Micro-MoB was made to simplify the task of model building for mosquito-borne pathogen transmission (MBPT) systems. It stands for "microsimulation for mosquito-borne pathogens". It is a modular framework to build discrete time MBPT models. It uses R's S3 object system to define a set of components and interfaces which can be filled by any specific model that implements the interface. These parts, along with certain invariants can be put together to define a full simulation model. Definitions for all these terms can be found in the documentation.
We hope it proves useful. Please visit the website to learn more.
remotes::install_github('dd-harp/MicroMoB')
Alternatively you can install Micro-MoB directly from CRAN, but be aware that the CRAN version may not be the most recent version of the package:
install.packages('MicroMoB')
To start learning more about the software design, the problems it was designed to solve,
and how to build new models in Micro-MoB, please read vignette("MicroMoB").
Next, vignette("bloodmeal") describes how the bloodmeal algorithm computes
the distribution of bites using each component's interface, allowing different models
to be linked in a consistent framework.
We also have articles describing some well-known models of specific components of MBPT models that are implemented in Micro-MoB:
-
vignette("RM_mosquito"): read about an implementation of a flexible Ross-Macdonald model of adult mosquito dynamics. -
vignette("MOI_human"): read about an implementation of the$(M/M/\infty)$ queuing model for superinfection in humans. -
vignette("BH_aqua"): read about a simple non-linear model of aquatic (immature) stage mosquito dynamics based on the well known Beverton-Holt model from ecology. -
vignette("BQ_mosquito"): read about a behavioral state model of adult mosquito dynamics. -
vignette("RM_transmission"): read about how we put together models fulfilling each component to run a simple Ross-Macdonald style model of pathogen transmission between human hosts and mosquito vectors.
The article vignette("Advanced") contains information on how to extend Micro-MoB
by linking to it from a new package, and how to write new models that interact with
the rest of the system. It also contains information on how to use the
Plumber web API which is supported for some models in Micro-MoB.
Thank you for your interest in Micro-MoB! If you have a bug to report, please
open an issue on GitHub. If you would like
to open a pull request or have further questions, please see our guide to
contributing to the project at vignette("Contributing").
Please note that the Micro-MoB project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.