Atomica
1.25.12
General content
Initializing compartments
Characteristics to Compartments
Problems and solutions
Negative initial compartment sizes
Underdetermined system
Inconsistent system
Inconsistent overdetermined system
Resolving inconsistencies - initialization weight
Computing initial values at arbitrary times
Contextual overview
Logging cookbook
Changing the amount of output
Dumping output to a log file
Optimization
Optimization
class
Performing an optimization
Adjustments
Implementation specifics
Constraints
Implementation specifics
Total spending constraint
Measurables
Measurables vs. constraints
Optimization examples
Maximize people alive
Minimize deaths
Minimize spending
Optimization calling structure
Parameters
Types of parameter
Functions
Value precedence
Performance considerations
Timescales
Derivatives
Interpolation and smoothing
Maximum compartment duration
Junction overview
Population types
Framework population types
Databook population types
Programs and population types
Running simulations
Plotting
Program System
Data and structural overview
Coverage computation
Capacity
Coverage
Number covered
Outcome computation
Coverage interaction
Impact interactions
Parameters in Number units
Targeting transfers
Stochastic models
Timed transitions
Motivation
Use cases
Basic implementation
Initialization
Normal transitions
Duration groups
Architecture
Transfers
Junctions
Examples
Basic workflow
Starting an application
Creating a project
Calibrating the model
Manual calibration
Automatic calibration
Adding programs
Reconciliation
Scenarios
Parameter scenarios
Budget scenarios
Coverage scenarios
Optimization
Data and Databooks
TimeSeries
objects
Population table
TimeDependentConnections
TimeDependentValuesEntry
Modifying databooks
Creating a blank databook
Pre-populating data
Adding a variable
Removing a variable
Add/remove populations
Add/remove transfers and interactions
Changing databook years
Further spreadsheet modification
Frameworks
ProjectFramework
basics
Accessing the data
Exporting a Framework
Making a new Framework
Validating the input
Adding a quantity to the Framework
Convenience methods
Iterating over items
Models (implementation)
Model object structure
Compartment
Link
Characteristic
Parameter
Population
Model
Building
Integrating
Linking and unlinking
Results and Models
Pre-specified plots
Exporting results
Exporting raw results
Accessing raw values
Traversing the graph
Plotting Documentation
Quick Reference
Just give me a plot
FAQs
Data manipulation
General issues
Bar graphs
Legends
Plotting system design
Data preparation and aggregation
Function aggregations
Axis units
Flow rate aggregations and disaggregations
Plotting series
Overriding data
Stacked plots and data
Plotting transition parameters and flow rates
Setting full names
Further formatting
Module-level settings and separate legends
Time accumulation
Saving figures
Plotting bars
Time aggregation
Stacking bars
Negative values
Horizontal bars
Labelling bars
Working with legends
Controlling legend order
Relabeling legend entries
Making a new legend
Time aggregation options
Flow rates
Setting colors
Colour design patterns
Plotting programs
Creating
PlotData
from programs
Plotting spending and coverage
Bar plots and selecting times
Time aggregation
Output aggregation
Plot unit conversions
Parameters
Programs
Probability rescaling
Geometric vs Exponential distribution for durations
Preserving durations vs preserving annual flows
Atomica models
Conclusions
Scenarios
Parameter scenarios
Using the
ParameterScenario
class
Scenario start year
Scenario end year
Smoothing
Step changes
Parameter interpolation prior to the start year
Inspecting the
ParameterSet
Modifying a
ParameterSet
Overwriting function parameters
Uncertainty
Specifying uncertainty
Sampling inputs
Analysis
Basic plotting
Comparing sampled results
Distributions of differences between results
Cascade ensembles
Virtual stages
Memory-limited environments
Parallization
Experimental plots
Overriding coverage calculations
Add a new population type
Overwriting coverage
Tutorials
T1 - Defining a model
Generating a databook
Exercise
T2 - Calibration
Calibration tips
T3 - Multiple populations
Transfers
Interactions
Exercises
T4 - Characteristics
T5 - Junctions
Exercise
T6 - Programs
Reconciliation
Common intervention types
Vaccines
Diagnosis screening program
Diagnosis
Screening with confirmatory test
One-off treatment
Sustained treatment
Exercise
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
atomica.cascade
