> For the complete documentation index, see [llms.txt](https://iddynamics.gitbook.io/flepimop/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://iddynamics.gitbook.io/flepimop/gempyor.md).

# gempyor: modeling infectious disease dynamics

- [Modeling infectious disease dynamics](https://iddynamics.gitbook.io/flepimop/gempyor/model-description.md)
- [Model Implementation](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation.md)
- [flepiMoP's configuration file](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/introduction-to-configuration-files.md)
- [Specifying population structure](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/specifying-population-structure.md): This page describes how users specify the names, sizes, and connectivities of the different subpopulations comprising the total population to be modeled
- [Specifying compartmental model](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/compartmental-model-structure.md): This section describes how to specify the compartmental model of infectious disease transmission.
- [Specifying initial conditions](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/specifying-initial-conditions.md): This section describes how to specify the values of each model state at the time the simulation starts, and how to make instantaneous changes to state values at other times (e.g., due to importations)
- [Specifying seeding](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/specifying-seeding.md): This section describes how to specify the values of each model state at the time the simulation starts, and how to make instantaneous changes to state values at other times (e.g., due to importations)
- [Specifying observational model](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/outcomes-for-compartments.md): This page describes how to specify the outcomes section of the configuration file
- [Distributions](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/distributions.md): This page describes the configuration schema for specifying distributions
- [Specifying time-varying parameter modifications](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/intervention-templates.md): This section describes how to specify modifications to any of the parameters of the transmission model or observational model during certain time periods.
- [Other configuration options](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/other-configuration-options.md)
- [Code structure](https://iddynamics.gitbook.io/flepimop/gempyor/model-implementation/code-structure.md)
- [Model Output](https://iddynamics.gitbook.io/flepimop/gempyor/output-files.md): (This section describes the location and contents of each of the output files produced during a non-inference model run)


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://iddynamics.gitbook.io/flepimop/gempyor.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.