Atomica
  • General content
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      • Atomica models
      • Conclusions
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      • Parameter scenarios
        • Using the ParameterScenario class
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      • Add a new population type
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  • Tutorials
    • T1 - Defining a model
      • Generating a databook
      • Exercise
    • T2 - Calibration
      • Calibration scale factors
      • Calibrating compartment sizes
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      • Automatic calibration
        • Automated calibration of transfers
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    • T3 - Multiple populations
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    • T4 - Characteristics
    • T5 - Junctions
      • Exercise
    • T6 - Programs
      • Reconciliation
      • Common intervention types
        • Vaccines
        • Diagnosis screening program
        • Diagnosis
        • Screening with confirmatory test
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      • Exercise
    • T7 - YAML calibration
      • YAML files
      • Basic calibration example
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      • Sections
        • Repeating a section
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      • Types of Action Blocks
        • Calibration blocks
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      • Exercise: Worked Example
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        • Epidemiological calibration
        • Documentation
  • Model library
    • Cervical cancer
      • Contents
      • Compartments
        • Compartment: Source
        • Compartment: Without cervical cancer
        • Compartment: Undiagnosed
        • Compartment: Screened
        • Compartment: Diagnosed
        • Compartment: Treated
        • Compartment: Dead (other)
        • Compartment: Dead (cervical cancer)
      • Characteristics
        • Characteristic: Population size
        • Characteristic: Estimated number of women with cervical cancer
        • Characteristic: Estimated number of women with cervical cancer who have ever been screened
        • Characteristic: Estimated number of women with cervical cancer who have ever been diagnosed
        • Characteristic: Estimated number of women being treated for cervical cancer
      • Parameters
        • Parameter: Annual number of births
        • Parameter: Estimated number of new cervical cancer cases annually
        • Parameter: Acquisition rate
        • Parameter: Annual number screened
        • Parameter: Screening yield
        • Parameter: Annual number screened positive
        • Parameter: Screening sensitivity
        • Parameter: Annual number of new diagnoses
        • Parameter: Probability of a positive confirmation following screening
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Mortality rate
        • Parameter: Mortality rate for those with untreated cervical cancer
      • Interactions
      • Cascades
        • Cascade: Cervical cancer cascade
    • Diabetes
      • Contents
      • Compartments
        • Compartment: Source
        • Compartment: Susceptible
        • Compartment: Unaware & uncomplicated
        • Compartment: Unaware & vascular damage
        • Compartment: Screened & uncomplicated
        • Compartment: Screened & vascular damage
        • Compartment: Diagnosed & uncomplicated
        • Compartment: Diagnosed & vascular damage
        • Compartment: Successful treatment & uncomplicated
        • Compartment: Successful treatment & vascular damage
        • Compartment: Treatment failure & uncomplicated
        • Compartment: Treatment failure & vascular damage
        • Compartment: Dead (diabetes)
        • Compartment: Dead (other)
      • Characteristics
        • Characteristic: Population size
        • Characteristic: All people with T2DM
        • Characteristic: People screened for T2DM
        • Characteristic: People diagnosed with T2DM
        • Characteristic: People treated for T2DM
        • Characteristic: People with HbA1c control
        • Characteristic: Proportion screened for T2DM
        • Characteristic: Proportion diagnosed with T2DM
        • Characteristic: Proportion treated for T2DM
        • Characteristic: Proportion with HbA1c control
      • Parameters
        • Parameter: Annual number of births
        • Parameter: Estimated number of new diabetes cases annually
        • Parameter: Acquisition rate
        • Parameter: Time before progression to vascular damage
        • Parameter: Annual number screened
        • Parameter: Yield among those screened
        • Parameter: Annual number screened positive
        • Parameter: Screening sensitivity
        • Parameter: Annual number of new diagnoses
        • Parameter: Diagnosis sensitivity
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Treatment failure rate
        • Parameter: Proportion of those experiencing treatment failure who are offered support
        • Parameter: Death rate for diabetes with vascular damage
        • Parameter: Background mortality rate
      • Interactions
      • Cascades
        • Cascade: Diabetes care cascade
        • Cascade: Diabetes care cascade - vascular damage
        • Cascade: Diabetes care cascade - uncomplicated cases
    • Diagnosis-Treated
      • Contents
      • Compartments
        • Compartment: Diagnosed, not treated
        • Compartment: Treated
      • Characteristics
        • Characteristic: All diagnosed
        • Characteristic: Currently treated
      • Parameters
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Annual number lost to follow-up
        • Parameter: Proportion of those on treatment lost-to-follow-up
      • Interactions
      • Cascades
        • Cascade: Cascade
    • HIV without dynamics
      • Contents
      • Compartments
        • Compartment: Undiagnosed
        • Compartment: Diagnosed
        • Compartment: Linked to care
        • Compartment: Treated
        • Compartment: Lost to follow-up
        • Compartment: Virally suppressed (comp)
      • Characteristics
        • Characteristic: All PLHIV
        • Characteristic: Aware of their status
        • Characteristic: Ever in care
        • Characteristic: Currently in care
        • Characteristic: Currently treated
        • Characteristic: Virally suppressed
      • Parameters
        • Parameter: Annual number of new diagnoses
        • Parameter: Diagnosis rate
        • Parameter: Average time taken to be linked to care (years)
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Loss-to-follow-up rate
        • Parameter: Time after initiating ART to achieve viral suppression (years)
        • Parameter: Treatment failure rate
      • Interactions
      • Cascades
        • Cascade: main
    • HIV with dynamics
      • Contents
      • Compartments
        • Compartment: Source
        • Compartment: Susceptible
        • Compartment: Undiagnosed
        • Compartment: Diagnosed
        • Compartment: Linked to care
        • Compartment: Treated
        • Compartment: Lost to follow-up
        • Compartment: Virally suppressed (comp)
        • Compartment: Dead (HIV/AIDS)
        • Compartment: Dead (other)
      • Characteristics
        • Characteristic: Population size
        • Characteristic: All PLHIV
        • Characteristic: Aware of their status
        • Characteristic: Ever in care
        • Characteristic: Currently in care
        • Characteristic: Currently treated
        • Characteristic: Virally suppressed
      • Parameters
        • Parameter: Annual number of births
        • Parameter: Estimated number of new HIV infections annually
        • Parameter: Acquisition rate
        • Parameter: Annual number of tests done
        • Parameter: Test yield
        • Parameter: Annual number tested positive
        • Parameter: Test sensitivity
        • Parameter: Average time taken to be linked to care (years)
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Loss-to-follow-up rate
        • Parameter: Time after initiating ART to achieve viral suppression (years)
        • Parameter: Treatment failure rate
        • Parameter: Death rate for those with untreated HIV
        • Parameter: Death rate for those with on unsuppressive ART
