# Eloranta et al. (2023) Effects of temporal abiotic drivers on the dynamics of an allometric trophic network model - software codes and simulation outputs --- Author and correspondence: Tommi Perälä, tommi.a.perala@jyu.fi, https://orcid.org/0000-0002-4995-5997 Contents: Data: Simulation outputs Software: Simulator software and codes for running the simulations and producing the figures in the manuscript. ## Data This section consists of the following files and directories "1_LakeConstance_colors.txt" - List of food web node colors. Used for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi "1_LakeConstance_labels.txt" - List of food web node labels. Used for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi "1_LakeConstance_links.txt" - Adjacency matrix describing the trophic interactions in the food web as a comma separated list. Used for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi "1_LakeConstance_TL.txt" - List of prey-averaged trophic levels of the nodes in the food web. Used for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi "README.md" - This readme file "Results.mat" - MATLAB formatted binary file containing simulation outputs and input variables In MATLAB, Results.mat can be loaded using the load command. In R, loading of a mat-file is done using the readMat function from the R.matlab package. The Results.mat file contains the following variables: Name Size Bytes Class Data 1x1 82590 struct DefaultOptions 1x1 4352 struct OPTIONS 1x15 96396 cell RESULTS 1x15 210824120 struct Data is a structure array containing the necessary input information about the species and their interactions in the food web. "Data" "B0" - Half-saturation density parameters of the functional response [mugC/m3] "d" - Intraspecific consumer interference parameters of the functional response [m3/mugC] "y" - Maximum consumption rate scaling factor parameters "q" - Hill's exponent parameters of the functional response "e" - Assimilation efficiency parameters "Guilds" - 1x32 Structure array containing guild specific information with fields: "label" - Guild label "name" - Guild name "type" - Guild type (Detritus/Producer/Consumer/Fish) "igr" - Intrisict growth rate [1/day] (Producers only) "mbr" - Mass-specific metabolic rate [1/day] (Consumers and Fish only) "binit" - Initial biomass [mugC/m3] "age" - Age of fish age class "f_m" - Maintenance respiration coefficient "c" - Intraspecific producer competition coefficient "s" - Fraction of exudation (Producers only) "diss_rate" - Dissolution rate of POC to DOC [1/day] "hatchery" - The amount of fish stocked each year [mugC/m3] "f_a" - Activity respiration coefficient (Consumers and Fish only) "invest" - Strength of reproductive investment (Fish only) "Pmat" - Proportion of mature biomass (Fish only) "bodymass" - Individual body mass [mugC/individual] (Producer, Fish and Consumer only) "adjacencyMatrix" - Food web link structure "DefaultOptions" structure array contains the default options for the simulation that are overwritten by the scenario-specific options when needed. Contains the following nested structure "DefaultOptions" "Model" - Abiotic driver submodel options "CarryingCapacity" - Producer time-dependent carrying capacity model "Version" - Model version "Kc" - Original constant carrying capacity [mugC/m3] "z" - Decay component [1/day] "tmax" - Time of the average carrying capacity [day] "GrowthRate" - Producer light dependent intrinsic growth rate model "Version" - Model version "Iadj" - Adjustment to the mean irradiance level [W/m2] "h" - Epilimnion depth [m] "lambda" - Bulk attenuation coefficient [1/m] "I0" - Half-saturation irradiance [W/m2] "cL0" - Scaling coefficient "MetabolicRate" - Consumer temperature dependent metabolic rate model "Version" - Model version "T0" - Standard temperature [degreeC] "Q10" - Temperature-dependency coefficient "cT0" - Scaling factor "Temperature" - Time-dependent temperature model "Version" - Model version "Tadj" - Adjustment to the mean temperature [degreeC] "dTadj" - Yearly temperature rise increment [degreeC/year] "Simulation" - Simulation options "nGrowthDays" - Number of days in a growth season [day] "nYears" - Number of years in the simulation [year] "OPTIONS" is a 1×15 cell array containing the name of the scenario and the scenario-specific options in structure arrays for each of the 15 different scenarios, such as the used versions of the different abiotic driver submodels and their parameter values (see "DefaultOptions" above). "RESULTS" is a 1x15 struct array containing the simulation outputs for each of the 15 different scenarios specified in the OPTIONS cell array of structure arrays. RESULTS = 1×15 struct array with fields: "B" - Biomasses at the end of each simulation year [mugC/m3] "allbiomasses" - Biomasses at the end of each simulation day [mugC/m3] "GF" - Reproductive output of each fish guild for each simulation year [mugC/m3] "G" - Consumption gains for each simulation year for each consumer-resource pair [mugC/m3] "P" - Productivity of primary producers for each simulation year [mugC/m3] ## Code/Software This section consists of the zip-file called Eloranta_et_al_2023_EcolEvo.zip containing the simulator software. The contents of the zip-file are: "1_LakeConstance.mat" - MATLAB formatted binary file containing the simulation input variable "Data" as described above "addIndices.m" - Utility function for indexing different components in the ODE solution "adjacencyMatrixToFile.m" - Utility function for generating data for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi (see Data section) "atn_ode.m" - Gradient function of the model describing the dynamics during the growth season "compileOdeData.m" - Utility function for optimizing the model for the ODE solver "Figure2.m" - Generate Figure 2 of the manuscript "Figure3.m" - Generate Figure 3 of the manuscript "Figure4.m" - Generate Figure 4 of the manuscript "Figure5.m" - Generate Figure 5 of the manuscript "Figure6.m" - Generate Figure 6 of the manuscript "Figure7.m" - Generate Figure 7 of the manuscript "FigureS1.m" - Generate Figure S1 of the manuscript "FigureS2.m" - Generate Figure S2 of the manuscript "guildColorsToFile.m" - Utility function for generating data for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi (see Data section) "guildLabelsToFile.m" - Utility function for generating data for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi (see Data section) "main.m" - Run simulations and generate all figures "parseOptions.m" - Overwrites defaultOptions with scenario specific options "reproductionAndAging.m" - Age class transfer and reproduction of fish species "setScenarioOptions.m" - Specifies scenario-specific options "TP_PreyAveraged.m" - Calculates prey-averaged trophic positions of the nodes in the food web. "trophicLevelsToFile.m" - Utility function for generating data for producing Figure 1 of the manuscript using https://network-visualization.bio.jyu.fi (see Data section) "updateGuildInfo.m" - Utility function for indexing and size information of matrices "webdriver.m" - Main simulation script