Major update

New version of the script, now with shorter, faster, and easier to reproduce code.

.gitignore

@@ -0,0 +1,3 @@
+
+.DS_Store
+.Rhistory

README.md

@@ -1,17 +1,80 @@
-# How to draw and analyze multilayer networks in R
+# multilayer-networks
+
+A tutorial on how to draw and analyze multilayer networks in R.
 
 [Ecological Synthesis Lab](https://marcomellolab.wordpress.com) (SintECO).
 
 Authors: Marco Mello & Renata Muylaert.
 
 E-mail: marmello@usp.br. 
 
-How to cite: Mello MAR & Muylaert RL. 2017. Drawing and analyzing multilayer networks in R. Ecological Synthesis Lab of the University of São Paulo, Brazil.
-
-Published on November 23rd, 2017 (English version).
+First published on November 23rd, 2017 (English version).
 
 <a href="https://doi.org/10.5281/zenodo.1487539"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.1487539.svg" alt="DOI"></a>
 
-Run in R 3.4.2 (2017-09-28) -- "Short Summer"
+Run in R version 4.0.2 (2020-06-22) -- "Taking Off Again"
+
+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, talk, lecture or similar), please acknowledge the authors and cite the source, using the DOI or URL of this GitHub repository.
+
+
+## Functionality and origin
+
+The first version of this script was written as part of the analysis carried out by [Mello et al. (2019, NatureEcoEvo)](https://doi.org/10.1038/s41559-019-1002-3). Since then, we have been working on making the code shorter, faster, and easier to be used by other people interested in the same topics. You may use this code to learn how to input data on multilayer networks in R, as well to visualize those data as multilayer graphs.
+
+
+## List of folders and files
+
+1. data (folder)
+
+    a. net1.xlsx -> complete data set from Genrich et al. (2017). Interactions between marsupials, rodents, and plants.
+
+    b. net1an.txt -> angatonistic layer of net1. Seed destruction by marsupials and rodents.
+
+    c. net1links.txt -> the links (edges) of net1 with additional attributes.
+
+    d. net1mu.txt -> mutualistic layer of net1. Seed dispersal by marsupials and rodents.
+
+    e. net1nodes.txt -> the nodes (vertices) of net1 with additional attributes.
+
+
+2. figures (folder)
+
+    a.net1.png -> multilayer graph of net1.
+
+
+3. multilayer-networks -> script to draw and analyze multilayer networks.
+
+
+## Instructions
+
+Follow the instructions provided in the script "multilayer-networks.R".
+
+
+## Data source
+
+* Genrich, C. M., Mello, M. A. R., Silveira, F. A. O., Bronstein, J. L., & Paglia, A. P. (2017). [Duality of interaction outcomes in a plant-frugivore multilayer network](https://doi.org/10.1111/oik.03825). Oikos, 126(3), 361–368. doi: 10.1111/oik.03825
+
+
+## Feedback
+
+If you have any questions, corrections, or suggestions, please feel free to open and [issue](https://github.com/marmello77/multilayer-networks/issues) or make a [pull request](https://github.com/marmello77/multilayer-networks/pulls).
+
+
+## Acknowledgments
+
+We thank our labmates and our sponsors, especially the Alexander von Humboldt-Stiftung, CNPq, CAPES, and FAPESP, who gave us grants, fellowships, and scholarships. Pedro Jordano and Carsten Dormann helped us take our first steps in analyzing and drawing networks in R. Special thanks go to Katherine Ognyanova, who gave us invaluable tips on advanced network drawing in R. We strongly recommend her [online tutorial](http://kateto.net/network-visualization). Last, but not least, we thank the [Stack Overflow Community](https://stackoverflow.com), where we solve most of our coding dilemmas. A dilemma related to converting incidence matrices to make a multilayer network was solved [here](https://stackoverflow.com/questions/64486982/how-to-unite-two-graphs-in-r-to-form-a-multilayer-network).
+
+
+## Suggested readings
+
+* Barabasi, A.L. (2016) [Network Science](http://barabasi.com/networksciencebook/), 1st ed. Cambridge University Press, Cambridge.
+
+* Bianconi, G. (2018). [Multilayer Networks: Structure and Function](https://amzn.to/31SAdRl). (1st ed.). Oxford: Oxford University Press.
+
+* Mello MAR, Muylaert RL, Pinheiro RBP & Félix GMF. 2016. [Guia para análise de redes ecológicas](https://marcomellolab.wordpress.com/software/). Edição dos autores, Belo Horizonte. 112 p. ISBN-13: 978-85-921757-0-2.
+
+* Mello, M. A. R., Felix, G. M., Pinheiro, R. B. P., Muylaert, R. L., Geiselman, C., Santana, S. E., … Stevens, R. D. (2019). [Insights into the assembly rules of a continent-wide multilayer network](https://doi.org/10.1038/s41559-019-1002-3). Nature Ecology & Evolution, 3(11), 1525–1532.
+
+* Ognyanova K. 2019. [Static and dynamic network visualization with R](http://kateto.net/network-visualization).
 
