Major update

Several changes, shorter and faster code, new figures.

Author: marmello77

.gitignore

@@ -1,3 +1,5 @@
 
 .Rhistory
 .DS_Store
+README.html
+README.html

README.html

@@ -1,27 +1,94 @@
-# How to draw networks in R
+# network-drawing
+
+Script with different ways to draw monolayer and multilayer networks in R.
 
 [Ecological Synthesis Lab](https://marcomellolab.wordpress.com) (SintECO).
 
-Author: Marco Mello & Renata Muylaert.
+Authors: Marco Mello & Renata Muylaert.
 
 E-mail: [email protected].
 
-How to cite: Mello MAR. 2017. How to draw networks in R. Ecological Synthesis Lab of the University of São Paulo, Brazil.
-
-Published first on April 25th, 2017 (English version).
-
-Updated on September 18th, 2020 (English version).
+First published on April 25th, 2017 (English version).
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4036687.svg)](https://doi.org/10.5281/zenodo.4036687)
 
 Run in R version 4.0.2 (2020-06-22) -- "Taking Off Again".
 
-Disclaimer: You may use this script freely for any purpose 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 script 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.
+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 this repo's DOI or URL.
+
+
+## List of folders and files
+
+1. data (folder)
+
+    a. net1.txt -> interactions of pollination between oil-collecting bees and oil flowers (Bezerra et al. 2009).
+
+    b. net2.txt -> interactions of pollination between bats, hawkmoths, and plants (Queioz et al. 2020).
+
+    c. net3an.txt -> interactions of seed destruction (antagonism) between maruspials, rodents, and plants (Genrich et al. 2017).
+    
+    d. net3mu.txt -> interactions of seed dispersal (mutualism) between maruspials, rodents, and plants (Genrich et al. 2017).
+    
+    
+2. figures (folder)
+
+    a. net1_bipartite_graph.png -> monolayer network drawn as a bipartite graph.
+
+    b. net1_bipartite_matrix.png -> monolayer network drawn as an incidence matrix.
+    
+    c. net1_igraph_graph_multi.png -> multilayer network drawn as an energy-minimization graph, with node colors by taxonomic group.
+
+    d. net1_igraph_graph_taxon.png -> monolayer network drawn as an energy-minimization graph, with node colors by taxonomic group.
+
+    e. net1_igraph_graph.png -> monolayer network drawn as an energy-minimization graph.
+    
+    
+3. network-drawing.pdf -> tutorial in PDF format.
+
+4. network-drawing.R -> script with commented codes.
+
+5. network-drawing.Rmd -> tutorial in RMD format.
+
+
+## Data sources
+
+1. net1 -> Bezerra, E. L. S., Machado, I. C., & Mello, M. A. R. (2009). [Pollination networks of oil-flowers: a tiny world within the smallest of all worlds](https://doi.org/10.1111/j.1365-2656.2009.01567.x). Journal of Animal Ecology, 78(5), 1096–1101. 
+
+2. net2 -> Queiroz, J. A., Diniz, U. M., Vázquez, D. P., Quirino, Z. M., Santos, F. A. R., Mello, M. A. R., & Machado, I. C. (2020). Bats and hawkmoths form mixed modules with flowering plants in a nocturnal interaction network. Biotropica, *accepted*. See also this [repo](https://github.com/marmello77/queiroz-et-al-2020).
+
+3. net3an and net3mu -> 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
+
 
 ## Instructions
 
-If you are familiar with R, just run the scripts provided in the R file.
+If you are familiar with R, just run the scripts provided in "network-drawing.R".
+
+If you are not so familiar with R, follow the steps described in the RMD tutorial.
+
+If you just to take a look at the networks and their drawing solutions, read the PDF tutorial.
+
+
+## Feedback
+
+If you have any questions, corrections, or suggestions, please feel free to open and [issue](https://github.com/marmello77/network-drawing/issues) or make a [pull request](https://github.com/marmello77/network-drawing/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. 
+
+
+## Suggested readings
+
+* Ognyanova K. 2019. [Static and dynamic network visualization with R](http://kateto.net/network-visualization).
+
+* Pocock, M. J. O., D. M. Evans, C. Fontaine, M. Harvey, R. Julliard, Ó. McLaughlin, J. Silvertown, A. Tamaddoni-Nezhad, P. C. L. White, and D. A. Bohan. (2016) [The Visualisation of Ecological Networks, and Their Use as a Tool for Engagement, Advocacy and Management](http://linkinghub.elsevier.com/retrieve/pii/S0065250415000355). In G. Woodward and D. A. Bohan (Eds.) Advances in Ecological Research. pp. 41–85, Academic Press, Cambridge.
+
+* Marai, G. E., B. Pinaud, K. Bühler, A. Lex, and J. H. Morris. (2019) [Ten simple rules to create biological network figures for communication](https://doi.org/10.1371/journal.pcbi.1007244). PLOS Comput. Biol. 15: e1007244.
+
+* 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.
+
+* Barabasi, A.L. (2016) [Network Science](http://barabasi.com/networksciencebook/), 1st ed. Cambridge University Press, Cambridge.
 
