Example data | Filtering impact data | Filtering on touchstone | Filtering on diseases | Flagging duplicates | Filtering invalid trajectories | Identifying differences between datasets | Generating differences | Generate national IQRs | Flag large differences | Generate a combined dataset | Comparing national values to regional values | Plotting functions | Plotting significant differences | Plotting modelling group variation | Plotting GAVI vaccination | Plot cumulative values

Big picture | Function organisation | Package data | Package dependencies | Data frames and tibbles | Testing

Compare demography | Examine age patterns | Global burden by decade | Global burden timeseries | Coverage sets | Fully-vaccinated persons

References

Configuration | Use within a report | More on configuration | Environment variables for passwords | Advanced database configuration | Migrating from orderly v1 | Other differences in behaviour

Introduction | The problem | The process | Example | Running the report | Creating a report | Resources, sources and artefacts | Using artefacts from other reports | Parameterised reports | Using global resources | Using version control | Using SQL databases | Configuration | Use within a report | Advanced use | Customising the database configuration | Advanced database configuration | Using environment variables and secrets | Developing a report

Overview | The process | Limitations

The orderly changelog | User's perspective | Details

Individual researcher | Why not commit the archive to git? | Small group, sharing via shared disk | Some comments on collaboration | Group of researchers, sharing via server | Using staging environments | Dependency resolution | Looking forward, a fully decentralised approach

OrderlyWeb | Configuring orderly to talk to OrderlyWeb | Interacting with the remote server | Future developments | Deploying a remote server

References

Impact by calendar year & impact by birth year | Function interface | Recipe interface | Impact by year of vaccination | Comparison | HepB | Measles | Comparisons of HepB, Measles & YF

Data | Impact by calendar year (cross-sectional impact) | Impact by birth year (lifetime impact) | Impact by year of vaccination | Impact by year of vaccination: impact ratio stratified by activity type | Impact by year of vaccination: impact ratio stratified by birth cohort | Glossary

Combining schemas

Error handling | Increasing resilience via separate processes | Loss of workers | Retrying tasks | An example where retrying fixes an error | Performance considerations | Deleting tasks that have been retried | Going further

Messages and responses | PING | ECHO | INFO | EVAL | PAUSE / RESUME | SET_TIMEOUT / GET_TIMEOUT | Messages that are supported but use via wrappers:

Getting started | Hello world | Design | Running tasks | Configuring the worker environment | Scheduling options | Tasks that depend on other tasks | Multiple queues | Running tasks in separate processes | Coping with memory use | Orchestrating workers | Use (and limitations) of spawn | Start workers on another node, perhaps using a scheduler | Use docker | Waiting for workers to appear | Worker heartbeat | Getting a Redis server | Install Redis | Use Redis on a different machine

Handling lack of vault gracefully | Installing vault

Connecting to vault | Reading, writing, listing and deleting secrets | Alternative login approaches | Username and password (userpass) | GitHub (github) | LDAP (ldap)

Prerequisites | Declaring a simple endpoint | The basic syntax | Adding inputs | Binding state | Testing | An example

Frequently used functions communicating with Montagu database | Annex views (Susy to add) | Vaccine impact calculations

GET endpoint, inputs as query parameters, returning JSON | GET endpoint, inputs as path and query parameters, returning JSON | POST endpoint, inputs as JSON, returning JSON | POST endpoint, inputs as binary, returning binary

Motivation | Introduction - a porcelain approach to adding-as-a-service

ETL | Repository setup | dettl_config.yml | Creating a new ETL import | Developing the import | Extract | Transform | Load | Running the import | Run functions | Working with import object | Dry run | Other stuff | I want to write an import which creates a table | I want to write a custom load | I want to use the automatic load but make additional changes to the database | What about cycles?

Identify the Montagu Server | Basic Information | Touchstones | Scenarios | Expectations - years, ages, countries and outcomes | Demography | Gender | Format | Templates | Coverage | Long or Wide format | Returning the full range of countries | Burden Estimate Sets | Creating a new burden estimate set | Uploading data | Plotting previous burden estimate sets | Stochastic Runs | Model Run Parameter Sets | Appendix | Models | Demographic Sources

Introduction | Background | Usage - how? | Usage - why?