-Disclaimer: You may use this software freely for commercial or non-comercial 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 etc.), please acknowledge the authors and cite the source, using the DOI provided and the URL to this GitHub repository.
+* Pilosof, S., Porter, M. A., Pascual, M., & Kéfi, S. (2017). [The multilayer nature of ecological networks](https://doi.org/10.1038/s41559-017-0101). Nature Ecology & Evolution, 1(4), 0101.

data/net1an.txt

@@ -0,0 +1,10 @@
+	ByrSp	CamAda	CecHol	CecPac	CecGla	ChiAlb	CocAur	ErytSp	EuphSp	FicuSp	LeaAur	LeaCor	LeanSp	MicAlb	MicLig	MicPep	MicSp1	MorSp1	MorSp2	MorSp3	MorSp5	MorSp6	MorSp7	MorSp8	MorSp9	MyrSp1	MyrSp2	PsidSp	RubSp1	RubSp2	SabBra	SolaSp	TocFor	VisBra
+CerSco	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+CerSub	0	0	0	13	12	0	19	0	0	0	3	0	1	0	0	2	0	0	0	0	0	0	0	72	9	0	0	0	0	0	11	0	0	0
+DidAlb	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0
+DidAur	0	0	0	6	11	0	0	1	3	2	0	0	0	1	50	0	0	0	1	2	0	1	19	0	0	2	2	0	0	0	0	0	0	3
+MonDom	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
+NecLas	0	20	0	0	0	3	0	0	0	0	15	4	2	0	0	0	0	0	0	0	0	0	0	10	58	0	9	18	0	0	0	2	0	0
+OliSp	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+PhiFre	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
+GueIng	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

