Skip to content

Add axes top level key to configuration format#164

Open
TimothyWillard wants to merge 1 commit intomainfrom
push-ttxsmnxspmsw
Open

Add axes top level key to configuration format#164
TimothyWillard wants to merge 1 commit intomainfrom
push-ttxsmnxspmsw

Conversation

@TimothyWillard
Copy link
Collaborator

Added the concept of 'axes' to represent a single dimension for something that has shape. Axes can take the form of categorical like 'unvaccinated' and 'vaccinated' or 'low', 'medium', 'high' as well as numerical forms like ages being represented by integers or physical space being represented by a continuous (by discretized) axis. This provides a foundation for further structuring parameters and systems by giving them shape.

  • Added axes attribute to the ConfigurationModel class to contain a mapping of named axes that can be used throughout a configuration file.
  • Added CategoricalAxisModel, IntegerAxisModel, and ContinuousAxisModel classes to represent the three different kinds of axis provided by flepimop2. These classes represent the configuration form of these axes objects, including pydantic based validations.
  • Added an Axis class to represent a realized Axis object that can be handed off to parameters, systems, etc. This provides a unified interface for those modules to create objects of appropriate size.

Heavily inspired by work from @MacdonaldJoshuaCaleb on ACCIDDA/op_system. Closes #147.

Added the concept of 'axes' to represent a single dimension for
something that has shape. Axes can take the form of categorical like
'unvaccinated' and 'vaccinated' or 'low', 'medium', 'high' as well as
numerical forms like ages being represented by integers or physical
space being represented by a continuous (by discretized) axis. This
provides a foundation for further structuring parameters and systems by
giving them shape.

- Added `axes` attribute to the `ConfigurationModel` class to contain a
  mapping of named axes that can be used throughout a configuration
  file.
- Added `CategoricalAxisModel`, `IntegerAxisModel`, and
  `ContinuousAxisModel` classes to represent the three different kinds
  of axis provided by `flepimop2`. These classes represent the
  configuration form of these axes objects, including pydantic based
  validations. 
- Added an `Axis` class to represent a realized `Axis` object that can
  be handed off to parameters, systems, etc. This provides a unified
  interface for those modules to create objects of appropriate size.

Heavily inspired by work from @MacdonaldJoshuaCaleb on
`ACCIDDA/op_system`. Closes #147.
@pearsonca
Copy link
Member

I think we want something like this capability, but I'm not sure what that capability should look like because I'm uncertain of how we plan to use it.

I'm basically thinking of axes as:

  • something a system can advertise about itself
  • which parameters can be functions of (where the notion of parameter here is more expansive than value / distribution)
  • which engines can adjust their operations on
  • which observations / transformations can summarize along

What else do they get used for? When are they necessary (vs convenient)?

Can we get some concept documentation now? As "imagine your model is an ODE, then axes mean this, get expressed like this. Translate that model to a PDE, the axes mean this. An ABM, the axes mean ..."

@MacdonaldJoshuaCaleb need your perspective here as well

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Add axes TLK

2 participants