feeding.mat: Atlantis feeding tool

In jporobicg/ReactiveAtlantis: Multiple Reactive HTML tools to help in the calibration of the Atlantis ecosystem model (AEM)

Atlantis feeding tool

Description

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 shiny::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 shiny::observe online how these new values affect the predator-prey interaction.

Usage

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

Arguments

prm.file	Character string with the path to the biological parameter *.prm file (Atlantis input file).
grp.file	Character string with the path to the Groups *.csv file (Atlantis input file).
nc.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.
bgm.file	Character string with the path to the XY coordinates Atlantis input file *.bgm with the information in metres.
cum.depths	Vector with the cumulative depths of the different layers (e.g. cum.depths <- c(0, 20, 100, 200, 500))
quiet	(Default = TRUE) this parameter helps during the process of debugging.

Value

Shiny::Reactive shiny::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:

• Non-spatial: This tab allows the user to check and modify availability values from the pprey matrix. This Function provides 5 outputs:

  • Availability matrix (λ): Matrix of prey availability values (pprey) for each adult, young or biomass pool prey and predator.

  • Overlap matrix: Calculates if a predator is able to eat a prey given its gape size limitations. This function uses the knife-edge size selectivity, where availability of the prey is either available (1) or not available to the predator (0).

    (non-Latex version)

    were SN is the structural weight; KLP Minimum gape limit of the predator (age structured or biomass pool); KUP Maximum gape limit of the predator (age structured or biomass pool).

  • Effective Predation: this provides an approximation of the total biomass of prey consumed by a predator. It assumes a perfect spatial match between prey and predator.

    γ = B * λ * ω

    were γ is the effective predation; B is the biomass; λ is the predator-prey availability (pprey matrix); and ω is the predator-prey gape overlap.

  • Predation pressure: this function calculates the percentage of the predator diet corresponding to a specific prey.

  • Total biomass prey: this is the total biomass per functional group and maturity stage (adult and juvenile).

• Spatial Overlap- this tab allows the user to check the spatial overlap between the prey and the predator in all the boxes and layers based on the values in the initial conditions file and the parameterized gape limitation.

Author(s)

Demiurgo

jporobicg/ReactiveAtlantis documentation built on April 19, 2022, 3:24 a.m.