links1.txt → data/net1links.txt

@@ -1,73 +1,73 @@
-animals	plants	weight	layer
-GueIng	ByrSp	2	antagonistic
-NecLas	CamAda	20	antagonistic
-PhiFre	CecHol	1	antagonistic
-CerSub	CecPac	13	antagonistic
-DidAur	CecPac	6	antagonistic
-PhiFre	CecPac	1	antagonistic
-CerSub	CecGla	12	antagonistic
-DidAur	CecGla	11	antagonistic
-NecLas	ChiAlb	3	antagonistic
-CerSco	CocAur	6	antagonistic
-CerSub	CocAur	19	antagonistic
-DidAur	ErytSp	1	antagonistic
-DidAur	EuphSp	3	antagonistic
-DidAur	FicuSp	2	antagonistic
-CerSub	LeaAur	3	antagonistic
-NecLas	LeaAur	15	antagonistic
-NecLas	LeaCor	4	antagonistic
-CerSub	LeanSp	1	antagonistic
-NecLas	LeanSp	2	antagonistic
-DidAur	MicAlb	1	antagonistic
-DidAur	MicLig	50	antagonistic
-CerSub	MicPep	2	antagonistic
-DidAlb	MicSp1	3	antagonistic
-DidAlb	MorSp1	5	antagonistic
-DidAur	MorSp2	1	antagonistic
-DidAur	MorSp3	2	antagonistic
-PhiFre	MorSp5	1	antagonistic
-DidAur	MorSp6	1	antagonistic
-DidAur	MorSp7	19	antagonistic
-CerSub	MorSp8	72	antagonistic
-NecLas	MorSp8	10	antagonistic
-CerSub	MorSp9	9	antagonistic
-NecLas	MorSp9	58	antagonistic
-DidAur	MyrSp1	2	antagonistic
-DidAur	MyrSp2	2	antagonistic
-NecLas	MyrSp2	9	antagonistic
-MonDom	PsidSp	1	antagonistic
-NecLas	PsidSp	18	antagonistic
-DidAlb	RubSp1	1	antagonistic
-CerSub	SabBra	11	antagonistic
-NecLas	SolaSp	2	antagonistic
-DidAlb	TocFor	1	antagonistic
-DidAur	VisBra	3	antagonistic
-NecLas	CamAda	1	mutualistic
-CerSub	CecPac	9	mutualistic
-DidAur	CecPac	12	mutualistic
-CerSub	CecGla	3	mutualistic
-DidAur	CecGla	4	mutualistic
-NecLas	ChiAlb	1	mutualistic
-CerSco	CocAur	1	mutualistic
-CerSub	CocAur	2	mutualistic
-DidAur	CocAur	1	mutualistic
-DidAur	ErytSp	6	mutualistic
-DidAur	EuphSp	8	mutualistic
-NecLas	LeaAur	12	mutualistic
-NecLas	LeaCor	2	mutualistic
-DidAur	MicLig	5	mutualistic
-CerSub	MicPep	1	mutualistic
-DidAlb	MicSp1	1	mutualistic
-DidAlb	MorSp1	2	mutualistic
-DidAur	MorSp7	36	mutualistic
-OliSp	MorSp7	1	mutualistic
-MonDom	MorSp9	2	mutualistic
-NecLas	MorSp9	62	mutualistic
-DidAur	MyrSp2	7	mutualistic
-NecLas	MyrSp2	1	mutualistic
-CerSub	PsidSp	2	mutualistic
-MonDom	PsidSp	1	mutualistic
-NecLas	PsidSp	24	mutualistic
-DidAlb	RubSp1	3	mutualistic
-PhiFre	RubSp2	1	mutualistic
-NecLas	SolaSp	5	mutualistic
+animals	plants	weight	layer
+GueIng	ByrSp	2	antagonistic
+NecLas	CamAda	20	antagonistic
+PhiFre	CecHol	1	antagonistic
+CerSub	CecPac	13	antagonistic
+DidAur	CecPac	6	antagonistic
+PhiFre	CecPac	1	antagonistic
+CerSub	CecGla	12	antagonistic
+DidAur	CecGla	11	antagonistic
+NecLas	ChiAlb	3	antagonistic
+CerSco	CocAur	6	antagonistic
+CerSub	CocAur	19	antagonistic
+DidAur	ErytSp	1	antagonistic
+DidAur	EuphSp	3	antagonistic
+DidAur	FicuSp	2	antagonistic
+CerSub	LeaAur	3	antagonistic
+NecLas	LeaAur	15	antagonistic
+NecLas	LeaCor	4	antagonistic
+CerSub	LeanSp	1	antagonistic
+NecLas	LeanSp	2	antagonistic
+DidAur	MicAlb	1	antagonistic
+DidAur	MicLig	50	antagonistic
+CerSub	MicPep	2	antagonistic
+DidAlb	MicSp1	3	antagonistic
+DidAlb	MorSp1	5	antagonistic
+DidAur	MorSp2	1	antagonistic
+DidAur	MorSp3	2	antagonistic
+PhiFre	MorSp5	1	antagonistic
+DidAur	MorSp6	1	antagonistic
+DidAur	MorSp7	19	antagonistic
+CerSub	MorSp8	72	antagonistic
+NecLas	MorSp8	10	antagonistic
+CerSub	MorSp9	9	antagonistic
+NecLas	MorSp9	58	antagonistic
+DidAur	MyrSp1	2	antagonistic
+DidAur	MyrSp2	2	antagonistic
+NecLas	MyrSp2	9	antagonistic
+MonDom	PsidSp	1	antagonistic
+NecLas	PsidSp	18	antagonistic
+DidAlb	RubSp1	1	antagonistic
+CerSub	SabBra	11	antagonistic
+NecLas	SolaSp	2	antagonistic
+DidAlb	TocFor	1	antagonistic
+DidAur	VisBra	3	antagonistic
+NecLas	CamAda	1	mutualistic
+CerSub	CecPac	9	mutualistic
+DidAur	CecPac	12	mutualistic
+CerSub	CecGla	3	mutualistic
+DidAur	CecGla	4	mutualistic
+NecLas	ChiAlb	1	mutualistic
+CerSco	CocAur	1	mutualistic
+CerSub	CocAur	2	mutualistic
+DidAur	CocAur	1	mutualistic
+DidAur	ErytSp	6	mutualistic
+DidAur	EuphSp	8	mutualistic
+NecLas	LeaAur	12	mutualistic
+NecLas	LeaCor	2	mutualistic
+DidAur	MicLig	5	mutualistic
+CerSub	MicPep	1	mutualistic
+DidAlb	MicSp1	1	mutualistic
+DidAlb	MorSp1	2	mutualistic
+DidAur	MorSp7	36	mutualistic
+OliSp	MorSp7	1	mutualistic
+MonDom	MorSp9	2	mutualistic
+NecLas	MorSp9	62	mutualistic
+DidAur	MyrSp2	7	mutualistic
+NecLas	MyrSp2	1	mutualistic
+CerSub	PsidSp	2	mutualistic
+MonDom	PsidSp	1	mutualistic
+NecLas	PsidSp	24	mutualistic
+DidAlb	RubSp1	3	mutualistic
+PhiFre	RubSp2	1	mutualistic
+NecLas	SolaSp	5	mutualistic