        • Parameter: Death rate for those with on suppressive ART
        • Parameter: Background mortality rate
      • Interactions
      • Cascades
        • Cascade: HIV care cascade
    • Hypertension
      • Contents
      • Compartments
        • Compartment: Undiagnosed
        • Compartment: Screened
        • Compartment: Diagnosed
        • Compartment: Treated
        • Compartment: Controlled
      • Characteristics
        • Characteristic: All people with condition
        • Characteristic: Screened people
        • Characteristic: Diagnosed people
        • Characteristic: Currently treated
        • Characteristic: Blood pressure controlled
      • Parameters
        • Parameter: Annual number screened
        • Parameter: Screening rate
        • Parameter: Annual number of new diagnoses
        • Parameter: Diagnosis rate
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Loss-to-follow-up rate
        • Parameter: Time after initiating treatment to achieve BP control (years)
        • Parameter: Treatment failure rate
      • Interactions
      • Cascades
        • Cascade: main
    • Hypertension with dynamics
      • Contents
      • Compartments
        • Compartment: Source
        • Compartment: No hypertension
        • Compartment: Undiagnosed
        • Compartment: Screened, not diagnosed
        • Compartment: Diagnosed, not treated
        • Compartment: Treated, not controlled
        • Compartment: Controlled
        • Compartment: Dead (hypertension)
        • Compartment: Dead (other)
      • Characteristics
        • Characteristic: Population size
        • Characteristic: All people with condition
        • Characteristic: Screened people
        • Characteristic: Diagnosed people
        • Characteristic: Currently treated
        • Characteristic: Blood pressure controlled
      • Parameters
        • Parameter: Annual number of births
        • Parameter: Estimated number of new cases annually
        • Parameter: Acquisition rate
        • Parameter: Annual number screened
        • Parameter: Target population for screening programs
        • Parameter: Screening coverage shares
        • Parameter: Screening yield
        • Parameter: Annual number screened positive
        • Parameter: Annual number of new diagnoses
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Loss-to-follow-up rate
        • Parameter: Time after initiating treatment to achieve BP control (years)
        • Parameter: Treatment failure rate
        • Parameter: Death rate for those with untreated hypertension
        • Parameter: Background mortality rate
      • Interactions
      • Cascades
        • Cascade: Hypertension care cascade
    • Service modalities
      • Contents
      • Compartments
        • Compartment: Source
        • Compartment: Unaware of own need
        • Compartment: Aware but not linked to services
        • Compartment: Linked to service provider
        • Compartment: Receiving services
        • Compartment: Successful outcome
        • Compartment: Dead
      • Characteristics
        • Characteristic: All people
        • Characteristic: People aware of need
        • Characteristic: People linked to services
        • Characteristic: People receiving services
        • Characteristic: People with successful outcomes
        • Characteristic: Proportion aware of need
        • Characteristic: Proportion linked to services
        • Characteristic: Proportion receiving services
        • Characteristic: Proportion with successful outcomes
      • Parameters
        • Parameter: Number of new cases (annual)
        • Parameter: Number becoming aware of need (annual)
        • Parameter: Number linked to services (annual)
        • Parameter: Number initiated onto services (annual)
        • Parameter: Proportion of those without successful outcomes who are offered further support
        • Parameter: Probability of successful outcome among those receiving services
        • Parameter: Background mortality rate
      • Interactions
      • Cascades
        • Cascade: main
    • SIR model
      • Contents
      • Compartments
        • Compartment: Susceptible
        • Compartment: Infected
        • Compartment: Recovered
        • Compartment: Dead
      • Characteristics
        • Characteristic: Total number of entities
        • Characteristic: Prevalence
        • Characteristic: Number ever infected
        • Characteristic: Number infected or susceptible
        • Characteristic: Number not at risk of death
        • Characteristic: Proportion ever infected
        • Characteristic: Proportion infected or susceptible
        • Characteristic: Proportion not at risk of death
      • Parameters
        • Parameter: Transmission probability per contact
        • Parameter: Number of contacts annually
        • Parameter: Average duration of infections (years)
        • Parameter: Death rate for infected people
        • Parameter: Death rate for susceptible people
        • Parameter: Force of infection
      • Interactions
      • Cascades
        • Cascade: main
    • TB full model
      • Contents
      • Compartments
        • Compartment: Initialization population size
        • Compartment: Susceptible
        • Compartment: Vaccinated
        • Compartment: Early latent untreated (diagnosable)
        • Compartment: Early latent on treatment
        • Compartment: Junction: Latent early treatment outcome
        • Compartment: Late latent untreated (diagnosable)
        • Compartment: Late latent on treatment
        • Compartment: Junction: Latent late treatment outcome
        • Compartment: Susceptible (diagnosis restricted)
        • Compartment: Early latent untreated (diagnosis restricted)
        • Compartment: Late latent untreated (diagnosis restricted)
        • Compartment: Junction: Smear disaggregator for new active
        • Compartment: Junction: Strain disaggregator for new smear positive
        • Compartment: SP-DS undiagnosed
        • Compartment: SP-DS diagnosed but not on treatment
        • Compartment: SP-DS on treatment
        • Compartment: Junction: SP-DS treatment outcome
        • Compartment: SP-MDR undiagnosed
        • Compartment: SP-MDR diagnosed but not on treatment
        • Compartment: SP-MDR on treatment
        • Compartment: Junction: SP-MDR treatment outcome
        • Compartment: SP-XDR undiagnosed
        • Compartment: SP-XDR diagnosed but not on treatment
        • Compartment: SP-XDR on treatment
        • Compartment: Junction: SP-XDR treatment outcome
        • Compartment: Junction: Strain disaggregator for new smear negative
        • Compartment: SN-DS undiagnosed
        • Compartment: SN-DS diagnosed but not on treatment
        • Compartment: SN-DS on treatment
        • Compartment: Junction: SN-DS treatment outcome
        • Compartment: SN-MDR undiagnosed
        • Compartment: SN-MDR diagnosed but not on treatment
        • Compartment: SN-MDR on treatment
        • Compartment: Junction: SN-MDR treatment outcome
        • Compartment: SN-XDR undiagnosed
        • Compartment: SN-XDR diagnosed but not on treatment
        • Compartment: SN-XDR on treatment
        • Compartment: Junction: SN-XDR treatment outcome
        • Compartment: Completed treatment (active)
        • Compartment: Source: Origin of births
        • Compartment: Source: Origin of immigration
        • Compartment: Junction: Infection status of immigrants
        • Compartment: Sink: Cumulative TB deaths over simulation
        • Compartment: Sink: Cumulative non-TB deaths over simulation
        • Compartment: Sink: Cumulative emigration over simulation
      • Characteristics
        • Characteristic: Latent TB infections on treatment
        • Characteristic: Suspected diagnosis restricted latent infections
        • Characteristic: Suspected undiagnosed latent infections
        • Characteristic: Suspected early latent infections
        • Characteristic: Suspected late latent infections
        • Characteristic: Suspected latent infections
        • Characteristic: Known SP-DS infections
        • Characteristic: Known SP-MDR infections
        • Characteristic: Known SP-XDR infections
        • Characteristic: Known SN-DS infections
        • Characteristic: Known SN-MDR infections
        • Characteristic: Known SN-XDR infections
