A method for characterizing disease emergence curves from paired pathogen detection and serology data

Wildlife disease surveillance programs and research studies track infection and identify risk factors for wild populations, humans, and agriculture. Often, several types of samples are collected from individuals to provide more complete information about an animal's infection history. Methods that jointly analyze multiple data streams to study disease emergence and drivers of infection via epidemiological process models remain underdeveloped. Joint-analysis methods can more thoroughly analyze all available data, more precisely quantifying epidemic processes, outbreak status, and risks. We contribute a paired data modeling approach that analyzes multiple samples from individuals. We use \"characterization maps\" to link paired data to epidemiological processes through a hierarchical statistical observation model. Our approach can provide both Bayesian and frequentist estimates of epidemiological parameters and states. Our approach can also incorporate test sensitivity and specificity, and ..., , , # A method for characterizing disease emergence curves from paired pathogen detection and serology data

## Reproducibility strategy

The [`targets`](https://cran.r-project.org/web/packages/targets/index.html) workflow manager for `R` organizes the analysis. A thorough [tutorial](https://books.ropensci.org/targets/) and a quick [overview](https://cran.r-project.org/web/packages/targets/vignettes/overview.html) are available to learn `targets`. The `targets` package can make it easier to create and store project [artifacts](https://machine-learning.paperspace.com/wiki/artifacts), such as pre-processed datasets, fitted models, diagnostic and predictive output, and tables and figures. However, the tutorial describes ideal workflows that do not necessarily scale well to very large projects with many computationally expensive steps. So, the repository's use of the `targets` package will occasionally deviate from the tutorial's demonstration workflows.

The `targets` package creates and manip...