Uses

dated fairly regularly. As of December 15, 2017 this is what I’m using:

Writing

I permanently ditched Word as a writing environment in 2008 after starting grad school. I do all my writing in pandoc-flavored Markdown (including e-mails and paper-and-pencil writing)—it’s incredibly intuitive, imminently readable, flexible, future proof, and lets me ignore formatting and focus on content.
I live in Ulysses. At first I chafed at the fact that it stores everything in its own internal folder structure, since I store most of my writing in git repositories, but exporting a compiled Markdown file from a bunch of Ulysses sheets is trivial (and still easily trackable in version control).
Ulysses has decent HTML previewing powers, but when I need more editorial tools, I use Marked.
I use iA Writer to edit standalone Markdown files, since Ulysses uses its own syntax when using fancy things like footnotes.
The key to my writing workflow is the magical pandoc, which converts Markdown files into basically anything else. I use my own variation of Kieran Healy’s Plain Text Social Science workflow to convert Markdown to HTML, PDF (through LaTeX), and Word (through LibreOffice).
I store all my bibliographic references, books, and articles in a BibTeX file that I edit with BibDesk.
I read and annotate all my PDFs with Skim (and iAnnotate on iOS), since both export annotations as clean plain text.
I store all my notes in Evernote (after temporarily ditching them for OneNote because of their new prices and policies, and despite their ongoing privacy controversies).

I post almost everything I write or develop on GitHub.
I use R and RStudio for most of my statistical computing, and I’m a dedicated devotee of the tidyverse (especially ggplot2 and dplyr). I sometimes use knitr and RMarkdown, but I generally just export figures and tables from R and reference them in my writing rather than making full-blown literate documents.
I also use Python (3!) pretty regularly, especially for natural language processing (with nltk) and web scraping (with Requests + BeautifulSoup). Every few months I play with pandas and numpy and Jupyter, but I’m far more comfortable with R for scientific computing.
I use RStudio for editing R files, but I use Sublime Text 3 for everything else.

I run my main web server on a Host1Plus droplet, and I spin up temporary droplets all the time to offload scraping scripts, complicated R models, and to create on-the-fly VPNs.
I normally access my remote files through SSH in a terminal, but for more complicated things, I’ve found that Mountain Duck is indispensable.
My website uses Pelican.
I use Let’s Encrypt for SSL.

Though I regularly use LaTeX (through pandoc), I adore InDesign CC and use it to make fancier academic and policy documents. I also used it for all the typesetting I did for BYU’s Neal A. Maxwell Institute.
I use Illustrator CC all the time to enhance graphics I make in R and to make non-data-driven figures and diagrams.
I use Lightroom and Photoshop too, but less often nowadays.
Despite my dislike for Word and Excel, I use PowerPoint for all my presentations. It’s not my favorite, but in the apocryphal words of Churchill, “PowerPoint is the worst form of slide editor, except for all the others.”

My secret for avoiding the siren call of the internet is Freedom. I have two blocklists: (1) antisocial, which blocks Facebook and Twitter, and (2) nuclear, which blocks everything. I have the antisocial blocklist enabled on my laptop and phone from 8:00 AM–6:00 PM and 8:30 PM–11:30 PM. Since I accidentally discovered that it’s relatively easy to circumvent the blocking on the Mac, I also use Focus with the same schedule.
I use Vitamin-R as a souped-up Pomodoro timer.
I was an early convert to Todo.txt and used it for years until my tasks and projects got too unwieldy. I switched to Taskpaper for a while before recently settling on 2Do (due to incredibly positive reviews), and I’m in love.
Fantastical 2‘s natural language input is a glorious thing.
I keep a log of what I work on (and occasionally do more traditional diary-like entries) with Day One 2 on both iOS and macOS.
I use TextExpander to replace and expand a ton of snippets, and I use Keyboard Maestro to run dozens of little scripts that help control my computer with the keyboard.
I use Übersicht to show weather, iTunes track information, and my todo lists on my desktop.
I use Dropbox religiously and use Crashplan to back up all the computers in our house to the cloud.
With all these little helper apps, I use Bartender to keep my menubar clean.

I use a Dell Optiplex and Precison for all my gateway, servers and security needs.
I use Dell Optiplex and Precison for all my gateway, servers and security needs.
I use Dell Optiplex and Precison for all my gateway, servers and security needs.
I use 2016 13″ MacBook Pro, iPad Mini 2, and iPhone 6s.
I use Raspberry Pi for my Kerberos/LDAP ticketing and multiple window-session-login needs across all devices above (except for iPhone).