TB simple with dynamics

Name: TB with dynamics

Description: Framework for a simple TB model with vital dynamics and new cases

Compartments

Compartment: Source

  • Code name: source

  • Is source

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Susceptible

  • Code name: sus

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Vaccinated

  • Code name: vac

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Undiagnosed

  • Code name: undx

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Diagnosed

  • Code name: dx

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Notified and treated

  • Code name: tx

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Lost to follow-up

  • Code name: lost

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Successfully treated (comp)

  • Code name: txs

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Dead (TB)

  • Code name: dead_tb

  • Is sink

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Compartment: Dead (other)

  • Code name: dead_other

  • Is sink

  • Does not appear in the databook

  • Description:

  • Data entry guidance:

Characteristics

Characteristic: Population size

  • Code name: alive

  • Value can be used for calibration

  • Includes:

    • Susceptible

    • Vaccinated

    • Undiagnosed

    • Diagnosed

    • Notified and treated

    • Lost to follow-up

    • Successfully treated (comp)

  • Appears in the databook

  • Databook values will be used for model initialization

  • Description:

  • Data entry guidance:

Characteristic: TB burden

  • Code name: all_people

  • Value can be used for calibration

  • Includes:

    • Undiagnosed

    • Diagnosed

    • Notified and treated

    • Lost to follow-up

    • Successfully treated (comp)

  • Appears in the databook

  • Databook values will be used for model initialization

  • Description:

  • Data entry guidance:

Characteristic: Notified

  • Code name: all_dx

  • Value can be used for calibration

  • Includes:

    • Diagnosed

    • Notified and treated

    • Lost to follow-up

    • Successfully treated (comp)

  • Appears in the databook

  • Databook values will be used for model initialization

  • Description:

  • Data entry guidance:

Characteristic: In care

  • Code name: all_curr_linked

  • Value can be used for calibration

  • Includes:

    • Diagnosed

    • Notified and treated

    • Successfully treated (comp)

  • Appears in the databook

  • Databook values will be used for model initialization

  • Description:

  • Data entry guidance:

Characteristic: Treated

  • Code name: all_tx

  • Value can be used for calibration

  • Includes:

    • Notified and treated

    • Successfully treated (comp)

  • Appears in the databook

  • Databook values will be used for model initialization

  • Description:

  • Data entry guidance:

Characteristic: Successfully treated

  • Code name: all_vs

  • Value can be used for calibration

  • Includes:

    • Successfully treated (comp)

  • Appears in the databook

  • Databook values will be used for model initialization

  • Description:

  • Data entry guidance:

Parameters

Parameter: Annual number of births

  • Code name: birth_rate

  • Units/format: number

  • Value restrictions: At least 0

  • Contributes to transitions from:

    • “Source” to “Susceptible”

  • Default value: None

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Estimated number of new TB cases annually

  • Code name: num_acq

  • Units/format: number

  • Value restrictions: At least 0

  • Default value: None

  • Appears in the databook

  • Used to compute:

    • “Acquisition rate”

  • Description:

  • Data entry guidance:

Parameter: Acquisition rate

  • Code name: acq_rate

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Susceptible” to “Undiagnosed”

  • Default value: None

  • Does not appear in the databook

  • This parameter’s value is computed by a function: num_acq/max(sus,num_acq)

  • Depends on:

    • “Susceptible”

    • “Estimated number of new TB cases annually”

  • Description:

  • Data entry guidance:

Parameter: Natural recovery rate

  • Code name: rec_rate

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Undiagnosed” to “Susceptible”

    • “Diagnosed” to “Susceptible”

    • “Notified and treated” to “Susceptible”

    • “Lost to follow-up” to “Susceptible”

    • “Successfully treated (comp)” to “Susceptible”

  • Default value: 0.16

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Annual number vaccinated

  • Code name: num_vac

  • Units/format: number

  • Value restrictions: At least 0

  • Default value: None

  • Appears in the databook

  • Used to compute:

    • “Vaccination rate”

  • Description:

  • Data entry guidance:

Parameter: Vaccination rate

  • Code name: vac_rate

  • Value can be used for calibration

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Susceptible” to “Vaccinated”

  • Default value: None

  • Does not appear in the databook

  • This parameter’s value is computed by a function: num_vac/max(sus,num_vac)

  • Depends on:

    • “Annual number vaccinated”

    • “Susceptible”

