# FlepiMoP Documentation

## FlepiMoP Documentation

- [Home](https://iddynamics.gitbook.io/flepimop/readme.md)
- [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)
- [Inference Description](https://iddynamics.gitbook.io/flepimop/model-inference/inference-description.md): Methods for fitting model to data
- [Inference Implementation](https://iddynamics.gitbook.io/flepimop/model-inference/inference-implementation.md)
- [Specifying data source and fitted variables](https://iddynamics.gitbook.io/flepimop/model-inference/inference-implementation/specifying-data-source-and-fitted-variables.md)
- [(OLD) Configuration options](https://iddynamics.gitbook.io/flepimop/model-inference/inference-implementation/configuration-options.md)
- [(OLD) Configuration setup](https://iddynamics.gitbook.io/flepimop/model-inference/inference-implementation/old-configuration-setup.md)
- [Code structure](https://iddynamics.gitbook.io/flepimop/model-inference/inference-implementation/code-structure.md): Files where these algorithms are contained
- [Inference Model Output](https://iddynamics.gitbook.io/flepimop/model-inference/inference-model-output.md): (This section describes the location and contents of the additional output files produced during an inference model run)
- [Inference with EMCEE](https://iddynamics.gitbook.io/flepimop/model-inference/inference-with-emcee.md)
- [Setting up the model and post-processing](https://iddynamics.gitbook.io/flepimop/more/setting-up-the-model-and-post-processing.md): Setting up the model and post-processing data
- [Config writer](https://iddynamics.gitbook.io/flepimop/more/setting-up-the-model-and-post-processing/config-writer.md)
- [Diagnostic plotting scripts](https://iddynamics.gitbook.io/flepimop/more/setting-up-the-model-and-post-processing/plotting-scripts.md)
- [Create a post-processing script](https://iddynamics.gitbook.io/flepimop/more/setting-up-the-model-and-post-processing/create-a-post-processing-script.md): These scripts are run automatically after an inference run
- [Reporting](https://iddynamics.gitbook.io/flepimop/more/setting-up-the-model-and-post-processing/reporting.md)
- [Advanced](https://iddynamics.gitbook.io/flepimop/more/advanced.md): (Any more advanced mathematical or computational methods used, or possible configuration options, that only specialized users would need to change)
- [File descriptions](https://iddynamics.gitbook.io/flepimop/more/advanced/file-descriptions.md)
- [Numerical methods](https://iddynamics.gitbook.io/flepimop/more/advanced/numerical-methods.md)
- [Additional parameter options](https://iddynamics.gitbook.io/flepimop/more/advanced/additional-parameter-options.md): Aka “magic numbers” - fixed parameters that may or may not be in config, like MCMC step size, dt, etc . . .
- [Swapping model modules](https://iddynamics.gitbook.io/flepimop/more/advanced/swapping-model-modules.md): (Ie using a totally different compartmental model or outcomes model)
- [Using plug-ins 🧩\[experimental\]](https://iddynamics.gitbook.io/flepimop/more/advanced/using-plug-ins-experimental.md): How to plug-in your code/data directly into flepiMoP
- [Quick Start Guide](https://iddynamics.gitbook.io/flepimop/how-to-run/quick-start-guide.md): Quick instructions on how to install Prerequisites, install flepiMoP itself, and then run through a quick example of how to use flepiMoP.
- [Multiple Configuration Files](https://iddynamics.gitbook.io/flepimop/how-to-run/multiple-configuration-files.md)
- [Synchronizing Files](https://iddynamics.gitbook.io/flepimop/how-to-run/synchronization.md)
- [Advanced run guides](https://iddynamics.gitbook.io/flepimop/how-to-run/advanced-run-guides.md)
- [Running On A HPC With Slurm](https://iddynamics.gitbook.io/flepimop/how-to-run/advanced-run-guides/running-on-a-hpc-with-slurm.md): Tutorial on how to install and run flepiMoP on a supported HPC with slurm.
- [Running with Docker locally 🛳](https://iddynamics.gitbook.io/flepimop/how-to-run/advanced-run-guides/running-with-docker-locally.md): Short tutorial on running FlepiMop on your personal computer using a "Docker" container
- [Running on AWS 🌳](https://iddynamics.gitbook.io/flepimop/how-to-run/advanced-run-guides/running-on-aws.md): using Docker container
- [Environment Variables](https://iddynamics.gitbook.io/flepimop/how-to-run/environment-variables.md)
- [Common errors](https://iddynamics.gitbook.io/flepimop/how-to-run/common-errors.md): Common error messages and how to debug them
- [Useful commands](https://iddynamics.gitbook.io/flepimop/how-to-run/useful-commands.md)
- [Tips, tricks, FAQ](https://iddynamics.gitbook.io/flepimop/how-to-run/tips-tricks-faq.md): All the little things to save you time on the clusters
- [Installing flepiMoP For Development](https://iddynamics.gitbook.io/flepimop/development/installing-flepimop-for-development.md): Instructions on how to install \`flepiMoP\` for development purposes, which uses a specific utility script that installs extras and force reinstall.
- [Git and GitHub Usage](https://iddynamics.gitbook.io/flepimop/development/git-and-github-usage.md)
- [Guidelines for contributors](https://iddynamics.gitbook.io/flepimop/development/python-guidelines-for-developers.md)
- [Module specification](https://iddynamics.gitbook.io/flepimop/deprecated-pages/module-specification.md)
- [US specific How to Run](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run.md)
- [Running with Docker locally (outdated/US specific) 🛳](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/running-with-docker-locally.md): Short internal tutorial on running locally using a "Docker" container.
- [Running on Rockfish/MARCC - JHU 🪨🐠](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/slurm-submission-on-marcc.md): or any HPC using the slurm workload manager
- [Running with docker on AWS - OLD probably outdated](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/running-with-docker-on-aws.md)
- [Provisioning AWS EC2 instance](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/running-with-docker-on-aws/provisioning-aws-ec2-instance.md)
- [AWS Submission Instructions: Influenza](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/running-with-docker-on-aws/aws-submission-instructions-influenza.md)
- [AWS Submission Instructions: COVID-19](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/running-with-docker-on-aws/aws-submission-instructions-covid-19.md)
- [Running with RStudio Server on AWS EC2](https://iddynamics.gitbook.io/flepimop/jhu-internal/us-specific-how-to-run/running-with-rstudio-server-on-aws-ec2.md)
- [Inference scratch](https://iddynamics.gitbook.io/flepimop/jhu-internal/inference-scratch.md): This is just a place to play around with different inference algorithms. Gitbook markdown is very application-specific so can't copy this algorithm text into other apps to play around with!
- [click commands](https://iddynamics.gitbook.io/flepimop/technical-reference/click-commands.md)


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