food.web: Trophic level

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

Trophic level

Description

This function allows you to explore the changes in the food web structure and trophic level for an specific functional group through time. The estimation of the trophic position is based on the approach of Pauly et al.(1998)

TL_{i} = 1 + \frac{\sum_{j = 1}^{n}(DC_{i, j} * TL_{j})}{\sum_{j = 1}^{n} DC_{i, j}}

were TL_{i} in the trophic position of the predator, DC_{i, j} is the diet composition; TL_{j} is the trophic level of the prey, and n in the number of preys. These initial values for the trophic position were based on Pauly et al. (1998) and Tucker and Roger (2014) (Table 1).
Table 1 : Initial trophic position Assigned for each functional groups.

Functional Group	Trophic level
Small Phytoplankton	1.2
Large Phytoplankton	2
Coral	2.2
Small zooplankton	2.4
Medium zooplankton	2.5
Large zooplankton	2.7
Benthic invertebrates	2.52
Cephalopods	3.2
Fishes	3.24
Birds	3.5
Shark and Mammals	4.0

The flexibility of this function allows you to change: a) the focus functional group over which all calculations would be made; b) Maximum trophic connection, this allows for simplification of the food-web and the setting of the maximum number of connections from the focus functional group; c) the minimum proportion, which sets the minimum proportion of a functional group in a diet that is considered as prey for the analysis; and d) time step which sets the time step for the calculation of the food-web.

Usage

food.web(diet.file, grp.file, diet.file.bypol = NULL, quiet = TRUE)

Arguments

diet.file	Character string with the path to the Diet output file. This file contains the diets of each functional group at each (recorded) time step. If the Atlantis simulation is for several years, it is highly recommended that a low frequency of recording of this output is used (set using toutinc) otherwise file sizes can become substantial (which can be very difficult to handle in R).
grp.file	Character string with the path to the groups *.csv file (Atlantis input file).
diet.file.bypol	Detailed diet check file, this can be obtained as an extra output from Atlantis "DetailedDietCheck.txt". To get this file from Atlatnis turn on the option flagdietcheck on the Run.prm file on Atlantis.
quiet	(Default = TRUE) this parameter helps during the process of debugging.

Value

Shiny::Reactive output with the plot of the food web for the specific time step, and a table with the trophic level of each prey and predator in the food web

Author(s)

Javier Porobic

Atlantis-Ecosystem-Model/ReactiveAtlantis documentation built on April 16, 2024, 6:27 a.m.