From d53d43e2a519bed35bdc952a0c7262f0713236a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Franc=CC=A7ois?= Date: Tue, 12 Apr 2016 01:55:41 +0200 Subject: [PATCH] last additions for today --- README.md | 64 ++++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 54 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 75ff146..db4baea 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,9 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const - __[Professional groups](#professional-groups)__ - __[Review Articles](#review-articles)__ - __[Software](#software)__ + - __[C/C++](#c) - __[JavaScript](#javascript)__ + - __[MATLAB](#matlab)__ - __[Python](#python)__ - __[R](#r)__ - __[Tutorials](#tutorials)__ @@ -40,6 +42,7 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const ### Graph Theory 1. _[Graph Theory](http://www.cs.unibo.it/babaoglu/courses/cas00-01/tutorials/GraphTheory.pdf)_, by Reinhard Diestel - Full electronic version online (2000). +- [Graph Theory and Applications](http://www.hamilton.ie/ollie/Downloads/Graph.pdf), by Paul Van Dooren - Full lecture slides (Hamilton Institute, Dublin, 2009). ### Method-specific @@ -70,13 +73,17 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const ## Courses 1. [Complex Networks](https://www.uvm.edu/~pdodds/teaching/courses/2016-01UVM-303/), by Peter Sheridan Dodds (University of Vermont, 2016). -- [Graph Theory: Penn State Math 485 Lecture Notes](http://www.personal.psu.edu/cxg286/Math485.pdf), by Christopher Griffin - Full lecture notes online (2012). +- [Graph Theory: Penn State Math 485 Lecture Notes](http://www.personal.psu.edu/cxg286/Math485.pdf), by Christopher Griffin - Full lecture notes online (Penn State University, 2012). +- [Networks, Complexity and Its Applications](http://ocw.mit.edu/courses/media-arts-and-sciences/mas-961-networks-complexity-and-its-applications-spring-2011/), by Cesar Hidalgo (MIT, 2011). - [Networks (Economics)](http://ocw.mit.edu/courses/economics/14-15j-networks-fall-2009/), by Daron Acemoglu and Asu Ozdaglar (MIT, 2009). +- [Political Networks: Methods and Applications](http://vanity.dss.ucdavis.edu/~maoz/networks/Spring%202011/pol279-11.htm), by Zeev Maoz (University of California in Davis, 2012). - [Social and Economic Networks: Models and Analysis](https://www.coursera.org/course/networksonline), by Matthew O. Jackson (Stanford University via Coursera, 2015). - [Social Network Analysis](https://www.coursera.org/course/sna), by Lada Adamic (University of Michigan via Coursera, not yet run). ## Datasets +> See also [Mangal](http://mangal.io/), an online platform and collection of tools to analyze, archive and share ecological network data ([preprint](http://biorxiv.org/content/early/2015/02/24/002634), [Python package](https://github.com/mangal-wg/pymangal), [R package](https://github.com/mangal-wg/rmangal)). + 1. [Bill Cosponsorship Networks in European Parliaments](https://github.com/briatte/parlnet). - [Gephi Datasets](https://github.com/gephi/gephi/wiki/Datasets). - [igraphdata](https://cran.r-project.org/web/packages/igraphdata/index.html) - Data sets intended for use with the igraph R package. @@ -118,28 +125,42 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const ## Review Articles -1. "[Network Analysis and Political Science](http://www.annualreviews.org/doi/abs/10.1146/annurev.polisci.12.040907.115949)" (_Annual Review of Political Science_, 2011). +1. "[Graph Theory and Networks in Biology](http://dx.doi.org/10.1049/iet-syb:20060038)" ([preprint](http://arxiv.org/abs/q-bio/0604006); _IET Systems Biology_, 2007). +- "[Network Analysis and Political Science](http://www.annualreviews.org/doi/abs/10.1146/annurev.polisci.12.040907.115949)" (_Annual Review of Political Science_, 2011). - "[Statistical Models for Social Networks](http://www.annualreviews.org/doi/abs/10.1146/annurev.soc.012809.102709)" (_Annual Review of Sociology_, 2011). ## Software -1. [Cytoscape](http://www.cytoscape.org/) - Cross-platform Java program to build, analyze and visualize networks. +> Several links in this section come from the [NetWiki Shared Code](http://netwiki.amath.unc.edu/SharedCode/SharedCode) page. +> See also the [Social Network Analysis Project Survey](https://docs.google.com/spreadsheets/d/1Xo-ehJatzmxMek6gPG0h-d7yRSuiO6_flViTQNMAku0/edit#gid=0), an