Alvarenga etal. 2021 data set and project

 Individual behavior and local context are processes that can influence the structure and evolution of ecological interactions. In trophic interactions, consumers can increase their fitness by actively choosing resources that enhance their chances of exploring them successfully. Upon searching for potential resources, they are able to decide which one to choose according to their fitness benefit and maneuverability. Mathematical modeling is often employed in theoretical studies to understand the coevolutionary dynamics between these species. However, they often disregard the individual consumer behavior since the complexity of these systems usually requires simplifying assumptions about interaction details. Using an individual-based model, we model a community of several species that interact antagonistically. The trait of each individual is modeled explicitly and is subjected to the interaction pressure. In addition, consumers can actively choose the resources that guarantee greater fitness. We show that active consumer choice can generate coevolutionary units over time. It means that the traits of both consumers and resources converge into multiple groups with similar traits, exerting reciprocal selective pressure between them. We also observed that network structure has a greater dependence on the parameter that delimits active consumer choice than on the intensity of selective pressure. As a consequence, this parameter can closely match empirical networks. Thus, we consider that the inclusion of consumers' active choice behavior in the models plays an important role in the ecological and evolutionary processes that structure these communities.

We used a project-oriented Workflow with R-Studio to keep our paper reproducible. You need to install all the packages and their dependencies to achieve this goal. The project is organized according to the diagram below which highlights the main files (we try to make the names as self-explanatory as possible), followed by a brief description: 

/alvarenga-etal-2021 # root
├── 00-data-cleaning.Rmd        # Preparation of raw data
├── 01-introduction.Rmd
├── 02-methods.Rmd
├── 03-results.Rmd
├── 04-discussion.Rmd
├── Alvarenga-etal-2021.Rproj 
├── _book                       # Final files of project (.pdf, .tex)
├── _bookdown_files             # intermediate figures created in the process.
├── _bookdown.yml               # You can control which .Rmd file to compile 
├── data
│   ├── data-processed          # data cleaned, organized ans ready to use
│   ├── networks                # Interaction networks (output FORTRAN)
│   ├── output_fdif             # outputs FORTRAN (phenotype)
├── figs                        # figures of main and supplementary documents)
├── index.Rmd                   # Use to configurate the paper/ load the packages
├── output                      # analysis results, data to plot
│   ├── data
├── packages.bib
├── packrat                   # library with all packages necessary to run the project
├── proceedings-of-the-royal-society-b.csl # To control citations
├── R                         # scripts in R
│   └── fct                   # functions created
└── references.bib
 

You need to know a little about R, RStudio and projects with RStudio. If you understand a little bit of Rmarkdown it helps too. After installing the packages and dependencies, just click on the build book button in the build tab and all the work will be done in a few minutes.

The final products of this project are  .tex and .pdf archives (drafts) of the paper contains all sections.