DOI: 10.5061/dryad.g4f4qrfxn
title: Data from: Strong and weak environmental perturbations cause contrasting restructure of ant transportation networks

description: Dynamic transportation networks are embedded in all levels of biological
 organisation. Ever-growing anthropogenic disturbances and an increasingly
 variable climate highlight the importance of understanding how these
 networks restructure under environmental perturbations. Polydomous wood
 ants provide a convenient model system to study the resilience of
 self-organising multi-source multi-sink transportation networks. We used
 ten years of longitudinal empirical data on both unperturbed and
 experimentally manipulated colony networks to develop and validate a
 comprehensive dynamic simulation model to study network restructuring
 after resource removal. We performed simulation experiments to study the
 effects of excluding food sources with varying importance, either
 temporarily or permanently, imitating pulse and press perturbations of the
 networks. We found that removing heavily used resources, corresponding to
 a strong targeted perturbation, persistently decreased network efficiency,
 unlike random or weak perturbations. We also found that strong
 perturbations had excessively adverse effects on robustness and function,
 reducing the networks’ ability to withstand potential future
 perturbations. When transportation networks develop around the efficient
 use of a few key resources, they may be unable to quickly recover from the
 loss of these through self-organized restructuring. Our findings highlight
 the importance of considering the interaction of perturbation strength and
 network structure in studying transportation network dynamics.
description: <strong>Methods: How was this dataset
 collected?</strong> This dataset was collected
 from a long-term study on nine polydomous wood ant (<em>Formica
 lugubris</em>) colony networks at Longshaw Estate, Peak District, UK
 (N53°18’33”, E1°36’96”), spanning the period 2012–2021. Colony mapping
 followed the protocol of Ellis & Robinson (2015) and was conducted
 annually in late summer (July–August), coinciding with peak ant
 activity. Data collection involved:
 <strong>Nest and Foraging
 Mapping:</strong> Actively used nests and the trees they foraged on
 were recorded. <strong>Trail
 Measurement:</strong>  Internest and foraging trail lengths were
 measured, and trail strength was assessed by recording the distance
 required to count ten ants at the midpoint of each trail. This recorded
 distance was then converted into ants per millimeter (ants/mm) for further
 analysis. <strong>Nest Population
 Estimation:</strong> The mound-volume technique (Chen &
 Robinson, 2013) was used to estimate nest sizes. 
 <strong>Previous Empirical Perturbation Experiment
 (2017–2021):</strong> Five colonies underwent a tree exclusion
 experiment in a previously published study, where a major foraging tree
 was temporarily blocked for one year to analyze network adaptation. Five
 other colonies served as controls. See Burns et al. (2021) for
 details. <strong>How has it been
 processed?</strong> The dataset was
 pre-processed to extract relevant model parameters and validate
 simulations: <strong>2012–2016
 data</strong> were used for parameter estimation, defining network
 structures such as nest density, trail lengths, foraging behaviors, and
 colony size. <strong>2017–2021
 data</strong> were categorized for model validation, comparing
 control and exclusion-treated colonies to assess network
 adaptation. <strong> The original data are
 stored in CSV format.</strong> The csv files (empirical_edges.csv
 and empirical_nodes.csv) are available for direct download and are also
 contained in Ant_networks_Code_and_Data.zip (see the 'Input'
 folder inside the ZIP file).  For a
 complete description of the methodology and dataset structure, refer to
 the Supplementary Methods (S1.2) and the included README file.
 <strong>References</strong>
 <strong>Burns DDR, Franks DW, Parr C, Robinson
 EJH.</strong> 2021. <em>Ant colony nest networks adapt to
 resource disruption.</em> Journal of Animal Ecology
 <strong>90</strong>, 143–152.
 doi:10.1111/1365-2656.13198 <strong>Ellis S,
 Robinson EJH.</strong> 2015. <em>The role of non-foraging
 nests in polydomous wood ant colonies.</em> PLOS ONE
 <strong>10</strong>, e0138321.
 doi:10.1371/journal.pone.0138321 <strong>Chen
 Y-H, Robinson EJH.</strong> 2013. <em>A comparison of
 mark–release–recapture methods for estimating colony size in the wood ant
 Formica lugubris.</em> Insectes Sociaux
 <strong>60</strong>, 351–359.
 doi:10.1007/s00040-013-0300-z
description: # Strong and weak environmental perturbations cause contrasting
 restructure of ant transportation networks 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)