hatchR: A toolset to predict fish development
hatchR allows users to better understand when wild fish hatch and emerge, like this ESA threatened bull trout from Boise National Forest
For fishes, the timing of when eggs hatch and juveniles emerge from their nests is critical to their survival. These early life stages are when fish are immobile and most vulnerable to sedimentation, dewatering, and disturbance. Land managers and restoration planners need to know when these sensitive windows occur to avoid unintended harm during projects like road repairs, grazing, prescribed fire, or timber work. The need for accurate predictions is growing as climate shifts stream temperatures and flows.
To support these decisions, we built hatchR, a free software tool that helps users forecast fish hatch and emergence timing using stream temperature and spawning dates. hatchR is available as both an R package for technical users and an easy-to-use web app for managers and field staff.
Unlike traditional models that use fixed temperature thresholds, hatchR uses “effective value” models that account for how fish development speeds up or slows down with daily temperature changes. This makes it more accurate and flexible—especially in systems where temperatures are highly variable. hatchR includes a library of developmental models for common salmonid species, and it also allows users to build their own custom models if they have data for specific populations or new species.
hatchR is designed to be both accessible and flexible. In one case study, we use it to show how field crews can schedule road or culvert work outside of emergence windows, reducing risk to protected fish species. In another, we use it to analyze broad patterns in fish development across years and watersheds—useful for understanding how fish may respond to climate or land-use differences.
With hatchR, natural resource agencies, tribal biologists, researchers, and restoration planners now have a free, open-source tool to help protect fish during critical life stages, better time fieldwork, and anticipate ecological changes. The tool can support NEPA planning, grazing allotment reviews, infrastructure maintenance scheduling, or fundamental ecological research.
Explore the tool
Try the interactive demo using real Crooked River data: https://elifelts.shinyapps.io/hatchR_demo/
Visit the project site for documentation and source code: https://bmait101.github.io/hatchR/