • Appears in the databook
  • Description:
  • Data entry guidance:

Parameter: Death rate for susceptible people

  • Code name: susdeath
  • Value can be used for calibration
  • Units/format: probability
  • Contributes to transitions from:
    • “Susceptible” to “Dead”
    • “Infected” to “Dead”
    • “Recovered” to “Dead”
  • Default value: 0.008
  • Appears in the databook
  • Used to compute:
    • “Force of infection”
  • Description:
  • Data entry guidance:

Parameter: Force of infection

  • Code name: foi
  • Units/format: probability
  • Contributes to transitions from:
    • “Susceptible” to “Infected”
  • Default value: None
  • Does not appear in the databook
  • This parameter’s value is computed by a function: (1 - (1-ch_prev*transpercontact)**floor(contacts)*(1-ch_prev*transpercontact*(contacts-floor(contacts))))*(1-susdeath)
  • Depends on:
    • “Prevalence”
    • “Transmission probability per contact”
    • “Death rate for susceptible people”
    • “Number of contacts annually”
  • Description:
  • Data entry guidance:

Interactions

Cascades

Cascade: main

  • Description:
  • Stages:
    • Total number of entities
      • Total number of entities
    • Number ever infected
      • Infected
      • Recovered
    • Recovered
      • Recovered