README.txt file was generated on 2022-10-14 by Lucas P. Martins # For general queries, contact martinslucas.p@gmail.com * GENERAL INFORMATION 1. Title of Dataset: 'Data and code: Global and regional ecological boundaries explain abrupt spatial discontinuities in avian frugivory interactions.' 2. Author Information Corresponding Investigator and 1st author Name: Lucas Pereira Martins Institution: University of Canterbury, New Zealand 3. Date of data collection and scripts preparation: 2019-2022 * SCRIPTS AND DATASETS 1. Description The scripts and datasets presented here are part of the article "Global and regional ecological boundaries explain abrupt spatial discontinuities in avian frugivory interactions", Nature Communications. In this study, we show that both ecoregion and biome boundaries explain abrupt spatial discontinuities in the composition of species and their interactions. These effects are detectable on top of the effects of spatial and elevational gradients and after accounting for differences in sampling effort and methods. Similarly, we find evidence that human disturbance gradients also promote large-scale shifts in species and interaction composition. Interestingly, despite the large (often complete) changes observed in the composition of species and interactions, the structure of avian frugivory networks is relatively consistent across large-scale environmental gradients. 2. Folders, subfolders and files list and descriptions: # Martins et al: Main folder containing the scripts and datasets | |_ _ _ _## data: Subfolder containing instructions and the data necessary for running the analyses. | | | |_ _ _ ### clean_networks: subfolder containing the avian frugivory networks used in the analyses. Networks were cleaned according to three buffer zone sizes and scenarios. | | | | | |_ _ _ ### three buffer zone size subfolders: clean_networks_100km, clean_networks_500km and clean_networks_1000km. | | | | | |_ _ _ ### three scenarios subfolders: clean_networks_scenario1, clean_networks_scenario2 and clean_networks_scenario3. | | | | | |_ _ _ ### 196 csv files containing the avian frugivory networks. For the default buffer zone (500km) and scenario (3), | | networks are also saved as RData (mynetworks.RData). | | | | | |_ _ _ ### dataframe_networks.Rdata: Dataframe containing the predictor and response variables used in our models. | | | |_ _ _ ### dataframe_rewiring.Rdata: Dataframe containing the predictor and response variables used in our supplementary model. | | | |_ _ _ ### metadata_networks.Rdata: Dataframe containing the metadata of our local networks. | | | |_ _ _ ### README_dataframe_networks.pdf: description of the variables within the dataframe_networks.Rdata file. | | | |_ _ _ ### README_metadata_networks.pdf: description of the variables within the metadata_networks.Rdata file. | | |_ _ _ _## global_network_figures: Subfolder containing the figures (.pdf) generated in the '10_figure_global_network.R' script. | | |_ _ _ _## outputs: Subfolder containing the outputs of our scripts. | | | | | |_ _ _ ### gam_mrm_results: subfolder containing R files with the results of our GAM-based MRM models. Results are available for all buffer zone sizes (100km, 500km and 1000km) | | and data claeaning scenarios (1, 2 and 3). However, results obtained by using the quantitative version of ecoregion and biome | | distance matrices and jackknife outputs are only available for the default buffer zone (500km) and scenario (3). | | Similarly, results obtained by removing the study with the greatest number of networks in our dataset from the analyses are only available | | for the default buffer zone (500km) and scenario (3). These results can be found in the corresponding folders within the | | subfolder 'tanzania_removed'. | | | | | | | |_ _ _ ### sensitivity_analysis: subfolder containing R files with the results of our sensitivity analysis. | | | | _ _ _ _## new_results: subfolder to be filled with results obtained by running the analyses from scratch. | | | | _ _ _ _## sensitivity_analysis_interaction: results of sensitivity analysis using interaction dissimilarity as response variable. | | | | _ _ _ _## sensitivity_analysis_network: results of sensitivity analysis using network structural dissimilarity as response variable. | | | | _ _ _ _## shapefile: Subfolder created to storage the Ecoregions 2017 shapefile (available at https://ecoregions.appspot.com/). | | |_ _ _ _## 01_functions.R: Code - Functions to be used in the analyses of the paper. | | |_ _ _ _## 02_MRM_GAM.R: Code - Statistical analyses using Generalized Additive Models (GAMs) and Multiple Regression on Distance Matrices (MRMs). | | |_ _ _ _## 03_deviance_partitioning.R: Code - Evaluating the relative contributions of different predictor variables using deviance partitioning. | | |_ _ _ _## 04_jackknifing.R: Code - Using the jackknife function to run the models (MRMs/GAMs) using different subsets of the data. | | |_ _ _ _## 05_removing_study_76.R: Code - Running the models without the study 76 (Mt Kilimanjaro, Tanzania). | | |_ _ _ _## 06_rewiring_analysis.R: Code - Evaluating interaction rewiring across networks. | | |_ _ _ _## 07_sensitivity_analysis.R: Code - Sensitivity analysis to evaluate how sequentially removing networks based on their size would affect the estimates (t and F values) of our predictor variables. | | |_ _ _ _## 08_figures_sensitivity.R: Code - Figures of sensitivity analysis. | | |_ _ _ _## 09_plots.R: Code - Generating the plots presented in the paper. | | |_ _ _ _## 10_global_network_figure.R: Code - Generating the figure of the global network of frugivory. | | |_ _ _ _## General Information.pdf: General information about the analyses and results.