DOI: 10.5061/dryad.1hd6dg7
title: Data from: The role of fish life histories in allometrically scaled food-web dynamics

description: 1. Body size determines key ecological and evolutionary processes of
 organisms. Therefore, organisms undergo extensive shifts in resources,
 competitors and predators as they grow in body size. While empirical and
 theoretical evidence show that these size-dependent ontogenetic shifts
 vastly influence the structure and dynamics of populations, theory on how
 those ontogenetic shifts affect the structure and dynamics of ecological
 networks is still virtually absent. 2. Here, we expand the Allometric
 Trophic Network (ATN) theory in the context of aquatic food webs to
 incorporate size-structure in the population dynamics of fish species. We
 do this by modifying a food web generating algorithm, the niche model, to
 produce food webs where different fish life-history stages are described
 as separate nodes which are connected through growth and reproduction.
 Then, we apply a bioenergetic model that uses the food webs and the body
 sizes generated by our niche model to evaluate the effect of incorporating
 life-history structure into food web dynamics. 3. We show that the larger
 the body size of a fish species respective to the body size of its preys,
 the higher the biomass attained by the fish species and the greater the
 ecosystem stability. We also find that the larger the asymptotic body size
 attained by fish species the larger the total ecosystem biomass, a result
 that holds true or both the largest fish in the ecosystem and each fish
 species in the ecosystem. 4. This work provides an expanded ATN theory
 that generates food webs with life-history structure for chosen species.
 Our work offers a systematic approach for disentangling the effects of
 increasing life-history complexity in food-wed models.
description: START_RunCluster_2018May03_1We modified a the ATN model from Tonin (2011) and Martinez et al. (2012) by extending it to include life history structure. We use MATLAB version 2016b (The MathWorks). The main file within is called START_RunCluster.m.R code for data formattingThis R code inputs the simulation output and reformats it into tidy data (Wickham 2014), as contained in clean_phase1_2018May03_1.zip or clean_phase2_2018May03_1.zip. It also creates colnames_clean_2018May03_1.txt, which stores the column names for the data sets.reformat_data.RAppendix_AnalysisThis R code does all the analyses described in the main text. It requires clean_phase2_2018May03_1.txt, which is contained in clean_phase2_2018May03_1.zip, and colnames_clean_2018May03_1.txt.Column names for the simulation dataThis contains the column names for all the data sets. This file is called by Appendix_Analysis.R.colnames_clean_2018May03_1.txtData part 1This contains the compressed text file for the first phase (200 years) of the simulation during which food web dynamics reach the equilibrium.clean_phase1_2018May03_1.zipData part 2This contains the compressed text file for the second phase (100 years) of the simulation, after the food web dynamics have reached equilibrium. This is the data set we use in the analyses (Appendix_Analysis.R), as it is much smaller than the complete data set.clean_phase2_2018May03_1.zip