feeding.mat: Atlantis feeding tool

Description Usage Arguments Value Author(s)

View source: R/pprey.mat.R


This function helps the user to calibrate and explore different aspect of the predator-prey interaction. In Atlantis, interaction between the predator and the prey is mainly defined by the predator-prey matrix which represents the maximum availability of each prey (age) group to a specific predator (age group). This consumption can be strongly affected by different processes such as the spatial overlap, the biomass of the prey and the gape limitation of the predator. With this tool you can explore the availability matrix and the processes that affect consumption. This tool also allows you to explore new values for the predator-prey matrix and observe online how these new values affect the predator-prey interaction.


feeding.mat(prm.file, grp.file, nc.file, bgm.file, cum.depths,
  quiet = TRUE)



Character string with the path to the biological parameter *.prm file (Atlantis input file).


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


Character string with the path to the netcdf file to read in. This netcdf file contains the initial conditions for the Atlantis model usually ends in .nc.


Character string with the path to the XY coordinates Atlantis input file *.bgm with the information in metres.


Vector with the cumulative depths of the different layers (e.g. cum.depths <- c(0, 20, 100, 200, 500))


(Default = TRUE) this parameter helps during the process of debugging.


Reactive HTML that displays predator-prey information such as: the ppPREY matrix, the initial abundance of prey, the overlap matrix based on gape size, predator preference and predator prey spatial overlap. All this information is divided into two different tabs:



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