The population dynamics of clustered consumer-resource spatial patterns: insights from the demographics of a Turing mechanism

Code and data from:  “The population dynamics of clustered consumer-resource spatial  patterns: insights from the demographics of a Turing mechanism” (2024)  by Zachary Hajian-Forooshani, Iris Saraeny Rivera Salinas, Ivette  Perfecto and John Vandermeer. With these files all of the analysis can  be recreated.

R script: “2024_10_16_Phorid_survey_analysis_figures_final”

• Script for statistical analysis of the Phoridae field surveys.
   
• Relies on data from: “Azteca_DSP_Phorid_dynamics_survey_data.csv”
   

R script: “2024_10_16_DSP_test_for_empirical_data”

• Script for Demographic Spatial Patterning test and  randomization procedure as outlined in Figure 2 of the manuscript and  described in Supplementary Material
   
• Relies on data from:
   
  • “Azteca_census_data_Jan_2018.csv”
• Produces:
   
  • “dsp.df.final.csv”
  • “dsp.randomizations.df.final.csv”

R script: “2024_10_16_DSP_results_Fig3”

• Plots the results from the DSP test for Fig 3.
   
• Relies on data from:
   
  • “dsp.df.final.csv”
  • “dsp.randomizations.df.final.csv”

R script: “2024_10_16_Azteca_DSP_age_specific_mortality_calculations”

• Calculates the age specific mortalities in the empirical data.
   
• Produces: ”2023_11_15_Azteca_DSP_empirical_death_rates_full_df.csv”
   

R script: “2024_10_16_density_dependence_in_clusters_for_SupMat”

• Script with analysis to show that older nests tend to be in the center of clusters for supplementary material.
   
• Relies on data from:
   
  • “Azteca_census_data_Jan_2018.csv”

R script: “2024_10_16_Processing_death_rate_data_from_netlogo_model”

• Script to process death rate trends from the netlogo consumer-resource model.
   
• Relies on data from:
   
  • “Netlogo_consumer_resrouce_model_output.csv"
• Produces:
   
  • "2023_11_19_azteca_DSP_netlogo_mortality_df_with_replicates.csv"

R script: “2024_10_16_Netlogo_spatial_output_Fig6_landscape”

• Makes figures from the output of the netlogo  consumer-resource model. Data is embedded in the script which was copied  directly from runs of the netlogo model to get spatial explicit  information on consumers and resources.
   
• Relies on data from:
   
  • “Netlogo_consumer_resource_model_output.csv"

R script: “2024_10_16_Empirical_and_model_comparisions_Death_rates_and_Spatial_patterns_Fig5_Fig8_Fig9”

• Script to compare death rate and spatial patterning trends from empirical data and netlogo consumer-resource model.
   
• Relies on data from:
   
  • “azteca_phorid_model_data_for_paper_Feb27_202.csv”
  • “2023_11_15_Azteca_DSP_empirical_death_rates_full_df.csv”
  • “2023_11_19_azteca_DSP_netlogo_mortality_df_with_replicates.csv”

R script: “2024_10_16_Azteca_DSP_netlogo_age_specific_death_rate_threshold_sensitivity_analysis”

• Sensitivity analysis for the death rate trends in the empirical data and model as described in the supplementary material.
   
• Relies on data from:
   
  • “2023_11_19_azteca_DSP_netlogo_mortality_df_with_replicates.csv”
  • “Azteca_census_data_Jan_2018.csv”

R script: “2024_10_16_Frequency_distribution_empirical_model_comparison_Fig7"

• Script to make Fig 7 comparing the landscape scale spatial patterns between the model and the empirical data.
   
• Relies on data from:
   
  • “Netlogo_consumer_resource_model_output.csv”
  • “Azteca_census_data_Jan_2018.csv”

Netlogo file: “2024_10_16_Netlogo_consumer_resource_model.nlogo”

• Implementation of the spatially explicit consumer-resource model that tracks demography of resources.