food.web: Trophic level

Description Usage Arguments Value Author(s)

View source: R/food.web.R


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{∑_{j = 1}^{n}(DC_{i, j} * TL_{j})}{∑_{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.


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



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).


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


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


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



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