How does parasite environmental transmission stage concentration change before, during, and after disease outbreaks?

Outbreaks of environmentally transmitted parasites require that susceptible hosts encounter transmission stages in the environment and become infected, but we also know that transmission stages can be in the environment without triggering disease outbreaks. One challenge for understanding the relationship between environmental transmission stages and disease outbreaks is that the distribution and abundance of transmission stages outside of their hosts have been difficult to quantify. Thus, we have limited data about how changes in transmission stage abundance influence disease dynamics; moreover, we do not know whether the relationship between transmission stages and outbreaks differs among parasite species. We used digital PCR to quantify environmental transmission stages of five parasites in six lakes in southeastern Michigan every two weeks from June to November 2021. At the same time, we quantified infection prevalence in hosts and host density. Our study focused on eight zooplankto..., , , # Davenport et al. study on parasite environmental transmission stage concentration and disease outbreaks

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The files include all the data and code used to create the figures in the Davenport et al. manuscript. Data collection was led by Elizabeth Davenport and supported by Marcin Dziuba, Logan Jacobson, Siobhan Calhoun, and Kira Monell. Figures were created by Elizabeth Davenport and Meghan Duffy of the University of Michigan.

## Description of the data and file structure

There are three main folders in the zip file:

1. scripts: this contains the code used to create figures.
2. data: this contains the data collected during the study.
3. figures: this is the folder where plots will be saved from the output of the R markdown files.

## Sharing/Access information

During the review process, data and code were posted at:

# Spore Concentrations and Outbreak Data

Data and code for 2021 field study led by Elizabeth Davenport

Citation: How does parasite environmental transmission...