predation: Predation analysis

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

Predation analysis

Description

This function is useful for dynamically evaluating and visualizing predator-prey interaction from Atlantis. Providing information of the predation trough time for biomass pool and for age class functional groups. This tool can helps to analyze the predatory pressure from the predator and from the prey perspective.

Usage

predation(biom.file, groups.csv, diet.file, age.biomass = NULL)

Arguments

biom.file	Character string with the path to biomass output file from the Atlantis simulation. Usually this output has the name "output_Model_BiomIndx.txt", were Model is the name of your Atlantis model.
groups.csv	Character string with the path to the Groups *.csv file (Atlantis input file).
diet.file	Character string with the path to the diet output file. This file contain the diets of each functional group at each recorded time step. If the Atlantis simulation is for several years, it is highly recommended a low frequency recording periodicity of this output file (toutinc). General high frequency engravings very large files and are very difficult to handle in R.
age.biomass	Character string with the path to the output file biomass by age. This is a non-standard Atlantis output file, make sure to turn on the flag "flag_age_output" in the run.prm file if you want Atlantis to write this this output file.

Value

The output of this function is a shiny::reactive html, useful for dynamically evaluating and visualizing predator-prey relationships from an Atlantis output. The outputs of the predation analysis is divided in three parts:

• Biomass: This panel is divided in two sub-panels:

  • Total Biomass which displays the changes in total biomass for each functional group.

  • Relative Biomass displays the variation of the total biomass relative to the initial biomass (B_{0}).

• Predation through time: This panel displays in the upper section the proportion of prey ingested by a specific predator during the simulation. The lower section is the proportion of biomass that is predated from the selected functional group by different predators at each time step during the entire simulation. This function has different option that includes:

  • Threshold this option filters the predation values, only the values of proportion of predation greater than this limit are displayed;

  • Scale this option allows you to normalize the predation values between 0 and 1 for each time step. Otherwise, predation values are weighted by the predator's biomass. This allows to evaluate the impact of the predator on each prey at each time step.

• Predation by age group: This panel visualize the predation by an age group and it is composed by two sub-panels:

  • Total Biomass shows in the upper panel the time series of biomass of the functional group selected. The lower section shows the proportion of each prey in the diet of the selected predator at a given time step. The time step can be changed allowing the user to explore the diets of the functional at any point in the simulation; and

  • Biomass by age: This sub-panel shows the biomass of each prey consumed by each age class. This allows visualizing amount of biomass consumed from each prey by the predator at each time step. The upper panel shows the biomass of the prey throughout the simulation, indicating the selected time step.

Author(s)

Demiurgo

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