-If you are not so familiar with R, follow the steps described in the RMD file.
+* Bascompte, J. & Jordano, P. (2014) [Mutualistic Networks](https://amzn.to/2FLwhto), 1st ed. Princeton University Press, Princeton.
 
-If you have any questions, corrections, or suggestions, please feel free to open and *issue* or make a *pull request*.

README.md

@@ -0,0 +1,14 @@
+	Cenaen	Cenfus	Cencax	Centar	Cenfla	Centri	Cenobs	Episp2	Apimel	Censp3	Censp1	Xylsp	Xylgri
+Dippub	1368	1364	740	460	416	256	0	328	364	368	0	0	0
+Byrgar	924	320	2108	464	284	0	0	0	28	0	0	0	0
+Banmur	396	468	108	140	272	652	912	364	44	0	368	164	84
+Hetsp1	764	680	528	308	404	300	0	28	0	0	0	76	0
+Hetsp2	740	656	528	332	0	324	0	116	116	0	0	0	0
+Dicbra	556	512	356	132	524	0	0	0	0	0	0	0	0
+Carcha	604	452	432	200	0	0	0	0	0	0	0	0	0
+Stipar	504	816	0	0	0	0	0	0	0	0	0	0	0
+Banste	292	300	244	116	0	0	0	0	0	0	0	0	0
+Bansch	228	224	124	120	0	0	0	0	0	0	0	0	0
+Stiaur	240	164	68	0	196	0	0	0	0	0	0	0	0
+Sticil	268	196	0	0	164	0	0	0	0	0	0	0	0
+Janani	188	244	0	96	0	0	0	0	0	0	0	0	0

data/net1.txt

@@ -0,0 +1,20 @@
+	Pilgou	Encspe	Gueang	Bauche	Helbar	Pilchr	Psemar	Ambcea	Asppyr	Ipomar	Lirsp	Crosp	Ceigla	Tocfor	Cerjam	Comsp	Pipsti	Ind1	Allsp	Anacol	Caesp	Schbra	Alisp	Ind2
+Glosor	23	22	0	10	34	27	24	0	0	8	24	4	4	0	0	0	2	0	0	0	0	0	0	0
+Lonmor	14	10	0	9	16	23	14	0	0	18	2	0	4	0	0	1	1	1	0	0	0	0	0	0
+Phydis	0	8	0	5	0	0	9	0	0	0	6	0	5	0	0	0	0	0	0	0	0	0	0	0
+Artpla	3	0	0	0	0	2	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
+Calgri	13	0	26	3	0	0	0	8	13	2	0	11	0	0	0	6	4	1	3	1	0	2	0	1
+Eriell	20	9	28	18	5	0	0	3	15	0	0	11	1	3	0	0	1	0	0	0	2	0	1	0
+Eriswa	9	6	4	6	1	0	0	13	0	0	0	0	0	1	3	0	0	0	0	0	0	0	0	0
+Agrcin	7	0	0	2	3	0	0	0	0	4	2	0	0	2	5	0	0	2	0	0	0	0	0	0
+Eumvit	8	0	3	6	0	0	0	0	0	0	0	1	0	4	0	2	0	1	0	0	0	0	0	0
+Eumana	2	0	1	0	1	0	0	0	0	0	0	3	0	1	3	0	0	0	0	1	0	0	0	0
+Manrus	6	0	1	2	0	0	0	0	0	1	0	0	0	3	4	0	0	0	0	0	0	0	0	0
+Mansex	2	0	0	1	0	0	0	0	0	0	0	0	0	4	3	0	0	0	0	0	0	0	0	0
+Xylter	5	7	0	0	0	0	0	8	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0
+Prostr	6	8	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0
+Eriobs	2	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0
+Aelsp	0	0	5	0	0	0	0	15	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Cocant	2	0	0	1	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Calpar	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
+Psetet	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

data/net2.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

data/net3an.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