earlier attempt to chart social network analysis tools, which links to many commercial platforms not included in this list, such as [Detective.io](http://www.detective.io/) ([related blog post](http://pudo.org/blog/2013/12/21/sna-survey.html)). + +1. [CONGA and CONGO](http://www.cs.bris.ac.uk/~steve/networks/index.html) - Algorithms to detect overlapping communities in networks, written in Java. +- [Cytoscape](http://www.cytoscape.org/) - Cross-platform Java program to build, analyze and visualize networks. - [Discourse Network Analyzer (DNA)](http://www.philipleifeld.com/discourse-network-analyzer/discourse-network-analyzer-dna.html) - Qualitative content analysis tool with network export facilities, written in Java with R integration. -- [igraph](http://igraph.org/) - C library of network analysis tools; also exists as packages for Python and R. - [Gephi](https://gephi.github.io/) - Cross-platform, free and open source tool for network visualization. - [Graphviz](http://www.graphviz.org/) - Cross-platform software to draw graphs in the [DOT](http://www.graphviz.org/doc/info/lang.html) language. - [MuxViz](http://muxviz.net/) - Cross-platform, free and open source multilayer network analysis And visualization platform, based on R and GNU Octave. - [Neo4j](http://neo4j.com/) - Open source, scalable graph database, used by companies like [Linkurious](http://linkurio.us/). -- [networks.tb](http://networks-tb.sourceforge.net/) - C program designed for analyzing socio-semantic networks; runs on Linux and Mac OS X. - [NodeXL](http://nodexl.codeplex.com/) - Free, open-source template to explore network graphs with Microsoft Excel. - [ORA-LITE](http://www.casos.cs.cmu.edu/projects/ora/) - Windows program for dynamic meta-network assessment and analysis. - [Pajek](http://vlado.fmf.uni-lj.si/pub/networks/pajek/) - Windows program for large network analysis, free for noncommercial use. - [PNet](http://www.swinburne.edu.au/fbl/research/transformative-innovation/our-research/MelNet-social-network-group/PNet-software/index.html) - Simulation and estimation of exponential random graph models (ERGMs), written in Java for Windows. -- [Siena](http://www.stats.ox.ac.uk/~snijders/siena/) - Simulation Investigation for Empirical Network Analysis, formerly a Windows program, now an R package. -- [Stanford Network Analysis Project](http://snap.stanford.edu/) - C++ general purpose network analysis and graph mining library; available as a Python library and through NodeXL. +- [Siena](http://www.stats.ox.ac.uk/~snijders/siena/) - Simulation Investigation for Empirical Network Analysis. Formerly a Windows program, now developed as the RSiena R package. +- [SoNIA](http://web.stanford.edu/group/sonia/) (Social Network Image Animator) - Tool to visualize dynamic or longitudinal network data. Formerly a [Java program](https://sourceforge.net/projects/sonia/), now developed as the ndtv R package. - [UCINET](https://sites.google.com/site/ucinetsoftware/) - Windows commercial software package for the analysis of social network data. +- [vbmod: Variational Bayesian Inference for Network Modularity](http://vbmod.sourceforge.net/) - MATLAB and Python implementations of the [Bayesian community detection algorithm](http://arxiv.org/abs/0709.3512). - [Visone](http://visone.info/) - Cross-platform Java network analysis and visualization program, free for noncommercial use. - [VOSviewer](http://www.vosviewer.com/) - Cross-platform Java tool for constructing and visualizing bibliometric networks. +- [weighted-modularity-LPAwbPLUS](https://github.com/sjbeckett/weighted-modularity-LPAwbPLUS) - Julia, MATLAB and R implementations of two algorithms to find weighted modularity in bipartite networks. + +### C / C++ + +1. [Boost Graph Library (BGL)](http://www.boost.org/doc/libs/1_60_0/libs/graph/doc/) - C++ library that provides a generic interface to access graph structures. +- [igraph](http://igraph.org/) - C library of network analysis tools; also exists as packages for Python and R. +- [Louvain Method](https://sites.google.com/site/findcommunities/) - C++ code for the [Louvain multi-level community detection algorithm](http://arxiv.org/abs/0803.0476). +- [networks.tb](http://networks-tb.sourceforge.net/) - C