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fb4package

An R implementation of Fish Bioenergetics 4.0 (Deslauriers et al. 2017). The model partitions consumed energy among metabolism, waste, and growth to produce daily estimates of fish consumption and weight gain.

Installation

# Stable release from CRAN
install.packages("fb4package")

# Development version from GitHub
# install.packages("devtools")
devtools::install_github("HansTtito/fb4package")

Usage

library(fb4package)

data(fish4_parameters)
chinook <- fish4_parameters[["Oncorhynchus tshawytscha"]]

bio <- Bioenergetic(
  species_params     = chinook$life_stages$adult,
  species_info       = chinook$species_info,
  environmental_data = list(
    temperature = data.frame(Day = 1:100,
                             Temperature = 10 + 5 * sin(2 * pi * (1:100) / 365))
  ),
  diet_data = list(
    proportions = data.frame(Day = 1:100, Alewife = 0.7, Shrimp = 0.3),
    prey_names  = c("Alewife", "Shrimp"),
    energies    = data.frame(Day = 1:100, Alewife = 4900, Shrimp = 3200)
  ),
  simulation_settings = list(initial_weight = 1800, duration = 100)
)

# Fit p to a target final weight
res <- run_fb4(bio, strategy = "binary_search", fit_to = "Weight", fit_value = 3000)
print(res)

Full documentation, vignettes, and function reference are available at https://hansttito.github.io/fb4package/.

Documentation

• Introduction
• Statistical estimation strategies
• Case study: Chinook salmon
• Species database
• Temperature and climate
• Function reference

Reference

Deslauriers D, Chipps SR, Breck JE, Rice JA, Madenjian CP (2017). Fish Bioenergetics 4.0: An R-Based Modeling Application. Fisheries 42(11):586–596. https://doi.org/10.1080/03632415.2017.1377558

Code of Conduct

Please note that fb4package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

MIT

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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