data/net1mu.txt

@@ -0,0 +1,10 @@
+	ByrSp	CamAda	CecHol	CecPac	CecGla	ChiAlb	CocAur	ErytSp	EuphSp	FicuSp	LeaAur	LeaCor	LeanSp	MicAlb	MicLig	MicPep	MicSp1	MorSp1	MorSp2	MorSp3	MorSp5	MorSp6	MorSp7	MorSp8	MorSp9	MyrSp1	MyrSp2	PsidSp	RubSp1	RubSp2	SabBra	SolaSp	TocFor	VisBra
+CerSco	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+CerSub	0	0	0	9	3	0	2	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0
+DidAlb	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0
+DidAur	0	0	0	12	4	0	1	6	8	0	0	0	0	0	5	0	0	0	0	0	0	0	36	0	0	0	7	0	0	0	0	0	0	0
+MonDom	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	0	0	0
+NecLas	0	1	0	0	0	1	0	0	0	0	12	2	0	0	0	0	0	0	0	0	0	0	0	0	62	0	1	24	0	0	0	5	0	0
+OliSp	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+PhiFre	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
+GueIng	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

data/net1nodes.txt

@@ -0,0 +1,44 @@
+nodes	taxon	captures
+GueIng	Animal	1
+NecLas	Animal	34
+PhiFre	Animal	2
+CerSub	Animal	20
+DidAur	Animal	6
+CerSco	Animal	1
+DidAlb	Animal	2
+MonDom	Animal	9
+ByrSp	Plant	NA
+CamAda	Plant	NA
+CecHol	Plant	NA
+CecPac	Plant	NA
+CecGla	Plant	NA
+ChiAlb	Plant	NA
+CocAur	Plant	NA
+ErytSp	Plant	NA
+EuphSp	Plant	NA
+FicuSp	Plant	NA
+LeaAur	Plant	NA
+LeaCor	Plant	NA
+LeanSp	Plant	NA
+MicAlb	Plant	NA
+MicLig	Plant	NA
+MicPep	Plant	NA
+MicSp1	Plant	NA
+MorSp1	Plant	NA
+MorSp2	Plant	NA
+MorSp3	Plant	NA
+MorSp5	Plant	NA
+MorSp6	Plant	NA
+MorSp7	Plant	NA
+MorSp8	Plant	NA
+MorSp9	Plant	NA
+MyrSp1	Plant	NA
+MyrSp2	Plant	NA
+PsidSp	Plant	NA
+RubSp1	Plant	NA
+SabBra	Plant	NA
+SolaSp	Plant	NA
+TocFor	Plant	NA
+VisBra	Plant	NA
+OliSp	Animal	NA
+RubSp2	Plant	NA