catch: Analysis of the Harvest in Atlantis

Description Usage Arguments Value Author(s)

View source: R/catch.R


This tool allows for the visualization and analysis of the harvest output from an Atlantis model. This tool includes analysis of catch, bycatch, and discarding either at the level of the entire population or by age class. In addition to graphical output, it is also possible to perform a skill assessment of the model performance (currently only for the time series of catch and bycatch). The quantitative metrics used to analyze the performance of the model is based on the approach described by Olsen et al. (2016) and Stow et al. (2009) using: the correlation coefficient, root mean squared error, reliability index, average error, average absolute error and the modeling efficiency routines.


catch(grp.csv, fish.csv,, ext.catch.f = NULL)



Character string with the path to the Groups *.csv file (Atlantis input file).


Character string with the path to the fisheries *.csv file (Atlantis input file)

Character string with the path to the catch netcdf output file from Atlantis. Usually this file has the name of [Your_Model], where [Your_Model] is the name of your Atlantis model


(Default = NULL) Character string with the path to the external file with the observed catches and discards by year. This helps to calibrate the harvest section of Atlantis and it is required to perform the skill assessment of the model.


This function provides 3 different sets of analyzes of the catches in the following tabs:



Atlantis-Ecosystem-Model/ReactiveAtlantis documentation built on Dec. 7, 2018, 7:59 a.m.