TB simple with dynamics¶

Name: TB with dynamics

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

Contents¶

Compartments
Characteristics
Parameters
Interactions
Cascades

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