~/code/

Main application software

On Mac OSX, you first need to install XCode Command Line Tools: xcode-select --install.

You then want to install homebrew:

/usr/bin/ruby -e \
"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Homebrew then allows you to install R, R Studio, Julia, Python, PostgreSQL that we’ll use during the class:

  • R. Install using homebrew: brew install r.
  • R Studio. Install using homebrew: brew cask install rstudio.
  • Julia. Install using homebrew: brew cask install julia.
  • Python. Install using homebrew: brew install python. Install the package manager for python: sudo easy_install pip. Verify which version has been installed: python --version.
  • Anaconda. Install using homebrew: brew cask install anaconda
  • PostgreSQL. Install using homebrew: brew install postgresql.

Writing Papers

The following application software are recommended:

Communicating

  • Dropbox: to collaborate on projects. Very important to save your files as well. (coffee spills, etc.)
  • Skype: coauthor with anyone in the world.
  • Google Drive: cheaper online disk space than Dropbox, but also less reliable.

Other Useful applications

On Mac OSX, the following application software may prove useful:

  • Graphsketcher: Vector Graphing. brew cask install graphsketcher.

  • Tabula: extract tables from PDFs.

  • pdfsandwich: Optical Character Recognition (OCR) images to text. On Mac, use homebrew: brew install pdfsandwich.

  • Mathpix Snipping Tool: Take a screenshot of math and paste the LaTeX into your editor.

  • ffmpeg: convert images. brew install ffmpeg.

  • filezilla: FTP Client.

  • VLC Media Player: Better Video Player.

  • csvkit: convert from .xlsx to .csv. sudo pip install csvkit.

  • xlsx2csv: convert from .xlsx to .csv. pip install xlsx2csv.

  • imagemagick. brew install imagemagick. Exemple to convert pdf to png: convert -density 150 input.pdf -quality 90 output.png.

  • sshpass: pass password file or cleartext to ssh.

    brew install \
https://raw.githubusercontent.com/kadwanev/bigboybrew/master/Library/Formula/sshpass.rb

    Use at your own peril!