editor_options	title	description
markdown wrap 72	Bfiat, An R package for bottom fishing assessment	Bfiat, the Bottom Fisheries Impact Assessment Tool, is an R-package that estimates the impact of bottom trawling on sediment inhabiting organisms, and on sediment ecosystem functions. It contains data-driven mechanistic models that describe how species density is being reduced by bottom trawling, and then recovers till the next fishing event.

Karline Soetaert and Olivier Beauchard

Netherlands Institute for Sea Research

Introduction

 Bfiat (Bottom Fisheries Impact Assessment Tool) is an R-package that 
 estimates the impact of bottom trawling on sediment inhabiting organisms, 
 and on sediment ecosystem functions. 
 It contains data-driven mechanistic models that describe how species 
 density is being reduced by bottom trawling, and then recovers till 
 the next fishing event. 

The R-package Bfiat is created in the framework of the EMODnet biology project, the NECCTON (New Copernicus Capability for Trophic Ocean Networks) project, and in cooperation with the ICES Working Group on Fisheries Benthic Impact and Trade-offs (WGFBIT).

Installation

Before installing the Bfiat package, you need to first install the following R-packages and their dependencies:

• Btrait, to work with species data, and for the trait databases (to be found on github/EMODNET/btrait).
• deSolve, to solve the mechanistic model
• devtools, required for a seamless installation of the Bfiat and Btrait packages from this github repository.

Once the deSolve and devtools packages have been installed (from CRAN), type the following command in the R-console to install the Btrait and Bfiat package:

devtools::install_github("EMODnet/Btrait", depend=TRUE, build_vignettes=TRUE)
devtools::install_github("EMODnet/Bfiat", depend=TRUE, build_vignettes=TRUE)

If you do not want to install the vignettes, then you may delete the build_vignettes = TRUE part.

Then, type require(Bfiat) in the R-console to load the package in R.

That's it! After this step, you should be able to use the package.

Getting help

As for any other R-package, you can get extra help by entering ?Bfiat in the R console.

There is a vignette in the package, that can be triggered with vignette("Btrait") in the R console.

Uninstall

To uninstall the Bfiat package, locate it in the "Packages" tab in Rstudio, and click on the encircled "x" button ("Remove package") on the right margin.

To uninstall the package manually, type the following command in the R-console (the version of the library may differ, here we assume 4.1):

• Windows users:

  remove.packages("Bfiat", lib="~/R/win-library/4.1")
  

• Linux users:

  remove.packages("Bfiat", lib="~/R/x86_64-pc-linux-gnu-library/4.1")
  

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During the transition from version 0.01 to version 1.0.0 the names of many functions have changed. Also, the function names in package Btrait, used by Bfiat, have changed. This means that any code that uses these old versions will need to be adapted.

First upload: 22/02/2024

Last major change: 29/01/2025