Folder
ROOT
_ScienceBase Catalog
__Upper Midwest Environmental Sciences Center (UMESC)
___Upper Midwest Environmental Sciences Center Data
____Environmental DNA (eDNA)
This code supports the manuscript "Sampling designs for landscape-level eDNA monitoring programs using three-level occurrence models. Specifically, we used this code to examine different sampling methods for eDNA-based studies as well as the ability of a three-level occupancy model to recover parameters. Our code can be used to conduct power analysis of eDNA-based studies or analyzed eDNA-based models with a three-level occupancy model. (Both of these uses would require some adaption by the user and require the user understand the statistical assumptions of occupancy models, experimental design, the [R](https://www.r-project.org/) and [Stan](http://mc-stan.org/) languages, and eDNA-based studies).
Resource managers conduct landscape-level monitoring using environmental DNA (eDNA). These managers must contend with imperfect detection in samples and sub-samples (i.e., molecular analyses). This imperfect detection impacts their ability to both detect species and estimate occurrence. Although occurrence (synonymously occupancy) models can estimate these probabilities, most models and guidance for their application do not consider three levels. This simulated dataset assumes sites are occupied (probably psi =1, Z = 1 ) and simulates sample (probability theta, A = 0,1) and subsample (probability p, Y = 0, 1) occurrence probabilies and detections (1)/non-detections (0).