        • Characteristic: Known active TB infections
        • Characteristic: Diagnosed number of living people that developed active TB
        • Characteristic: Suspected SP-DS infections
        • Characteristic: Suspected SP-MD infections
        • Characteristic: Suspected SP-XDR infections
        • Characteristic: Suspected SN-DS infections
        • Characteristic: Suspected SN-MDR infections
        • Characteristic: Suspected SN-XDR infections
        • Characteristic: Suspected SP infections
        • Characteristic: Suspected SN infections
        • Characteristic: Estimated number of people with DS TB
        • Characteristic: Estimated number of people with MDR TB
        • Characteristic: Estimated number of people with XDR TB
        • Characteristic: Estimated number of people with DR TB
        • Characteristic: Estimated number of people with active TB
        • Characteristic: Estimated number of living people that developed active TB
        • Characteristic: Population size
        • Characteristic: Suspected untreated SP-DS infections
        • Characteristic: Suspected untreated SP-MDR infections
        • Characteristic: Suspected untreated SP-XDR infections
        • Characteristic: Suspected untreated SN-DS infections
        • Characteristic: Suspected untreated SN-MDR infections
        • Characteristic: Suspected untreated SN-XDR infections
        • Characteristic: Suspected untreated SP-DS prevalence
        • Characteristic: Suspected untreated SP-MDR prevalence
        • Characteristic: Suspected untreated SP-XDR prevalence
        • Characteristic: Suspected untreated SN-DS prevalence
        • Characteristic: Suspected untreated SN-MDR prevalence
        • Characteristic: Suspected untreated SN-XDR prevalence
        • Characteristic: Suspected LTBI prevalence
        • Characteristic: Suspected SP-DS prevalence
        • Characteristic: Suspected SP-MDR prevalence
        • Characteristic: Suspected SP-XDR prevalence
        • Characteristic: Suspected SN-DS prevalence
        • Characteristic: Suspected SN-MDR prevalence
        • Characteristic: Suspected SN-XDR prevalence
        • Characteristic: Suspected SP prevalence
        • Characteristic: Suspected SN prevalence
        • Characteristic: Suspected DS prevalence
        • Characteristic: Suspected DR prevalence
        • Characteristic: Suspected MDR prevalence
        • Characteristic: Suspected XDR prevalence
        • Characteristic: Suspected active TB prevalence
        • Characteristic: Suspected undiagnosed DS infections
        • Characteristic: Suspected undiagnosed MDR infections
        • Characteristic: Suspected undiagnosed XDR infections
        • Characteristic: Diagnosed DS infections
        • Characteristic: Diagnosed MDR infections
        • Characteristic: Diagnosed XDR infections
        • Characteristic: DS cases on treatment
        • Characteristic: MDR cases on treatment
        • Characteristic: XDR cases on treatment
        • Characteristic: Active TB cases on treatment
        • Characteristic: Number of living people that have recovered from active TB in the previous 2 years
        • Characteristic: Diagnosis sufficiency (known versus suspected infections)
        • Characteristic: Treatment sufficiency (on-treatment versus known infections)
      • Parameters
        • Parameter: Initialization proportion of the population with active TB
        • Parameter: Initialization proportion of the population with latent TB
        • Parameter: Initialization proportion of latent TB cases that are early latent
        • Parameter: Initialization proportion of latent TB cases that are on treatment
        • Parameter: Initialization proportion of active TB cases that are diagnosed
        • Parameter: Initialization proportion of diagnosed TB cases that are on treatment
        • Parameter: Initialization proportion of the population that have previously been vaccinated
        • Parameter: Initialization proportion of the population that have previously been infected with TB
        • Parameter: New active infections: proportion of population that are SP
        • Parameter: New active infections: proportion of population that are SN
        • Parameter: New SP infections: proportion of population that are SP-DS
        • Parameter: New SP infections: proportion of population that are SP-MDR
        • Parameter: New SP infections: proportion of population that are SP-XDR
        • Parameter: New SN infections: proportion of population that are SN-DS
        • Parameter: New SN infections: proportion of population that are SN-MDR
        • Parameter: New SN infections: proportion of population that are SN-XDR
        • Parameter: Infection vulnerability factor (relative population susceptibility)
        • Parameter: Infection vulnerability factor (vaccinated versus susceptible)
        • Parameter: Infection vulnerability factor (recovered versus susceptible)
        • Parameter: SP-DS infectiousness
        • Parameter: Relative infectiousness (SN versus SP)
        • Parameter: Relative infectiousness (MDR versus DS)
        • Parameter: Relative infectiousness (XDR versus DS)
        • Parameter: Initialization proportion: Early latent untreated (diagnosable)
        • Parameter: Initialization proportion: Early latent on treatment
        • Parameter: Initialization proportion: Late latent untreated (diagnosable)
        • Parameter: Initialization proportion: Late latent on treatment
        • Parameter: Initialization proportion: Early latent untreated (diagnosis restricted)
        • Parameter: Initialization proportion: Late latent untreated (diagnosis restricted)
        • Parameter: Initialization proportion: SP-DS undiagnosed
        • Parameter: Initialization proportion: SP-DS diagnosed but not on treatment
        • Parameter: Initialization proportion: SP-DS on treatment
        • Parameter: Initialization proportion: SP-MDR undiagnosed
        • Parameter: Initialization proportion: SP-MDR diagnosed but not on treatment
        • Parameter: Initialization proportion: SP-MDR on treatment
        • Parameter: Initialization proportion: SP-XDR undiagnosed
        • Parameter: Initialization proportion: SP-XDR diagnosed but not on treatment
        • Parameter: Initialization proportion: SP-XDR on treatment
        • Parameter: Initialization proportion: SN-DS undiagnosed
        • Parameter: Initialization proportion: SN-DS diagnosed but not on treatment
        • Parameter: Initialization proportion: SN-DS on treatment
        • Parameter: Initialization proportion: SN-MDR undiagnosed
        • Parameter: Initialization proportion: SN-MDR diagnosed but not on treatment
        • Parameter: Initialization proportion: SN-MDR on treatment
        • Parameter: Initialization proportion: SN-XDR undiagnosed
        • Parameter: Initialization proportion: SN-XDR diagnosed but not on treatment
        • Parameter: Initialization proportion: SN-XDR on treatment
        • Parameter: Initialization proportion: Completed treatment (active)
        • Parameter: Initialization proportion: Vaccinated
        • Parameter: Initialization proportion: Susceptible
        • Parameter: Initialization proportion: Susceptible (diagnosis restricted)
        • Parameter: Number of births
        • Parameter: Non-TB deaths
        • Parameter: Number of new immigrants
        • Parameter: Number of departing emigrants
        • Parameter: Number of vaccinations administered
        • Parameter: LTBI treatment initiations through mass screening
        • Parameter: LTBI treatment initiations through contact tracing
        • Parameter: LTBI treatment average duration of full course
        • Parameter: LTBI treatment proportion of lost to follow up
        • Parameter: LTBI treatment proportion of successful completions
        • Parameter: LTBI treatment average duration until outcome
        • Parameter: Early-LTBI annual number initiating treatment
        • Parameter: Early-LTBI (diagnosis restricted) annual number initiating treatment
        • Parameter: Late-LTBI annual number initiating treatment
        • Parameter: Early-LTBI treatment abandonment rate
        • Parameter: Early-LTBI treatment success rate
        • Parameter: Late-LTBI treatment abandonment rate
        • Parameter: Late-LTBI treatment success rate
        • Parameter: Early latency departure rate
