General

• Complex systems: https://bingweb.binghamton.edu/~sayama/textbook/.

• Network science: https://bingweb.binghamton.edu/~sayama/SSIE641/.

• Optimization: https://algorithmsbook.com/optimization/.

• Statistics: https://stats.oarc.ucla.edu/other/dae/

Network data

• https://networks.skewed.de/

• http://networkdata.schochastics.net/

• http://www.ecologia.ib.usp.br/iwdb/resources.html

• https://snap.stanford.edu/data/index.html

• http://www.sociopatterns.org/

• https://cran.r-project.org/package=igraphdata

R

• Networks: https://igraph.org/r/

• Principle component analysis tools (and more): http://www.sthda.com/english/

• Regression (in addition to base R; see below):

  • Hierarchical models, clustering: nlme, lme4, coxme, sandwich

  • Zero-inflated models: pscl

  • Regression support: lmtest, AER, car, arm

• Audio analysis: tuneR, seewave

• Parallel processing: See this blog post for an introduction.

• Documentation for the core R packages can be found here; this is the documentation for R’s equivalent of a standard library. These packages include the “base” packages (statistics, sample data sets, graphics, language utilities, but also parallel) and the “recommended” packages (e.g., boot, nlme, and survival).

Julia

• Manual: https://docs.julialang.org/en/v1/. Includes discussion on improving performance, multithreading, class/type management, and more.

• Numerical integration and simulations: https://diffeq.sciml.ai/dev/index.html

• Networks: https://juliagraphs.org/Graphs.jl/dev/

• Statistics: https://juliastats.org/

• Data visualization: https://docs.juliaplots.org/stable/

Python

• Networks: https://networkx.org/, https://graph-tool.skewed.de/, https://meh.imtlucca.it/ (statistical models of networks), https://www.raphtory.com/ (temporal networks)

• Numbers, arrays, calculations, vectorizing: https://numpy.org/

• Distributions, more calculations, curve fitting, etc.: https://scipy.org/

• Data manipulation: https://pandas.pydata.org/

• Statistics: https://www.statsmodels.org/stable/index.html

• Data visualization: https://matplotlib.org/

Video and Audio Annotation, Support

• Video annotation (for behavioral coding, etc.): https://archive.mpi.nl/tla/elan

• Audio editing, analysis, etc.: https://www.audacityteam.org/

• File conversion, etc.: https://ffmpeg.org/

Supporting Tasks

• LaTeX

  • Introduction and reference: https://en.wikibooks.org/wiki/LaTeX

  • For help with symbols: http://detexify.kirelabs.org/classify.html

  • For collaboration, use latexdiff for tracking changes (command line use: latexdiff originalfile.tex updatedfile.tex > diff.tex)

• PDFs

  • Viewers: Okular, Evince, MuPDF

  • Manipulator: pdftk

• Emacs

  • Wiki: https://www.emacswiki.org/emacs/SiteMap

  • Org Mode (notes, task scheduler/tracker, etc.): https://orgmode.org/

  • ESS (IDE for R and Julia): https://ess.r-project.org/

  • Magit (git porcelain): https://magit.vc/

  • MELPA (package manager): https://melpa.org/#/

• Visualization

  • Inkscape (SVG editor): https://inkscape.org/

  • Qualitative color palettes: R, Tableau, Okabe-Ito, and GNOME HIG

• Version control: git and git lfs (large files, such as data, in a git repository)