program designed for analyzing socio-semantic networks. Runs on Linux and Mac OS X. +- [Stanford Network Analysis Project](http://snap.stanford.edu/) - C++ general purpose network analysis and graph mining library; available as a Python library and through NodeXL. +- [Walktrap](https://www-complexnetworks.lip6.fr/~latapy/PP/walktrap.html) - C++ program that implements the [WalkTrap community detection algorithm](Computing communities in large networks using random walks (long version). ### JavaScript @@ -150,6 +171,12 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const - [Sigma](http://sigmajs.org/) - JavaScript library dedicated to graph drawing. - [vis.js](http://visjs.org/) - JavaScript library with network visualization capabilities. +### MATLAB + +1. [CONTEST](http://www.maths.strath.ac.uk/research/groups/numerical_analysis/contest) - Random network toolbox that implements nine network models. +- [Generalized Louvain](http://netwiki.amath.unc.edu/GenLouvain/GenLouvain) - A variant of the Louvain community detection algorithm. +- [MatlabBGL](http://dgleich.github.io/matlab-bgl/) - A graph library for Matlab, based on the Boost graph library. + ### Python > Most items below are from [a Google spreadsheet](https://docs.google.com/spreadsheets/d/1vJILk2EW1JnR3YAwTSSqAV5mPkeXaezy45wOoafBpfU/edit#gid=0) by Michał Bojanowski and others. @@ -169,6 +196,7 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const 1. [Bergm](https://cran.r-project.org/web/packages/Bergm/) - Tools to analyse Bayesian exponential random graph models (BERGM). - [CCAS](https://github.com/matthewjdenny/CCAS) - A statistical model for communication networks. - [concoR](https://github.com/aslez/concoR) - A translation of the CONCOR network blockmodeling algorithm ([blog post](http://badhessian.org/2015/05/concor-in-r/)). +- [ContentStructure](https://github.com/matthewjdenny/ContentStructure) - implements an extension to the [Topic-Partitioned Multinetwork Embeddings (TPME) model](http://dirichlet.net/pdf/krafft12topic-partitioned.pdf). - [ergm](https://cran.r-project.org/web/packages/ergm/) - Estimation of Exponential Random Graph Models (ERGM). - [GERGM](https://cran.r-project.org/web/packages/GERGM/) - Estimation and diagnosis of the convergence of Generalized Exponential Random Graph Models (GERGM). - [geomnet](https://cran.r-project.org/web/packages/geomnet/) - A single-geometry approach to network visualization with ggplot2. @@ -184,10 +212,11 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const - [networkDynamic](https://cran.r-project.org/web/packages/networkDynamic/) - Support for dynamic, (inter)temporal networks. - [rgexf](https://bitbucket.org/gvegayon/rgexf/wiki/Home) - Export network objects from R to [GEXF](http://gexf.net/format/), for manipulation with network software like Gephi or Sigma. - [Rgraphviz](https://bioconductor.org/packages/release/bioc/html/Rgraphviz.html) - Support for using the Graphviz library and its [DOT](http://www.graphviz.org/doc/info/lang.html) language from within R. -- [RSiena](https://cran.r-project.org/web/packages/RSiena/) - Simulation Investigation for Empirical Network Analysis; fits models to longitudinal network data. +- [RSiena](http://r-forge.r-project.org/R/?group_id=461) - Simulation Investigation for Empirical Network Analysis; fits models to longitudinal network data. - [sna](https://cran.r-project.org/web/packages/sna/) - Basic network measures and visualization tools. +- [spectralGOF](http://people.bu.edu/jccs/spectralGOF.html) - Compute the "spectral goodness of fit" (SGOF), a measure of how well a network model explains the structure of an observed network. - [spnet](http://cran.r-project.org/web/packages/spnet/) - Methods for dealing with spatial social networks. -- [statnet](http://statnet.org/) - The project behind many R network analysis packages. +- [statnet](http://statnet.org/) - The project behind many R network analysis packages ([mailing-list](https://mailman.u.washington.edu/mailman/listinfo/statnet_help)). - [tergm](https://cran.r-project.org/web/packages/tergm/) - Fit, simulate and diagnose models for temporal exponential-family random graph models (TERGM). - [tnet](https://cran.r-project.org/web/packages/tnet/) - Network measures