R package for modeling anadromous fish population responses to freshwater habitat changes
This package can be installed with the devtools package in R using the repository url:
devtools::install_github("danStich/anadrofish")
To install anadrofish, you will need to have devtools installed ahead of time in R, but that requires some special tools. To install on Windows, you will need to download and install the appropriate version of Rtools. To install on Mac, you will need to have the XCode command-line tools installed. And, if running from Linux, you will need to install the developer version of R (r-base-dev) if you have not already.
The purpose of this package is to distribute code and provide a user interface for modeling anadromous fish population responses to dam passage and fisheries in Atlantic coastal rivers of Canada and the United States. The main sim_pop function uses various helper functions (see ?anadrofish in R) that links dam passage to habitat availability and stochastic population models to simulate species-specific responses to dams and fisheries.
Existing models for each river can be implemented using the sim_pop function. New models can theoretically be constructed using the existing functions within anadrofish and appropriately structured habitat data.
Currently, these models are available for American shad (Alosa sapidissima) in 167 Atlantic Coastal rivers of North America from Florida (St. Johns River) to Quebec (St. Lawrence drainage). The full list of rivers available for assessment can be viewed with anadrofish::get_rivers(...) once the package is installed.
Implementation of river herring models has not yet been through peer-review. It is currently undergoing revision in preparation for review and thus may be updated at any time, after which it will be submitted to CRAN with the hope of providing a stable, backward-compatible version of the software moving forward. Until that time, please consult directly with the package maintainer(s) before use in management or research applications.
data/ Built-in data sets for the package
inst/examples/ Examples for those requiring more than a one-liner
man/ Help files and documentation
R/ R functions in scripts