The original empirical data used in this study, including network edges and nodes, is available for direct download as empirical_edges.csv and empirical_nodes.csv within the uploaded files and is also contained in Ant_networks_Code_and_Data.zip (see the 'Input' folder inside the ZIP file). A detailed description of all uploaded data, code, and results is listed below.

The study aims to improve our understanding of the structural changes happening in multi-sink multi-source transport networks in response to environmental perturbations. We designed to model to accurately describe the structure, dynamics, and perturbation responses of wood ant (Formica lugubris) colony networks.

We provide a complete, detailed model description, following the ODD (Overview, Design concepts, Details) protocol [1–3] in the Supplementary Material document.

The project is implemented in R 4.2.3. See Supplementary Methods S1.4 and sessionInfo.txt for more details. Execute Run_simulations.R to run simulation experiments. The results will be saved in "./Output/" in a folder named by the date and time when the simulations started. 

List of files in 'Ant_networks_Code_and_Data.zip'

• Input

  • Empirical data
    • empirical_edges.csv - Empirical data: network edges. ATTENTION! This file must be copied to the location ./Input/Empirical data/ for the code to run.
    • empirical_nodes - Empirical data: network nodes. ATTENTION! This file must be copied to the location ./Input/Empirical data/ for the code to run.
    • Colony_6.png - Example empirical colony map. See S1.2.4 Colony maps
    • Colony_10.png - Example empirical colony map. See S1.2.4 Colony maps
  • Empirical_network_statistics.R - Calculation of network measures on the empirical networks
  • Model_parameters.R - Estimates empirical and defines non-estimated parameters

• Output

  • Empirical_statistics - The calculated empirical network measures
    • empirical_stats.csv - Empirical network measures
    • empirical_stats.rds - Empirical network measures
  • Model_parameters
    • estimated_parameters.csv - List of parameters estimated from the empirical data
    • estimated_parameters.rds - List of parameters estimated from the empirical data
    • gravity_parameters.csv - Estimated parameters for the gravity model
    • gravity_parameters.rds - Estimated parameters for the gravity model
    • not_estimated_parameters.csv - List of not estimated parameters
    • not_estimated_parameters.rds - List of not estimated parameters
  • MS_Figures
    • Figure_ERC.pdf - Figure 2
    • Figure_ERC.png - Figure 2
    • Figure_NT.pdf - Figure 3
    • Figure_NT.png - Figure 3
  • Simulation run 2023-06-27 15_29_43 - The simulation results used for the study. Extract the zip file before use!

• Supplementary_Methods.pdf - Detailed model description

• Supplementary_Methods.Rmd - Rmarkdown files preparing Supplementary Methods S1

• Supplementary_Results.Rmd - Rmarkdown files preparing Supplementary Methods S2

• Supplementary_references.bib - BibLatex file with the references for the Supplementary Materials

• Validation_report_template.Rmd - Rmarkdown template called by Run_simulations.R to prepare the validation report

• Experiment_report_template.Rmd - Rmarkdown template called by Run_simulations.R to prepare individual reports on the experiments

• List_of_parameters.Rmd - Rmarkdown template called by Run_simulations.R to prepare a list of the used parameters

• Model_code.R - The codebase for running simulation experiments

• Run_simulations.R - Runs the exclusion experiments, prepares the validation and result reports, and generates individual reports for the experiments

• sessionInfo.txt - Information on R and package versions

• sessionInfo_all.txt - Detailed information on packages

• Simulation_results_template.Rmd - Rmarkdown template called by Run_simulations.R to prepare the results report

  Data file Description:

  empirical_nodes.csv

  This dataset contains information about the nodes in the network, including nests and trees, across different years. Each row represents a nest or tree at a specific time.