for weighted, two-mode and longitudinal networks. - [tsna](https://cran.r-project.org/web/packages/tsna/) - Tools for temporal social network analysis. @@ -211,12 +240,27 @@ An [awesome list](https://github.com/sindresorhus/awesome) of resources to const ## Varia -1. [Blog Posts About Networks by Baptiste Coulmont](http://coulmont.com/index.php?s=r%C3%A9seaux), in French. +1. [A Sociology Citation Network](http://nealcaren.web.unc.edu/a-sociology-citation-network/) and [A Co-citation Network for Philosophy](https://kieranhealy.org/blog/archives/2013/06/18/a-co-citation-network-for-philosophy/) - Examples of scientific co-citation networks. +- [Basic Notions for the Analysis of Large Two-mode Networks](https://www-complexnetworks.lip6.fr/~latapy/Publis/socnet07.pdf) - Efficient introduction to bipartites network analysis ([related code](https://www-complexnetworks.lip6.fr/~latapy/Bip/)). +- [Blog Posts About Networks on the Bad Hessian Blog](http://badhessian.org/category/networks/), by various contributors. +- [Blog Posts About Networks by Baptiste Coulmont](http://coulmont.com/index.php?s=r%C3%A9seaux), in French. - [Blog Posts About Networks by Pierre Mercklé](http://pierremerckle.fr/category/reseaux/), in French. - [Center for Network Science](http://cns.ceu.edu/) - A research center with a PhD in Network Science program at the Central European University in Budapest. +- [David Knoke on Network Analysis](https://thesocietypages.org/methods/2015/01/30/david-knoke-on-network-analysis/) - A 20-minute interview that discusses the uses and benefits of network analysis, drawing upon Knoke's research on terrorist networks. +- [How Small is the World, Really?](https://medium.com/@duncanjwatts/how-small-is-the-world-really-736fa21808ba#.kyr90lhyo) - A discussion of the "x degrees of separation" experiments (both [Milgram's original one](https://en.wikipedia.org/wiki/Small-world_experiment) and the [recent one](https://research.facebook.com/blog/three-and-a-half-degrees-of-separation/) by Facebook). +- [How to Draw Graphs in LaTeX?](https://tex.stackexchange.com/questions/57152/how-to-draw-graphs-in-latex) - A simple illustration of how to use [PGF/TikZ](https://en.wikipedia.org/wiki/PGF/TikZ) to draw graphs in the [LaTeX](https://latex-project.org/) typesetting environment. - [Interdependence in Governance and Policy](https://sites.psu.edu/desmaraisgroup/) - Network-oriented research group led by Bruce Desmarais at Penn State University. +- [Large Graphs and Networks](http://sites.uclouvain.be/networks/) - Research group at the Catholic University of Louvain. +- [Lessons on Exponential Random Graph Modeling from _Grey’s Anatomy_ hook-ups](http://badhessian.org/2012/09/lessons-on-exponential-random-graph-modeling-from-greys-anatomy-hook-ups/) - A step-by-step explanation of how exponential-family random graph models work. +- [NetWiki](http://netwiki.amath.unc.edu/Main/HomePage) - Wiki of various network analysis resources. +- [Networks Demystified](http://scottbot.net/tag/networks-demystified/), a series of blog posts by Scott B. Weingart. - [Network Fact](https://twitter.com/networkfact) - Twitter account about networks, graph theory, and related topics. +- [Patterns in the Ivy: The Small World of Metal](http://badhessian.org/2013/09/patterns-in-the-ivy-the-small-world-of-metal/) - An example of a two-mode network analysis based on metal artists and bands. +- [The Performativity of Networks](http://kieranhealy.org/files/papers/performativity.pdf) - A paper that connects network theory to the sociology of science. +- [Peter J. Mucha's Research Group at the University of North Carolina at Chapel Hill](http://mucha.web.unc.edu/networks/) - As it says on the box. +- [Social Network Analysis Group @ Stanford](http://sna.stanford.edu/) - As it says on the box. - [Social Network Analysis Software](https://en.wikipedia.org/wiki/Social_network_analysis_software) - Wikipedia English entry with links to many commercial and often outdated software. +- [Star Wars Social Networks: The Force Awakens](http://evelinag.com/blog/2016/01-25-social-network-force-awakens/index.html) - An example of a social network analysis written in F#. - [Videos from the Political Networks 2009 Conference](https://vimeo.com/user2690333). * * *