        • Parameter: Late latency departure rate
        • Parameter: Probability of early-active versus early-late progression
        • Parameter: Early-late LTBI progression rate (diagnosable)
        • Parameter: Early-late LTBI progression rate (diagnosis restricted)
        • Parameter: LTBI-active progression rate (early diagnosable)
        • Parameter: LTBI-active progression rate (early diagnosis restricted)
        • Parameter: LTBI-active progression rate (late diagnosable)
        • Parameter: LTBI-active progression rate (late diagnosis restricted)
        • Parameter: SP-MDR infectiousness
        • Parameter: SP-XDR infectiousness
        • Parameter: SN-DS infectiousness
        • Parameter: SN-MDR infectiousness
        • Parameter: SN-XDR infectiousness
        • Parameter: Force of infection from SP prevalence
        • Parameter: Force of infection from SN prevalence
        • Parameter: Force of infection imparted by population
        • Parameter: Force of infection experienced by population
        • Parameter: Infection rate (susceptible to diagnosable latent)
        • Parameter: Infection rate (vaccinated to diagnosis restricted latent)
        • Parameter: Reinfection rate (susceptible to diagnosis restricted for diagnosis restricted)
        • Parameter: Relapse rate for completed treatment (active) cases
        • Parameter: Full recovery rate for completed treatment (active) cases
        • Parameter: Proportion of new immigrants with LTBI
        • Parameter: Early latent proportion of new immigrants
        • Parameter: Late latent proportion of new immigrants
        • Parameter: Proportion of new immigrants with active TB infections
        • Parameter: Susceptible proportion of immigrants
        • Parameter: SP-DS diagnosis notifications
        • Parameter: SP-MDR diagnosis notifications
        • Parameter: SP-XDR diagnosis notifications
        • Parameter: SN-DS diagnosis notifications
        • Parameter: SN-MDR diagnosis notifications
        • Parameter: SN-XDR diagnosis notifications
        • Parameter: DS treatment number of initiations
        • Parameter: SP-DS treatment number of initiations
        • Parameter: SN-DS treatment number of initiations
        • Parameter: DS treatment average duration of completed treatment
        • Parameter: DS treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: DS treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: DS treatment proportion failed (escalation to MDR, require re-diagnosis)
        • Parameter: DS treatment proportion of treatments completed + success
        • Parameter: DS treatment proportion of deaths
        • Parameter: DS treatment average duration until outcome
        • Parameter: SP-DS treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: SP-DS treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: SP-DS treatment proportion failed (escalation to MDR, require re-diagnosis)
        • Parameter: SP-DS treatment proportion of treatments completed + success
        • Parameter: SP-DS treatment proportion of deaths
        • Parameter: SN-DS treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: SN-DS treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: SN-DS treatment proportion failed (escalation to MDR, require re-diagnosis)
        • Parameter: SN-DS treatment proportion of treatments completed + success
        • Parameter: SN-DS treatment proportion of deaths
        • Parameter: MDR treatment number of initiations
        • Parameter: SP-MDR treatment number of initiations
        • Parameter: SN-MDR treatment number of initiations
        • Parameter: MDR treatment average duration of completed treatment
        • Parameter: MDR treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: MDR treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: MDR treatment proportion failed (escalation to XDR, require re-diagnosis)
        • Parameter: MDR treatment proportion of treatments completed + success
        • Parameter: MDR treatment proportion of deaths
        • Parameter: MDR treatment average duration until outcome
        • Parameter: SP-MDR treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: SP-MDR treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: SP-MDR treatment proportion failed (escalation to XDR, require re-diagnosis)
        • Parameter: SP-MDR treatment proportion of treatments completed + success
        • Parameter: SP-MDR treatment proportion of deaths
        • Parameter: SN-MDR treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: SN-MDR treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: SN-MDR treatment proportion failed (escalation to XDR, require re-diagnosis)
        • Parameter: SN-MDR treatment proportion of treatments completed + success
        • Parameter: SN-MDR treatment proportion of deaths
        • Parameter: XDR treatment number of initiations
        • Parameter: SP-XDR treatment number of initiations
        • Parameter: SN-XDR treatment number of initiations
        • Parameter: XDR treatment average duration of completed treatment
        • Parameter: XDR treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: XDR treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: XDR treatment proportion of treatments completed + success
        • Parameter: XDR treatment proportion of deaths
        • Parameter: XDR treatment average duration until outcome
        • Parameter: SP-XDR treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: SP-XDR treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: SP-XDR treatment proportion of treatments completed + success
        • Parameter: SP-XDR treatment proportion of deaths
        • Parameter: SN-XDR treatment proportion of loss to follow up (require re-diagnosis)
        • Parameter: SN-XDR treatment proportion failed (no escalation, no need to re-diagnose)
        • Parameter: SN-XDR treatment proportion of treatments completed + success
        • Parameter: SN-XDR treatment proportion of deaths
        • Parameter: SP-DS natural recovery rate
        • Parameter: SP-MDR natural recovery rate
        • Parameter: SP-XDR natural recovery rate
        • Parameter: SN-DS natural recovery rate
        • Parameter: SN-MDR natural recovery rate
        • Parameter: SN-XDR natural recovery rate
        • Parameter: SP-DS death rate (untreated)
        • Parameter: SP-MDR death rate (untreated)
        • Parameter: SP-XDR death rate (untreated)
        • Parameter: SN-DS death rate (untreated)
        • Parameter: SN-MDR death rate (untreated)
        • Parameter: SN-XDR death rate (untreated)
        • Parameter: Disutility weight for active TB
        • Parameter: YLD rate
        • Parameter: Estimated number of years of life remaining
        • Parameter: YLL rate
        • Parameter: DALYs
      • Interactions
        • Interaction: Preference weighting for one population interacting with another
      • Plots
        • Plot: Population size
        • Plot: Latent infections
        • Plot: Active TB
        • Plot: Active DS-TB
        • Plot: Active MDR-TB
        • Plot: Active XDR-TB
        • Plot: New active TB infections
        • Plot: Activated TB infections inc. relapse and immigration
        • Plot: Smear negative active TB
        • Plot: Smear positive active TB
        • Plot: Latent diagnoses
        • Plot: New active TB diagnoses
        • Plot: Latent treatment
        • Plot: Active treatment
        • Plot: TB-related deaths
        • Plot: Latent prevalence
        • Plot: Active prevalence
        • Plot: DR prevalence
        • Plot: New active SP-DS diagnoses
        • Plot: New active SP-MDR diagnoses
        • Plot: New active SP-XDR diagnoses
        • Plot: New active SN-DS diagnoses
        • Plot: New active SN-MDR diagnoses
        • Plot: New active SN-XDR diagnoses
        • Plot: DS number initiating treatment
        • Plot: MDR number initiating treatment
        • Plot: XDR number initiating treatment
      • Cascades
        • Cascade: TB treatment (including recovered)
        • Cascade: SP treatment
        • Cascade: SN treatment
    • TB simple model
      • Contents
      • Compartments
        • Compartment: Undiagnosed
        • Compartment: Diagnosed
        • Compartment: Notified and treated
        • Compartment: Lost to follow-up
        • Compartment: Successfully treated (comp)