  • network_ID (Character): Unique identifier for the colony network on a specific date (e.g., "10_2012-07-26").
  • colony (Character): Unique identifier for the colony (e.g., "10", "2b", "6").
  • date (Character, format: DD/MM/YYYY): Date when data was collected.
  • node_ID (Character): Unique identifier for the node, including colony information (e.g., "10_N1").
  • ID (Character): Simple identifier for the node within the colony (e.g., "N1", "N10").
  • x (Numeric, relative spatial coordinate): X-coordinate of the node.
  • y (Numeric, relative spatial coordinate): Y-coordinate of the node.
  • species (Character): Node type, either "nest" (ant nest) or "tree" (foraging tree).
  • nest_size (Numeric, mound volume in cm³): Estimated size of the nest based on mound volume. Trees have a value of 1.
  • year (Integer): Year of data collection.
  • tree_type (Character): Type of tree, either "regular" or "excl. tree" (excluded from foraging in the experiment).
  • treatment (Character): Experimental treatment type, either "exclusion" (tree excluded from foraging) or "control" (unmanipulated colony).
  • dataset (Character): Classification of the data as "Estimation" (2012–2016 pre-experiment), "Empirical exclusion" (2017–2021 exclusion treatment), or "Empirical control" (2017–2021 control treatment).
    empirical_edges.csv

  This dataset contains information about foraging and internest trails between wood ant nests and trees across multiple years. Each row represents an edge (trail) in the network.

  • colony (Character): Unique identifier for the colony (e.g., "2b", "6", "9").
  • date (Character, format: DD/MM/YYYY): Date when data was collected.
  • distance (Numeric, meters): Length of the trail between two nodes (nest-to-nest or nest-to-tree).
  • from (Character): Identifier of the starting node (nest or tree) of the trail.
  • from_ID (Character): Unique identifier for the starting node, including colony information (e.g., "2b_N1").
  • from_ID_date (Character): Unique identifier for the starting node with date information (e.g., "2b_N1_2012-07-26").
  • from_nest_size (Numeric, mound volume in cm³): Estimated size of the starting nest based on mound volume.
  • from_x (Numeric, relative spatial coordinate): X-coordinate of the starting node.
  • from_y (Numeric, relative spatial coordinate): Y-coordinate of the starting node.
  • network_ID (Character): Unique identifier for the colony network on a specific date (e.g., "2b_2012-07-26").
  • strength (Numeric, ants/mm): Trail strength measured as the number of ants per millimeter.
  • to (Character): Identifier of the ending node (nest or tree) of the trail.
  • to_ID (Character): Unique identifier for the ending node, including colony information (e.g., "2b_T1").
  • to_ID_date (Character): Unique identifier for the ending node with date information (e.g., "2b_T1_2012-07-26").
  • to_nest_size (Numeric, mound volume in cm³): Estimated size of the ending nest based on mound volume.
  • to_x (Numeric, relative spatial coordinate): X-coordinate of the ending node.
  • to_y (Numeric, relative spatial coordinate): Y-coordinate of the ending node.
  • trail_ID (Character): Unique identifier for the trail, including colony and date (e.g., "2b_2012-07-26_N1_T1").
  • trail_type (Character): Type of trail, either "foraging" (nest-to-tree) or "internest" (nest-to-nest).
  • tree_type (Character): Type of tree used, either "regular" or "focal" (for experimental purposes).
  • year (Integer): Year of data collection.
  • treatment (Character): Experimental treatment type, either "exclusion" (tree excluded from foraging) or "control" (unmanipulated colony).
  • dataset (Character): Classification of the data as "Estimation" (2012–2016 pre-experiment), "Empirical exclusion" (2017–2021 exclusion treatment), or "Empirical control" (2017–2021 control treatment).

References

1. Grimm V et al. 2006 A standard protocol for describing individual-based and agent-based models. Ecol. Model. 198, 115–126. (doi:10.1016/j.ecolmodel.2006.04.023)
2. Grimm V, Berger U, DeAngelis DL, Polhill JG, Giske J, Railsback SF. 2010 The ODD protocol: A review and first update. Ecol. Model. 221, 2760–2768. (doi:10.1016/j.ecolmodel.2010.08.019)
3. Grimm V et al. 2020 The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism. J. Artif. Soc. Soc. Simul. 23. (doi:10.18564/jasss.4259)