Published December 1, 2025 | Version v3
Dataset Open

Data for Coevolution and temporal dynamics of species interactions shape species coexistence

Authors/Creators

  • 1. ROR icon Estación Biológica de Doñana

Description

This folder contains all the data and R codes used to reproduce simulations and analyses.

# Project structure
.
└── data_zenodo
    ├── data
    ├── scripts
        ├── functions and secondary scripts
        | numbered scripts
    ├── README.md
The folder "functions and secondary scripts" contains some functions that are called in the main scripts or alternative scripts that have been used while building up the project, for exploration.

# Codes

### Initial conditions

Scripts 1.1 & 1.2 defined initial conditions for theoretical and empirical communities, respectively, to allows the reproducibility of the simulations.

### Simulations under Julia

Script 2 & 2bis are Julia scripts that were used to perform the coevolution simulations, using theoretical and empirical initial conditions, respectively. The ran on a HPC plateform.

### Extracts and plot the results of theoretical simulations

Script 3 extracts community measures from theoretical simulations. The middle part of script 3, was also ran on a HPC plateform to gain time.

Script 4 plots the results, from figure 2 to figure 4. Figure 1 was done in a sepate scripts labelled *Figure1.r*

### Analyse empirical data and simulations with empirical initial conditions (=with empirical network dimensions)

Scripts 5 extracts communitiy measures from empirical networks and from simulations performed with initial empirical network sizes.

Script 6 merges community measures from empirical networks and simulations to do figure 5.

# Empirical data

*flow_pheno_empirical.csv* and *poll_pheno_empirical.csv* contain the empirical phenological parameters for plant and pollinator species, respectively: the mean activity day (mu) and its standard deviation (sde) representing the duration of the activity period.

*matrices_empirical_networks.RData* contains an R object with the 17 networks used. Plants are in rows and pollinators in columns, with each cell representing the average interaction value across sampling rounds, corrected by abundances.

You can access it in R via:

#load data
load("matrices_empirical_networks.RData")

#see the structure (a list of 17 networks)
str(networks)

#access the first network
networks[[1]]
 

Files

data_zenodo.zip

Files (2.8 GB)

Name Size
md5:4c449ef19680bda3bc1c2e14ac72da40
2.8 GB Preview Download

Additional details

Software

Repository URL
https://github.com/f-duchenne/Evolution_pheno_vs_morpho
Programming language
R , Julia