      • Characteristics
        • Characteristic: TB burden
        • Characteristic: Notified
        • Characteristic: In care
        • Characteristic: Treated
        • Characteristic: Successfully treated
      • Parameters
        • Parameter: Annual number of tests done
        • Parameter: Test yield
        • Parameter: Annual number tested positive
        • Parameter: Test sensitivity
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Loss-to-follow-up rate
        • Parameter: Time after initiating treatment to treatment success (years)
        • Parameter: Treatment failure rate
      • Interactions
      • Cascades
        • Cascade: TB care cascade
    • TB simple with dynamics
      • Contents
      • Compartments
        • Compartment: Source
        • Compartment: Susceptible
        • Compartment: Vaccinated
        • Compartment: Undiagnosed
        • Compartment: Diagnosed
        • Compartment: Notified and treated
        • Compartment: Lost to follow-up
        • Compartment: Successfully treated (comp)
        • Compartment: Dead (TB)
        • Compartment: Dead (other)
      • Characteristics
        • Characteristic: Population size
        • Characteristic: TB burden
        • Characteristic: Notified
        • Characteristic: In care
        • Characteristic: Treated
        • Characteristic: Successfully treated
      • Parameters
        • Parameter: Annual number of births
        • Parameter: Estimated number of new TB cases annually
        • Parameter: Acquisition rate
        • Parameter: Natural recovery rate
        • Parameter: Annual number vaccinated
        • Parameter: Vaccination rate
        • Parameter: Annual number of tests done
        • Parameter: Test yield
        • Parameter: Annual number tested positive
        • Parameter: Test sensitivity
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Loss-to-follow-up rate
        • Parameter: Time after initiating treatment to treatment success (years)
        • Parameter: Treatment failure rate
        • Parameter: Death rate for those with untreated TB
        • Parameter: Death rate for those unsuccessfully treated
        • Parameter: Death rate for those successfully treated
        • Parameter: Background mortality rate
      • Interactions
      • Cascades
        • Cascade: TB care cascade
    • UDT model
      • Contents
      • Compartments
        • Compartment: Undiagnosed
        • Compartment: Diagnosed
        • Compartment: Treated
      • Characteristics
        • Characteristic: All people with condition
        • Characteristic: Diagnosed people
        • Characteristic: Currently treated
      • Parameters
        • Parameter: Annual number of new diagnoses
        • Parameter: Diagnosis rate
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Annual number lost to follow-up
        • Parameter: Loss-to-follow-up rate
      • Interactions
      • Cascades
        • Cascade: Cascade
    • UDT model with dynamics
      • Contents
      • Compartments
        • Compartment: Births
        • Compartment: Undiagnosed
        • Compartment: Diagnosed
        • Compartment: Treated
        • Compartment: dead
      • Characteristics
        • Characteristic: All people with condition
        • Characteristic: Diagnosed people
        • Characteristic: Currently treated
      • Parameters
        • Parameter: Annual number of new diagnoses
        • Parameter: Diagnosis rate
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Annual number lost to follow-up
        • Parameter: Loss-to-follow-up rate
        • Parameter: Birth rate
        • Parameter: Untreated death rate
        • Parameter: Treated death rate
      • Interactions
      • Cascades
        • Cascade: Cascade
    • USDT model
      • Contents
      • Compartments
        • Compartment: Undiagnosed
        • Compartment: Screened
        • Compartment: Diagnosed
        • Compartment: Treated
      • Characteristics
        • Characteristic: All people with condition
        • Characteristic: Screened people
        • Characteristic: Diagnosed people
        • Characteristic: Currently treated
      • Parameters
        • Parameter: Annual number screened
        • Parameter: Screening rate
        • Parameter: Annual number of new diagnoses
        • Parameter: Diagnosis rate
        • Parameter: Annual number newly initiated onto treatment
        • Parameter: Initiation rate
        • Parameter: Annual number lost to follow-up
        • Parameter: Loss-to-follow-up rate
      • Interactions
      • Cascades
        • Cascade: main

API Reference

  • atomica
    • atomica.calibration
      • atomica.calibration.calibrate
        • calibrate()
    • atomica.cascade
      • atomica.cascade.cascade_summary
        • cascade_summary()
      • atomica.cascade.get_cascade_data
        • get_cascade_data()
      • atomica.cascade.get_cascade_vals
        • get_cascade_vals()
      • atomica.cascade.plot_cascade
        • plot_cascade()
      • atomica.cascade.plot_multi_cascade
        • plot_multi_cascade()
      • atomica.cascade.plot_single_cascade
        • plot_single_cascade()
      • atomica.cascade.plot_single_cascade_series
        • plot_single_cascade_series()
      • atomica.cascade.sanitize_cascade
        • sanitize_cascade()
      • atomica.cascade.sanitize_pops
        • sanitize_pops()
      • atomica.cascade.validate_cascade
        • validate_cascade()
      • atomica.cascade.CascadeEnsemble
        • CascadeEnsemble
          • CascadeEnsemble.add()
          • CascadeEnsemble.baseline
          • CascadeEnsemble.boxplot()
          • CascadeEnsemble.get_vals()
          • CascadeEnsemble.mapping_function
          • CascadeEnsemble.n_samples
          • CascadeEnsemble.outputs
          • CascadeEnsemble.plot_bars()
          • CascadeEnsemble.plot_distribution()
          • CascadeEnsemble.plot_multi_cascade()
          • CascadeEnsemble.plot_series()
          • CascadeEnsemble.pops
          • CascadeEnsemble.results
          • CascadeEnsemble.run_sims()
          • CascadeEnsemble.samples
          • CascadeEnsemble.set_baseline()
          • CascadeEnsemble.tvec
          • CascadeEnsemble.update()
      • atomica.cascade.InvalidCascade
        • InvalidCascade
    • atomica.data
      • atomica.data.ProjectData
        • ProjectData
          • ProjectData.add_interaction()
          • ProjectData.add_pop()
          • ProjectData.add_transfer()
          • ProjectData.change_tvec()
          • ProjectData.end_year
          • ProjectData.from_spreadsheet()
          • ProjectData.get_tdve_page()
          • ProjectData.get_ts()
          • ProjectData.gitinfo
          • ProjectData.interpops
          • ProjectData.new()
          • ProjectData.pops
          • ProjectData.remove_interaction()
          • ProjectData.remove_transfer()
          • ProjectData.rename_pop()
          • ProjectData.rename_transfer()
          • ProjectData.save()
          • ProjectData.start_year
          • ProjectData.tables()
          • ProjectData.tdve
          • ProjectData.tdve_pages
          • ProjectData.to_spreadsheet()
          • ProjectData.to_workbook()
          • ProjectData.transfers
          • ProjectData.tvec
          • ProjectData.validate()
          • ProjectData.version
      • atomica.data.InvalidDatabook
        • InvalidDatabook
    • atomica.demos
      • atomica.demos.demo
        • demo()
      • atomica.demos.make_demo_scenarios
        • make_demo_scenarios()
    • atomica.excel
      • atomica.excel.apply_widths
        • apply_widths()
      • atomica.excel.cell_get_number
        • cell_get_number()
      • atomica.excel.cell_get_string
        • cell_get_string()
      • atomica.excel.copy_sheet
        • copy_sheet()
      • atomica.excel.read_dataframes
        • read_dataframes()
      • atomica.excel.read_tables
        • read_tables()
      • atomica.excel.standard_formats
        • standard_formats()
      • atomica.excel.transfer_comments
        • transfer_comments()
      • atomica.excel.update_widths
        • update_widths()
      • atomica.excel.validate_category
        • validate_category()
      • atomica.excel.TimeDependentConnections
        • TimeDependentConnections
          • TimeDependentConnections.assumption_heading
          • TimeDependentConnections.attributes
          • TimeDependentConnections.from_tables()
