Supplementary data 1 of the preprint Mello et al. (2018, bioRxiv), later published as Mello et al. (2019, Nature Ecology and Evolution).
Ecological Synthesis Lab (SintECO).
Authors: Marco A. R. Mello, Gabriel M. Felix, Rafael B. P. Pinheiro, Renata L. Muylaert, Cullen Geiselman, Sharlene E. Santana, Marco Tschapka, Nastaran Lotfi, Francisco A. Rodrigues & Richard D. Stevens.
E-mail: marmello@usp.br.
Created on October 16th, 2018 (English version).
Run in R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Disclaimer: You may use this software freely for any purposes at your own risk. We assume no responsibility or liability for the use of this software, convey no license or title under any patent, copyright, or mask work right to the product. We reserve the right to make changes in the software without notification. We also make no representation or warranty that such application will be suitable for the specified use without further testing or modification. If this software helps you produce any academic work (paper, book, chapter, dissertation, report, etc.), please acknowledge the authors and cite the source.
This repo contains all supplementary material from our paper, including processed data and code.
Recently, we've updated and improved the database used in our analysis, and published it as a new data paper. Check out its new repo.
In this paper we used a combination of codes produced in our lab to run different kinds of numerical and graphical analysis. These codes have been further developed since the paper was published. Now their stand-alone versions are available in other repos:
If you have any questions, suggestions, or corrections, please feel free to open an issue or send a pull request.
We are deeply grateful to all naturalists who carried out fieldwork in the Neotropics over several decades and collected the information used to build our dataset. Judith Bronstein gave invaluable suggestions for an early draft of this study. Paulo Guimarães Jr., Tiago Quental, and Thomas Lewinsohn discussed with us the assembly rules of interaction networks. Pedro Jordano, Carsten Dormann, and Katherine Ognyanova gave us invaluable tips on how to analyze and draw networks in R. Mark White and the StackOverflow community helped us build the model used in the latent variable analysis. MARM was funded by the São Paulo Research Foundation (FAPESP: 2018/20695-7), Research Dean of the University of São Paulo (PRP-USP: 18.1.660.41.7), Brazilian Council for Scientific and Technological Development (CNPq: 302700/2016-1), Minas Gerais Research Foundation (FAPEMIG: PPM-00324-15), and Alexander von Humboldt Foundation (AvH: 3.4-8151/15037). GMF and RBPP received scholarships from the Brazilian Coordination for the Improvement of Higher Education Personnel (CAPES) and CNPq through the Graduate School in Ecology of the Federal University of Minas Gerais (ECMVS). RLM received scholarships from FAPESP (2015/17739-4, 2017/01816-0). SES was supported by the National Science Foundation (NSF-1456375). NL received a scholarship from CNPq and The World Academy of Sciences (312518/2015-3). FAR acknowledges CNPq (307974/2013-8) and FAPESP (17/50144-0 and 16/25682-5) for the financial support given for his research, and the Leverhulme Trust for the Visiting Professorship provided.