rooperc4/MEHRSI: Habitat Model Estimates of Survey Abundances

The purpose of this package and its associated functions is to allow the user to compute annual indices of abundance from survey data using a habitat model based on Rooper and Martin (2012). It is designed to be a 2-stage model, with the first stage setting the biological limits for a species (such as depth ranges from 85-250 m for Pacific Ocean perch or geographical limits on Northern rockfish distribution). In the second stage a iterative modeling process fits CPUE data to habitat variables chosen by the user. Individual habitat variables are constrained to using one of 3 shapes for the fitting (dome, asymptotic or linear). Model fitting is completed using the optim function in R and parameters and variables are removed sequentially until there is no improvement in model AIC. Full details of the modeling and the manuscript can be found at https://www.st.nmfs.noaa.gov/spo/FishBull/1101/rooper.pdf and the preceeding papers where the method was developed (Rooper and Martin 2009 - http://www.int-res.com/articles/meps2009/379/m379p253.pdf, Rooper 2008 - http://fishbull.noaa.gov/1061/rooper.pdf, and Rooper and Zimmermann 2005 - http://www.int-res.com/articles/meps2005/290/m290p251.pdf).

install.packages("remotes")
remotes::install_github("rooperc4/MEHRSI")