README.md

In cfree14/splink: Covariate-linked biomass dynamic models

splink: Covariate-linked population dynamics models

Installation

The "splink" R package can be installed from GitHub with:

# Run if you don't already have devtools installed
install.packages("devtools")

# Run once devtools is successfully installed
devtools::install_github("cfree14/splink", force=T)
library(splink)

Functions

The package implements functions to:

• Fit covariate-linked stock recruit models: ?fit_sr
• Fit covariate-linked surplus production models: ?fit_sp
• Extract parameter estimates and confidence intervals from model fits: ?get_results
• Plot parameter estimates and confidence intervals: ?plot_results
• Plot covariate influence estimates and confidence intervals: ?plot_thetas
• Plot model fits on top of data: ?plot_fits
• Predict covariate-linked maximum sustainable yield (MSY): ?calc_msy

The fitting functions allow covariate estimates to be estimated as either fixed or random effects. The production model can be fit using a user-specified shape parameter and the stock recruit model can be fit using either a Ricker or Beverton-Holt stock recruit relationship.

Citation

Free CM (2021) splink: Covariate-linked population dynamics models. Available at: https://github.com/cfree14/splink/

cfree14/splink documentation built on Dec. 19, 2021, 2:57 p.m.