  • Description:

  • Data entry guidance:

Parameter: Annual number of tests done

  • Code name: num_test

  • Units/format: number

  • Value restrictions: At least 0

  • Default value: None

  • Appears in the databook

  • Used to compute:

    • “Annual number tested positive”

  • Description:

  • Data entry guidance:

Parameter: Test yield

  • Code name: test_yield

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Default value: None

  • Does not appear in the databook

  • This parameter’s value is computed by a function: undx/(undx+sus)

  • Depends on:

    • “Susceptible”

    • “Undiagnosed”

  • Used to compute:

    • “Annual number tested positive”

  • Description:

  • Data entry guidance:

Parameter: Annual number tested positive

  • Code name: pos_test

  • Units/format: number

  • Value restrictions: At least 0

  • Default value: None

  • Does not appear in the databook

  • This parameter’s value is computed by a function: num_test*test_yield

  • Depends on:

    • “Annual number of tests done”

    • “Test yield”

  • Used to compute:

    • “Test sensitivity”

  • Description:

  • Data entry guidance:

Parameter: Test sensitivity

  • Code name: diag

  • Value can be used for calibration

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Undiagnosed” to “Diagnosed”

  • Default value: None

  • Does not appear in the databook

  • This parameter’s value is computed by a function: pos_test/max(undx,pos_test)

  • Depends on:

    • “Undiagnosed”

    • “Annual number tested positive”

  • Description:

  • Data entry guidance:

Parameter: Annual number newly initiated onto treatment

  • Code name: num_initiate

  • Units/format: number

  • Value restrictions: At least 0

  • Default value: None

  • Appears in the databook

  • Used to compute:

    • “Initiation rate”

  • Description:

  • Data entry guidance:

Parameter: Initiation rate

  • Code name: initiate

  • Value can be used for calibration

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Diagnosed” to “Notified and treated”

    • “Lost to follow-up” to “Notified and treated”

  • Default value: None

  • Does not appear in the databook

  • This parameter’s value is computed by a function: num_initiate/max(dx,num_initiate)

  • Depends on:

    • “Diagnosed”

    • “Annual number newly initiated onto treatment”

  • Description:

  • Data entry guidance:

Parameter: Loss-to-follow-up rate

  • Code name: loss

  • Value can be used for calibration

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Notified and treated” to “Lost to follow-up”

    • “Successfully treated (comp)” to “Lost to follow-up”

  • Default value: None

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Time after initiating treatment to treatment success (years)

  • Code name: supp_rate

  • Units/format: duration

  • Value restrictions: At least 0

  • Contributes to transitions from:

    • “Notified and treated” to “Successfully treated (comp)”

  • Default value: 0.2

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Treatment failure rate

  • Code name: fail_rate

  • Value can be used for calibration

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Successfully treated (comp)” to “Notified and treated”

  • Default value: 0.16

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Death rate for those with untreated TB

  • Code name: death_tb

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Undiagnosed” to “Dead (TB)”

    • “Diagnosed” to “Dead (TB)”

    • “Lost to follow-up” to “Dead (TB)”

  • Default value: 0.12

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Death rate for those unsuccessfully treated

  • Code name: death_tbtx

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Notified and treated” to “Dead (TB)”

  • Default value: 0.06

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Death rate for those successfully treated

  • Code name: death_tbtxs

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Successfully treated (comp)” to “Dead (TB)”

  • Default value: 0.03

  • Appears in the databook

  • Description:

  • Data entry guidance:

Parameter: Background mortality rate

  • Code name: death_other

  • Units/format: probability

  • Value restrictions: 0-1.0000

  • Contributes to transitions from:

    • “Susceptible” to “Dead (other)”

    • “Vaccinated” to “Dead (other)”

    • “Undiagnosed” to “Dead (other)”

    • “Diagnosed” to “Dead (other)”

    • “Notified and treated” to “Dead (other)”

    • “Lost to follow-up” to “Dead (other)”

    • “Successfully treated (comp)” to “Dead (other)”

  • Default value: 0.015

  • Appears in the databook

  • Description:

  • Data entry guidance:

Interactions

Cascades

Cascade: TB care cascade

  • Description:

  • Stages:

    • TB burden

      • TB burden

    • Notified

      • Notified

    • In care

      • In care

    • Treated

      • Treated

    • Successfully treated

      • Successfully treated