Setting up stage

Installing and configuring Ubuntu distro

• For installation, follow self notes by Steven V Miller. SV Miller is a political science professor at clemson university. He has a regularly updated repertoire of blog posts, including those that instruct student writers. As it could be glened from his self note blog posts, he is an avid user of Linux, R and Latex.

• git (if not already installed, for windows) sudo apt-get install git

• tmux (sudo apt-get install tmux)

• zsh (sudo apt-get install zsh)

  • Configure z-shell with ohmyzsh configuration.

• R (described in @r-environment-setup)

• Rstudio (described in @r-environment-setup)

• Miniconda

• Vim (sudo apt-get install vim)

• Notepad++

• Jupyter with miniconda in base environment

• Python3 distribution site

• pip

• youtube-dl

• Sagemath in miniconda environment

• Configure dotfiles (https://github.com/deependrad/ProgrammingNotes/dotfiles/)

  • clone and paste the dotfiles directory of this repo to home
  • run make.sh file. It backs up existing dotfiles and copies the links for new dotfiles to home directory. Before running the make.sh change the permission to grant it execution rights (chmod +x .make.sh).

• pdfgrep (preferably expenimental)

  • With required dependencies (libpoppler-dev, libunac1-dev, …)

• Install calibre

• Rtools (for windows)

• OpenJDK

R environment setup

• To install R (described in https://cran.r-project.org/bin/linux/ubuntu/README.html):
  • Add secure APT
  • Add (for xenial) entry like the one below to /etc/apt/sources.list. Note the sources.list file is read only, so edit it as root.

deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/

• To install Rstudio:
  • Install gdebi-core sudo apt-get install gdebi-core
  • Download the debian file available at https://rstudio.com/products/rstudio/download/#download
  • sudo gdebi rstudio*.deb
• Pandoc (Rstudio comes readybuilt with it). Installing latest pandoc externally alongside is a good option.
• Tinytex
• R packages (tidyverse, tidymodels, tidyselect, bookdown, blogdown, lme4, janitor, tidytext, gt, ggdag, pdftools, forecast, ape, gganimate, tsibble, binb, xaringan, ggrepel, ggraph, bezier, tint)

TeX distribution

• TeX distribution with tinytex (from Rstudio)
  • For installation, follow instructions at: https://yihui.org/tinytex/
• Install it as normal user from R tinytex::install_tinytex()
• Use scheme-full to download all collection of latex packages (dont worry for download interruption because installation resumes where it was left before interruption)