          • TimeDependentConnections.ts_attributes
          • TimeDependentConnections.write()
          • TimeDependentConnections.write_assumption
          • TimeDependentConnections.write_uncertainty
          • TimeDependentConnections.write_units
      • atomica.excel.TimeDependentValuesEntry
        • TimeDependentValuesEntry
          • TimeDependentValuesEntry.assumption_heading
          • TimeDependentValuesEntry.comment
          • TimeDependentValuesEntry.default_all
          • TimeDependentValuesEntry.from_rows()
          • TimeDependentValuesEntry.has_data
          • TimeDependentValuesEntry.name
          • TimeDependentValuesEntry.ts_attributes
          • TimeDependentValuesEntry.tvec
          • TimeDependentValuesEntry.write()
          • TimeDependentValuesEntry.write_assumption
          • TimeDependentValuesEntry.write_uncertainty
          • TimeDependentValuesEntry.write_units
    • atomica.framework
      • atomica.framework.generate_framework_doc
        • generate_framework_doc()
      • atomica.framework.ProjectFramework
        • ProjectFramework
          • ProjectFramework.cascades
          • ProjectFramework.characs
          • ProjectFramework.comps
          • ProjectFramework.created
          • ProjectFramework.get_charac()
          • ProjectFramework.get_charac_includes()
          • ProjectFramework.get_comp()
          • ProjectFramework.get_databook_units()
          • ProjectFramework.get_interaction()
          • ProjectFramework.get_label()
          • ProjectFramework.get_par()
          • ProjectFramework.get_variable()
          • ProjectFramework.gitinfo
          • ProjectFramework.interactions
          • ProjectFramework.modified
          • ProjectFramework.name
          • ProjectFramework.pars
          • ProjectFramework.pop_types
          • ProjectFramework.save()
          • ProjectFramework.sheets
          • ProjectFramework.spreadsheet
          • ProjectFramework.to_spreadsheet()
          • ProjectFramework.uid
          • ProjectFramework.version
      • atomica.framework.InvalidFramework
        • InvalidFramework
    • atomica.function_parser
      • atomica.function_parser.parse_function
        • parse_function()
      • atomica.function_parser.sdiv
        • sdiv()
      • atomica.function_parser.vector_max
        • vector_max()
      • atomica.function_parser.vector_min
        • vector_min()
    • atomica.migration
      • atomica.migration.all_frameworks
        • all_frameworks()
      • atomica.migration.all_progsets
        • all_progsets()
      • atomica.migration.all_results
        • all_results()
      • atomica.migration.migrate
        • migrate()
      • atomica.migration.migration
        • migration()
      • atomica.migration.register_migration
        • register_migration()
      • atomica.migration.Migration
        • Migration
    • atomica.model
      • atomica.model.run_model
        • run_model()
      • atomica.model.Characteristic
        • Characteristic
          • Characteristic.id
          • Characteristic.name
          • Characteristic.plot()
          • Characteristic.pop
          • Characteristic.preallocate()
          • Characteristic.set_dynamic()
          • Characteristic.units
          • Characteristic.update()
      • atomica.model.Compartment
        • Compartment
          • Compartment.connect()
          • Compartment.id
          • Compartment.name
          • Compartment.outflow
          • Compartment.plot()
          • Compartment.pop
          • Compartment.preallocate()
          • Compartment.resolve_outflows()
          • Compartment.set_dynamic()
          • Compartment.units
          • Compartment.update()
      • atomica.model.JunctionCompartment
        • JunctionCompartment
          • JunctionCompartment.balance()
          • JunctionCompartment.connect()
          • JunctionCompartment.duration_group
          • JunctionCompartment.id
          • JunctionCompartment.initial_flush()
          • JunctionCompartment.name
          • JunctionCompartment.outflow
          • JunctionCompartment.plot()
          • JunctionCompartment.pop
          • JunctionCompartment.preallocate()
          • JunctionCompartment.resolve_outflows()
          • JunctionCompartment.set_dynamic()
          • JunctionCompartment.units
          • JunctionCompartment.update()
      • atomica.model.Link
        • Link
          • Link.create()
          • Link.id
          • Link.name
          • Link.plot()
          • Link.pop
          • Link.preallocate()
          • Link.set_dynamic()
          • Link.units
          • Link.update()
      • atomica.model.Model
        • Model
          • Model.build()
          • Model.dt
          • Model.flush_junctions()
          • Model.get_pop()
          • Model.process()
          • Model.relink()
          • Model.t
          • Model.unlink()
          • Model.update_comps()
          • Model.update_links()
          • Model.update_pars()
      • atomica.model.Parameter
        • Parameter
          • Parameter.constrain()
          • Parameter.deps
          • Parameter.derivative
          • Parameter.fcn_str
          • Parameter.id
          • Parameter.limits
          • Parameter.links
          • Parameter.name
          • Parameter.plot()
          • Parameter.pop
          • Parameter.pop_aggregation
          • Parameter.preallocate()
          • Parameter.scale_factor
          • Parameter.set_dynamic()
          • Parameter.set_fcn()
          • Parameter.skip_function
          • Parameter.timescale
          • Parameter.units
          • Parameter.update()
      • atomica.model.Population
        • Population
          • Population.build()
          • Population.charac_lookup
          • Population.characs
          • Population.comp_lookup
          • Population.comps
          • Population.get_charac()
          • Population.get_comp()
          • Population.get_links()
          • Population.get_par()
          • Population.get_variable()
          • Population.initialize_compartments()
          • Population.label
          • Population.link_lookup
          • Population.links
          • Population.name
          • Population.par_lookup
          • Population.pars
          • Population.popsize()
          • Population.type
      • atomica.model.ResidualJunctionCompartment
        • ResidualJunctionCompartment
          • ResidualJunctionCompartment.balance()
          • ResidualJunctionCompartment.connect()
          • ResidualJunctionCompartment.duration_group
          • ResidualJunctionCompartment.id
          • ResidualJunctionCompartment.initial_flush()
          • ResidualJunctionCompartment.name
          • ResidualJunctionCompartment.outflow
          • ResidualJunctionCompartment.plot()
          • ResidualJunctionCompartment.pop
          • ResidualJunctionCompartment.preallocate()
          • ResidualJunctionCompartment.resolve_outflows()
          • ResidualJunctionCompartment.set_dynamic()
          • ResidualJunctionCompartment.units
          • ResidualJunctionCompartment.update()
      • atomica.model.SinkCompartment
        • SinkCompartment
          • SinkCompartment.connect()
          • SinkCompartment.id
          • SinkCompartment.name
          • SinkCompartment.outflow
          • SinkCompartment.plot()
          • SinkCompartment.pop
          • SinkCompartment.preallocate()
          • SinkCompartment.resolve_outflows()
          • SinkCompartment.set_dynamic()
          • SinkCompartment.units
          • SinkCompartment.update()
      • atomica.model.SourceCompartment
        • SourceCompartment
          • SourceCompartment.connect()
          • SourceCompartment.id
          • SourceCompartment.name
          • SourceCompartment.outflow
          • SourceCompartment.plot()
          • SourceCompartment.pop
          • SourceCompartment.preallocate()
          • SourceCompartment.resolve_outflows()
          • SourceCompartment.set_dynamic()
          • SourceCompartment.units
          • SourceCompartment.update()
      • atomica.model.TimedCompartment
        • TimedCompartment
          • TimedCompartment.connect()
          • TimedCompartment.flush_link
          • TimedCompartment.id
          • TimedCompartment.name
          • TimedCompartment.outflow
          • TimedCompartment.parameter
          • TimedCompartment.plot()
          • TimedCompartment.pop
