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README.Rmd

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[![commit activity](https://img.shields.io/github/commit-activity/m/canmod/macpan2)](https://github.com/canmod/macpan2/commits)
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[![contributors](https://img.shields.io/github/contributors/canmod/macpan2)](https://github.com/canmod/macpan2/graphs/contributors)
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`macpan2` is a software platform for building and calibrating compartmental models of infectious disease. It supports flexible model specification and fast parameter calibration, making it easier for modellers to respond to emerging public health threats. Developed through collaboration with the [Public Health Agency of Canada](https://www.canada.ca/en/public-health.html), `macpan2` is being used to support responses to diseases such as mpox [@milwid2023mpox], measles [@phac2024measles], and COVID-19 [@simmons2025cost;@miranda2024strategies], and generally to assist with internal work on [pandemic preparedness](https://phac-nml-phrsd.github.io/EPACmodel/). PHAC published an [interactive measles model](https://wzmli.shinyapps.io/two_pop_measles_shiny/) using `macpan2`.
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`macpan2` is a software platform for building and calibrating compartmental models of infectious disease. It supports flexible model specification and fast parameter calibration, making it easier for modellers to respond to emerging public health threats. Developed through collaboration with the [Public Health Agency of Canada (PHAC)](https://www.canada.ca/en/public-health.html), `macpan2` is being used to support responses to diseases such as mpox [@milwid2023mpox], measles [@phac2024measles], and COVID-19 [@simmons2025cost;@miranda2024strategies], and generally to assist with internal work on [pandemic preparedness](https://phac-nml-phrsd.github.io/EPACmodel/). PHAC published an [interactive measles model](https://wzmli.shinyapps.io/two_pop_measles_shiny/) using `macpan2`.
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The precursor to `macpan2` was [McMasterPandemic](https://github.com/mac-theobio/McMasterPandemic), which was developed to provide [forecasts](https://mac-theobio.github.io/covid-19) and insights to Canadian public health agencies throughout the COVID-19 pandemic [@phac_modelling_group]. Much was [learned](https://canmod.github.io/macpan-book/index.html#vision-and-direction) about developing general purpose compartmental modelling software during this experience, but the pressure to deliver regular forecasts made it difficult to focus on the software itself. The goal of this `macpan2` project is to re-imagine `McMasterPandemic`, building it from the ground up with architectural and technological decisions that address the many lessons that we learned from COVID-19 about software.
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* [Project history and trajectory](https://canmod.net/misc/pyRC) [slides]
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* [Instructional videos](https://drive.google.com/drive/folders/1NEQf2sy6QLxMiiWBN5Yn9U7wiPMs1jiS)
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* [Publications and Reports using `macpan2` and `McMasterPandemic`](#publications-and-reports)
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* [Visual `macpan2` model builder](https://canmod.github.io/macpan2-model-builder/) [proof of concept]
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## Installation
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README.md

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compartmental models of infectious disease. It supports flexible model
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specification and fast parameter calibration, making it easier for
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modellers to respond to emerging public health threats. Developed
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through collaboration with the [Public Health Agency of
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Canada](https://www.canada.ca/en/public-health.html), `macpan2` is being
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through collaboration with the [Public Health Agency of Canada
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(PHAC)](https://www.canada.ca/en/public-health.html), `macpan2` is being
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used to support responses to diseases such as mpox ([Milwid et al.
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2023](#ref-milwid2023mpox)), measles ([PHAC
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2024](#ref-phac2024measles)), and COVID-19 ([Simmons et al.
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videos](https://drive.google.com/drive/folders/1NEQf2sy6QLxMiiWBN5Yn9U7wiPMs1jiS)
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- [Publications and Reports using `macpan2` and
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`McMasterPandemic`](#publications-and-reports)
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- [Visual `macpan2` model
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builder](https://canmod.github.io/macpan2-model-builder/) \[proof of
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concept\]
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## Installation
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