atomica.cascade.cascade_summary
atomica.cascade.get_cascade_data
atomica.cascade.get_cascade_vals
atomica.cascade.plot_cascade
atomica.cascade.plot_multi_cascade
atomica.cascade.plot_single_cascade
atomica.cascade.plot_single_cascade_series
atomica.cascade.sanitize_cascade
atomica.cascade.sanitize_pops
atomica.cascade.validate_cascade
atomica.cascade.CascadeEnsemble
atomica.cascade.InvalidCascade
atomica.data
atomica.data.ProjectData
atomica.demos
atomica.demos.demo
atomica.demos.make_demo_scenarios
atomica.excel
atomica.excel.apply_widths
atomica.excel.cell_get_number
atomica.excel.cell_get_string
atomica.excel.copy_sheet
atomica.excel.read_dataframes
atomica.excel.read_tables
atomica.excel.standard_formats
atomica.excel.transfer_comments
atomica.excel.update_widths
atomica.excel.validate_category
atomica.excel.TimeDependentConnections
atomica.excel.TimeDependentValuesEntry
atomica.framework
atomica.framework.generate_framework_doc
atomica.framework.ProjectFramework
atomica.framework.InvalidFramework
atomica.function_parser
atomica.function_parser.parse_function
atomica.function_parser.sdiv
atomica.function_parser.vector_max
atomica.function_parser.vector_min
atomica.migration
atomica.migration.all_frameworks
atomica.migration.all_progsets
atomica.migration.all_results
atomica.migration.migrate
atomica.migration.migration
atomica.migration.register_migration
atomica.migration.Migration
atomica.model
atomica.model.run_model
atomica.model.Characteristic
atomica.model.Compartment
atomica.model.JunctionCompartment
atomica.model.Link
atomica.model.Model
atomica.model.Parameter
atomica.model.Population
atomica.model.ResidualJunctionCompartment
atomica.model.SinkCompartment
atomica.model.SourceCompartment
atomica.model.TimedCompartment
atomica.model.TimedLink
atomica.model.Variable
atomica.model.BadInitialization
atomica.model.ModelError
atomica.optimization
atomica.optimization.constrain_sum_bounded
atomica.optimization.optimize
atomica.optimization.Adjustable
atomica.optimization.Adjustment
atomica.optimization.AtLeastMeasurable
atomica.optimization.AtMostMeasurable
atomica.optimization.Constraint
atomica.optimization.DecreaseByMeasurable
atomica.optimization.ExponentialSpendingAdjustment
atomica.optimization.IncreaseByMeasurable
atomica.optimization.MaximizeCascadeConversionRate
atomica.optimization.MaximizeCascadeStage
atomica.optimization.MaximizeMeasurable
atomica.optimization.Measurable
atomica.optimization.MinimizeMeasurable
atomica.optimization.Optimization
atomica.optimization.PairedLinearSpendingAdjustment
atomica.optimization.SpendingAdjustment
atomica.optimization.SpendingPackageAdjustment
atomica.optimization.StartTimeAdjustment
atomica.optimization.TotalSpendConstraint
atomica.optimization.FailedConstraint
atomica.optimization.InvalidInitialConditions
atomica.optimization.UnresolvableConstraint
atomica.parameters
atomica.parameters.Parameter
atomica.parameters.ParameterSet
atomica.plotting
atomica.plotting.plot_bars
atomica.plotting.plot_legend
atomica.plotting.plot_series
atomica.plotting.relabel_legend
atomica.plotting.reorder_legend
atomica.plotting.save_figs
atomica.plotting.PlotData
atomica.plotting.Series
atomica.programs
atomica.programs.Covout
atomica.programs.Program
atomica.programs.ProgramInstructions
atomica.programs.ProgramSet
atomica.project
atomica.project.Project
atomica.project.ProjectSettings
atomica.reconciliation
atomica.reconciliation.reconcile
atomica.results
atomica.results.export_results
atomica.results.Ensemble
atomica.results.Result
atomica.scenarios
atomica.scenarios.BudgetScenario
atomica.scenarios.CombinedScenario
atomica.scenarios.CoverageScenario
atomica.scenarios.ParameterScenario
atomica.scenarios.Scenario
atomica.system
atomica.system.atomica_path
atomica.system.FrameworkSettings
atomica.system.NotFoundError
atomica.utils
atomica.utils.datetime_to_year
atomica.utils.evaluate_plot_string
atomica.utils.fast_gitinfo
atomica.utils.format_duration
atomica.utils.nested_loop
atomica.utils.parallel_progress
atomica.utils.parent_dir
atomica.utils.start_logging
atomica.utils.stop_logging
atomica.utils.NDict
atomica.utils.NamedItem
atomica.utils.Quiet
atomica.utils.TimeSeries
atomica.version
Atomica
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atomica
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atomica.framework
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atomica.framework.InvalidFramework
atomica.framework.InvalidFramework
¶
exception
atomica.framework.
InvalidFramework
[source]
¶