          • TimedCompartment.preallocate()
          • TimedCompartment.resolve_outflows()
          • TimedCompartment.set_dynamic()
          • TimedCompartment.units
          • TimedCompartment.update()
          • TimedCompartment.vals
      • atomica.model.TimedLink
        • TimedLink
          • TimedLink.create()
          • TimedLink.id
          • TimedLink.name
          • TimedLink.plot()
          • TimedLink.pop
          • TimedLink.preallocate()
          • TimedLink.set_dynamic()
          • TimedLink.units
          • TimedLink.update()
          • TimedLink.vals
      • atomica.model.Variable
        • Variable
          • Variable.id
          • Variable.name
          • Variable.plot()
          • Variable.pop
          • Variable.preallocate()
          • Variable.set_dynamic()
          • Variable.units
          • Variable.update()
      • atomica.model.BadInitialization
        • BadInitialization
      • atomica.model.ModelError
        • ModelError
    • atomica.optimization
      • atomica.optimization.constrain_sum_bounded
        • constrain_sum_bounded()
      • atomica.optimization.optimize
        • optimize()
      • atomica.optimization.Adjustable
        • Adjustable
          • Adjustable.get_hard_bounds()
      • atomica.optimization.Adjustment
        • Adjustment
          • Adjustment.adjustables
          • Adjustment.get_initialization()
      • atomica.optimization.AtLeastMeasurable
        • AtLeastMeasurable
          • AtLeastMeasurable.get_baseline()
          • AtLeastMeasurable.get_objective_val()
      • atomica.optimization.AtMostMeasurable
        • AtMostMeasurable
          • AtMostMeasurable.get_baseline()
          • AtMostMeasurable.get_objective_val()
      • atomica.optimization.Constraint
        • Constraint
          • Constraint.constrain_instructions()
          • Constraint.get_hard_constraint()
      • atomica.optimization.DecreaseByMeasurable
        • DecreaseByMeasurable
          • DecreaseByMeasurable.get_baseline()
          • DecreaseByMeasurable.get_objective_val()
      • atomica.optimization.ExponentialSpendingAdjustment
        • ExponentialSpendingAdjustment
          • ExponentialSpendingAdjustment.adjustables
          • ExponentialSpendingAdjustment.get_initialization()
      • atomica.optimization.IncreaseByMeasurable
        • IncreaseByMeasurable
          • IncreaseByMeasurable.get_baseline()
          • IncreaseByMeasurable.get_objective_val()
      • atomica.optimization.MaximizeCascadeConversionRate
        • MaximizeCascadeConversionRate
          • MaximizeCascadeConversionRate.get_baseline()
          • MaximizeCascadeConversionRate.get_objective_val()
      • atomica.optimization.MaximizeCascadeStage
        • MaximizeCascadeStage
          • MaximizeCascadeStage.get_baseline()
          • MaximizeCascadeStage.get_objective_val()
      • atomica.optimization.MaximizeMeasurable
        • MaximizeMeasurable
          • MaximizeMeasurable.get_baseline()
          • MaximizeMeasurable.get_objective_val()
      • atomica.optimization.Measurable
        • Measurable
          • Measurable.get_baseline()
          • Measurable.get_objective_val()
      • atomica.optimization.MinimizeMeasurable
        • MinimizeMeasurable
          • MinimizeMeasurable.get_baseline()
          • MinimizeMeasurable.get_objective_val()
      • atomica.optimization.Optimization
        • Optimization
          • Optimization.compute_objective()
          • Optimization.constrain_instructions()
          • Optimization.get_adjustment()
          • Optimization.get_baselines()
          • Optimization.get_hard_constraints()
          • Optimization.get_initialization()
          • Optimization.maxiters
          • Optimization.maxtime
          • Optimization.method
          • Optimization.update_instructions()
      • atomica.optimization.PairedLinearSpendingAdjustment
        • PairedLinearSpendingAdjustment
          • PairedLinearSpendingAdjustment.adjustables
          • PairedLinearSpendingAdjustment.get_initialization()
      • atomica.optimization.SpendingAdjustment
        • SpendingAdjustment
          • SpendingAdjustment.adjustables
          • SpendingAdjustment.get_initialization()
      • atomica.optimization.SpendingPackageAdjustment
        • SpendingPackageAdjustment
          • SpendingPackageAdjustment.adjust_total_spend
          • SpendingPackageAdjustment.adjustables
          • SpendingPackageAdjustment.get_initialization()
      • atomica.optimization.StartTimeAdjustment
        • StartTimeAdjustment
          • StartTimeAdjustment.adjustables
          • StartTimeAdjustment.get_initialization()
      • atomica.optimization.TotalSpendConstraint
        • TotalSpendConstraint
          • TotalSpendConstraint.constrain_instructions()
          • TotalSpendConstraint.get_hard_constraint()
      • atomica.optimization.FailedConstraint
        • FailedConstraint
      • atomica.optimization.InvalidInitialConditions
        • InvalidInitialConditions
      • atomica.optimization.UnresolvableConstraint
        • UnresolvableConstraint
    • atomica.parameters
      • atomica.parameters.Initialization
        • Initialization
          • Initialization.apply()
          • Initialization.from_excel()
          • Initialization.from_result()
          • Initialization.hash_y_factors()
      • atomica.parameters.Parameter
        • Parameter
          • Parameter.has_values()
          • Parameter.interpolate()
          • Parameter.pops
          • Parameter.sample()
          • Parameter.smooth()
      • atomica.parameters.ParameterSet
        • ParameterSet
          • ParameterSet.all_pars()
          • ParameterSet.apply_initialization()
          • ParameterSet.calibration_spreadsheet()
          • ParameterSet.get_par()
          • ParameterSet.initialization
          • ParameterSet.load_calibration()
          • ParameterSet.make_constant()
          • ParameterSet.sample()
          • ParameterSet.save_calibration()
          • ParameterSet.y_factors
    • atomica.plotting
      • atomica.plotting.plot_bars
        • plot_bars()
      • atomica.plotting.plot_legend
        • plot_legend()
      • atomica.plotting.plot_series
        • plot_series()
      • atomica.plotting.relabel_legend
        • relabel_legend()
      • atomica.plotting.reorder_legend
        • reorder_legend()
      • atomica.plotting.save_figs
        • save_figs()
      • atomica.plotting.separatelegend
        • separatelegend()
      • atomica.plotting.PlotData
        • PlotData
          • PlotData.__getitem__()
          • PlotData.accumulate()
          • PlotData.interpolate()
          • PlotData.programs()
          • PlotData.set_colors()
          • PlotData.time_aggregate()
          • PlotData.tvals()
      • atomica.plotting.Series
        • Series
          • Series.data_label
          • Series.data_pop
          • Series.interpolate()
          • Series.timescale
          • Series.unit_string
          • Series.units
    • atomica.programs
      • atomica.programs.Covout
        • Covout
          • Covout.compute_impact_interaction()
          • Covout.get_outcome()
          • Covout.n_progs
          • Covout.sample()
          • Covout.update_outcomes()
      • atomica.programs.Program
        • Program
          • Program.baseline_spend
          • Program.capacity_constraint
          • Program.coverage
          • Program.get_capacity()
          • Program.get_prop_covered()
          • Program.get_spend()
          • Program.is_one_off
          • Program.label
          • Program.name
          • Program.sample()
          • Program.saturation
          • Program.spend_data
          • Program.target_comps
          • Program.target_pops
          • Program.unit_cost
      • atomica.programs.ProgramInstructions
        • ProgramInstructions
          • ProgramInstructions.scale_alloc()
      • atomica.programs.ProgramSet
        • ProgramSet
          • ProgramSet.add_comp()
          • ProgramSet.add_par()
          • ProgramSet.add_pop()
          • ProgramSet.add_program()
          • ProgramSet.from_spreadsheet()
          • ProgramSet.get_alloc()
          • ProgramSet.get_capacities()
          • ProgramSet.get_outcomes()
          • ProgramSet.get_prop_coverage()
          • ProgramSet.new()
          • ProgramSet.remove_comp()
          • ProgramSet.remove_par()
          • ProgramSet.remove_pop()
          • ProgramSet.remove_program()
          • ProgramSet.sample()
          • ProgramSet.to_spreadsheet()
          • ProgramSet.to_workbook()
          • ProgramSet.validate()
      • atomica.programs.InvalidProgramBook
        • InvalidProgramBook
    • atomica.project
      • atomica.project.Project
        • Project
          • Project.calibrate()
          • Project.create_databook()
          • Project.load()
          • Project.load_databook()
          • Project.load_progbook()
          • Project.make_parset()
          • Project.make_progbook()
          • Project.make_scenario()
          • Project.optim()
          • Project.parset()
          • Project.parsets
          • Project.progset()
          • Project.result()
          • Project.run_optimization()
          • Project.run_sampled_sims()
          • Project.run_scenarios()
          • Project.run_sim()
          • Project.save()
          • Project.scen()
          • Project.update_settings()
      • atomica.project.ProjectSettings
        • ProjectSettings
          • ProjectSettings.tvec
          • ProjectSettings.update_time_vector()
    • atomica.reconciliation
      • atomica.reconciliation.reconcile
        • reconcile()
    • atomica.results
      • atomica.results.export_results
        • export_results()
      • atomica.results.Ensemble
        • Ensemble
          • Ensemble.add()
          • Ensemble.baseline
          • Ensemble.boxplot()
          • Ensemble.mapping_function
          • Ensemble.n_samples
          • Ensemble.outputs
          • Ensemble.plot_bars()
          • Ensemble.plot_distribution()
          • Ensemble.plot_series()
          • Ensemble.pops
          • Ensemble.results
          • Ensemble.run_sims()
          • Ensemble.samples
          • Ensemble.set_baseline()
          • Ensemble.tvec
          • Ensemble.update()
      • atomica.results.Result
        • Result
          • Result.charac_names()
          • Result.check_for_nans()
          • Result.comp_names()
          • Result.dt
          • Result.export_raw()
          • Result.framework
          • Result.get_alloc()
          • Result.get_coverage()
          • Result.get_equivalent_alloc()
          • Result.get_variable()
          • Result.link_names()
          • Result.par_names()
          • Result.plot()
          • Result.pop_labels
          • Result.t
          • Result.used_programs
    • atomica.scenarios
      • atomica.scenarios.BudgetScenario
        • BudgetScenario
          • BudgetScenario.active
          • BudgetScenario.get_instructions()
          • BudgetScenario.get_parset()
          • BudgetScenario.get_progset()
          • BudgetScenario.parsetname
          • BudgetScenario.progsetname
          • BudgetScenario.run()
      • atomica.scenarios.CombinedScenario
        • CombinedScenario
          • CombinedScenario.active
          • CombinedScenario.get_instructions()
          • CombinedScenario.get_parset()
          • CombinedScenario.get_progset()
          • CombinedScenario.interpolation
          • CombinedScenario.parsetname
          • CombinedScenario.progsetname
          • CombinedScenario.run()
          • CombinedScenario.scenario_values
      • atomica.scenarios.CoverageScenario
        • CoverageScenario
          • CoverageScenario.active
          • CoverageScenario.get_instructions()
          • CoverageScenario.get_parset()
          • CoverageScenario.get_progset()
          • CoverageScenario.parsetname
          • CoverageScenario.progsetname
          • CoverageScenario.run()
      • atomica.scenarios.ParameterScenario
        • ParameterScenario
          • ParameterScenario.active
          • ParameterScenario.add()
          • ParameterScenario.get_instructions()
          • ParameterScenario.get_parset()
          • ParameterScenario.get_progset()
          • ParameterScenario.interpolation
          • ParameterScenario.parsetname
          • ParameterScenario.progsetname
          • ParameterScenario.run()
          • ParameterScenario.scenario_values
      • atomica.scenarios.Scenario
        • Scenario
          • Scenario.active
          • Scenario.get_instructions()
          • Scenario.get_parset()
          • Scenario.get_progset()
          • Scenario.parsetname
          • Scenario.progsetname
          • Scenario.run()
    • atomica.system
      • atomica.system.atomica_path
        • atomica_path()
      • atomica.system.FrameworkSettings
        • FrameworkSettings
      • atomica.system.NotFoundError
        • NotFoundError
    • atomica.utils
      • atomica.utils.datetime_to_year
        • datetime_to_year()
      • atomica.utils.evaluate_plot_string
        • evaluate_plot_string()
      • atomica.utils.format_duration
        • format_duration()
      • atomica.utils.get_sigfigs_necessary
        • get_sigfigs_necessary()
      • atomica.utils.nested_loop
        • nested_loop()
      • atomica.utils.parallel_progress
        • parallel_progress()
      • atomica.utils.parent_dir
        • parent_dir()
      • atomica.utils.start_logging
        • start_logging()
      • atomica.utils.stop_logging
        • stop_logging()
      • atomica.utils.NDict
        • NDict
          • NDict.__add__()
          • NDict.append()
          • NDict.clear()
          • NDict.copy()
          • NDict.dict_items()
          • NDict.dict_keys()
          • NDict.dict_values()
          • NDict.disp()
          • NDict.enumitems()
          • NDict.enumkeys()
          • NDict.enumvals()
          • NDict.enumvalues()
          • NDict.export()
          • NDict.filter()
          • NDict.filtervals()
          • NDict.findbykey()
          • NDict.findbyval()
          • NDict.findkeys()
          • NDict.fromeach()
          • NDict.fromkeys()
          • NDict.get()
          • NDict.getnested()
          • NDict.index()
          • NDict.insert()
          • NDict.items()
          • NDict.iteritems()
          • NDict.iternested()
          • NDict.keys()
          • NDict.make()
          • NDict.makefrom()
          • NDict.makenested()
          • NDict.map()
          • NDict.pop()
          • NDict.popitem()
          • NDict.promote()
          • NDict.remove()
          • NDict.rename()
          • NDict.reverse()
          • NDict.reversed()
          • NDict.setdefault()
          • NDict.setitem()
          • NDict.setnested()
          • NDict.sort()
          • NDict.sorted()
          • NDict.toeach()
          • NDict.update()
          • NDict.valind()
          • NDict.values()
      • atomica.utils.NamedItem
        • NamedItem
      • atomica.utils.Quiet
        • Quiet
      • atomica.utils.TimeSeries
        • TimeSeries
          • TimeSeries.assumption
          • TimeSeries.copy()
          • TimeSeries.get()
          • TimeSeries.get_arrays()
          • TimeSeries.has_data
          • TimeSeries.has_time_data
          • TimeSeries.insert()
          • TimeSeries.interpolate()
          • TimeSeries.remove()
          • TimeSeries.remove_after()
          • TimeSeries.remove_before()
          • TimeSeries.remove_between()
          • TimeSeries.sample()
          • TimeSeries.sigma
          • TimeSeries.t
          • TimeSeries.units
          • TimeSeries.vals
    • atomica.version
    • atomica.yaml_calibration
      • atomica.yaml_calibration.build
        • build()
      • atomica.yaml_calibration.run
        • run()
      • atomica.yaml_calibration.BaseNode
        • BaseNode
          • BaseNode.apply()
          • BaseNode.validate()
      • atomica.yaml_calibration.CalibrationNode
        • CalibrationNode
          • CalibrationNode.apply()
          • CalibrationNode.validate()
      • atomica.yaml_calibration.ClearInitializationNode
        • ClearInitializationNode
          • ClearInitializationNode.apply()
          • ClearInitializationNode.validate()
      • atomica.yaml_calibration.InitializationNode
        • InitializationNode
          • InitializationNode.apply()
          • InitializationNode.validate()
      • atomica.yaml_calibration.SaveCalibrationNode
        • SaveCalibrationNode
          • SaveCalibrationNode.apply()
          • SaveCalibrationNode.validate()
      • atomica.yaml_calibration.SectionNode
        • SectionNode
          • SectionNode.apply()
          • SectionNode.validate()
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