Ramblings and Resources

I’ll start with R. My personal philosophy is that R can do anything, and I’ve yet to be proven wrong. I want to share the wonders of R, but I should start by saying there are thousands of amazing resources online for R, coding, data analysis, GitHub, etc., some of which I’ll link below. What I share here is definitely repeated. So maybe this is more a resource for myself than anyone else. But much of what I have learned came from others’ personal websites, blogs, and answers on stack exchange. So maybe someone out there googling random things on the interweb will find these resources.. I can only hope.

Please contact me if you have questions or want help!

My Git Workflow

I use GitHub Desktop for my workflow. But you can also use the command line or RStudio to do everything I’m doing below. I’ll share how I use GitHub Desktop, and maybe later I’ll share some other workflows, so stay tuned! This workflow was adapted from Eli Holmes’ Practical R Workflow for Scientists Course, which you can follow along with online. It’s a GREAT resource for begining your GitHub and RStudio journey!

Create a repository

  1. Go to GitHub and create a new repository (the + in the top right)
  2. Check:
  • add Readme.md
  • add .gitignore (type R to get the R .gitignore)

Clone your repository

  1. Copy the url of your new repo
  2. Open GitHub Desktop
  3. Click File > Clone Repository…
  4. In the popup window, click the URL tab to the right and paste in the URL of your repository
  5. Double check that you have the right folder for the Local Path. I keep all my repositories in Documents/GitHub so they are easier to find.
  6. Click Clone.
  7. Open RStudio and click New Project (upper right, blue cube with R)
  8. Click New Project… > Existing Directory
  9. Navigate to the folder you just cloned from above and click Create Project

Make changes, commit, and push

  1. Make changes to your code or add a file (this can also be done by simply adding a file to that folder, doesn’t have to be done in RStudio)
  2. Switch to GitHub Desktop
  3. Click the changes that you want to commit (check the little checkbox next to the file). Add a comment to the first line and click Commit.
  4. Click the green up arrow to Push to GitHub.
  5. Go back to your GitHub repo online, your changes are now there!

How I built this website

R and GitHub did this, not me! Here’s a step-by-step of how I built this website, so that even someone with little to no experience with R or GitHub can do it too - because not all scientists use these platforms, but I think all scientists should have a personal website that they don’t have to wrestle with wordpress, wix, squarespace, etc. to build (believe me, I’ve been there). I first learned of this in Ben Best’s R3 Workshop. All the workshop materials and recordings are online, so check it out if you want more RStudio learnings.

picture step-by-step coming soon

Create a repo

Like I showed above, create a new repo in GitHub.

Clone the repo to your computers directory

Use your workflow of choice to clone the repo from GitHub to your computers directory. If you’ve never used GitHub before, and you created it to make this website (go you!), the easiest way is to do this all in RStudio,

  1. Copy the URL of your new repo
  2. Open an RStudio window
  3. Go to File > New Project… > Version Control > GIT > Clone
  4. Paste the URL and set the directory to where you want this project to land on your computer

Create a home page and a _site.yml

Your RStudio project is now open! Congrats! In the top right corner you should see the R cube with the name of your repo next to it. In the bottom right window you should see, in the ‘Files’ tab, you are in the project directory. Now,

  1. Go to File > New File > R Markdown…
  2. Give this a name, not super important, and click ‘OK’
  3. There will be a bunch of text in this file. Delete it all and put a header with your webpage name, here’s what mine looks like:
---
title: "Haley Oleynik (she/her)"
---

  1. Type all your info below this, here’s what my whole index file looks like for reference. Here’s a great short-and-sweet guide on R Markdown, if you’ve never done it. It’s seriously very easy, it just takes a little while to remember all the formatting tricks.

  2. Add more pages! Save another page, maybe research.Rmd:

---
title: "Research"
---

Research description, publications, etc.

Now we’ll make a _site.yml page. RStudio needs this to build the website.

  1. Create a new text file by File > New File > Text File and paste the following:
name: "Haley Oleynik"
navbar:
  title: "Haley Oleynik"
  left:
    - text: "Home"
      href: index.html
    - text: "Research"
      href: research.Rmd
output_dir: "."
  1. Save the file as _site.yml

Render your webpage

  1. Now, to build the website all you’ll need to do is run rmarkdown::render_site() in your R console.

  2. To see how it looks, knit your index.Rmd or Research.Rmd. You’ll be able to view the whole site locally, in your viewer pane (or in a pop up window).

  3. Now commit and push the changes you’ve made to the files.

Activate GitHub Pages

Back in your online GitHub repository:

  1. Go to Settings at the far right
  2. Scroll down and click on Pages on the left sidebar
  3. Choose Branch: main, folder / (root)
  4. Click Save
  5. The URL for your new website will show up, yay! Copy it and paste it where you need it.

Make it fancy

Now to the fun stuff! These are things I learned slowly while building my website. Since you’re on my website you can see some of these details in action. For example, the theme (journal) and all the icons on the top menu!

Webpage style / theme

Okay this is the easiest, but for me it was surprisingly hard to find all my options. I finally found this awesome resource: A THEME GALLERY.

Another way to try them out is to just change the theme and knit locally to see how they look (I think I did this with almost every theme…)

Here’s a list of all the theme options:

“default”, “bootstrap”, “cerulean”, “cosmo”, “darkly”, “flatly”, “journal”, “lumen”, “paper”, “readable”, “sandstone”, “simplex”, “spacelab”, “united”, “yeti”

To implement a theme, go to your recently created _site.yml and add the last few lines:

name: "Haley Oleynik"
navbar:
  title: "Haley Oleynik"
  left:
    - text: "Home"
      href: index.html
    - text: "Research"
      href: research.Rmd
output_dir: "."
output:
  html_document:
    theme: journal

Now rmarkdown::render_site() in your R console and knit one of your pages again to view it locally. Don’t forget to commit and push to GitHub so these changes are made on your real site!

Add icons

Okay, this is super easy, there are a bunch of font awesome icons built in so you can just call them in your _site.yml. Here is the ICON GALLERY (just be sure to choose the free icons). Once you’ve picked out your icons, all you do is add them to your _site.yml like I have below:

name: "Haley Oleynik"
navbar:
  title: "Haley Oleynik"
  left:
    - text: "Home"
      icon: fa-ship
      href: index.html
    - text: "Research"
      icon: fa-fish
      menu:
        - text: "Publications"
          icon: fa-copy
          href: Publications.html
        - text: "Presentations"
          icon: fa-file-powerpoint 
          href: Presentations.html
    - text: "CV"
      icon: fa-paperclip     
      href: collaborate.html
    - text: "Contact"
      icon: fa-at
      href: Contact.html
  right:
    - icon: fa-github fa-lg
      href: https://github.com/haleyoleynik-noaa     
    - icon: fa-twitter fa-lg
      href: https://twitter.com/fish_follower       
    - icon: fa-info-circle fa-la
      href: info.html 
output_dir: "."
output:
  html_document:
    theme: journal
    highlight: textmate
    #css: style.css
    fig_caption: true
    toc: true
    toc_float: true

You can even have only icons with no text, shown under the right header for my github and twitter links.

And if you want a drop down menu, like I have for my research, you can add that second level menu as shown above.

Add images

This is easy, just save them to an images folder in your GitHub repo and then call them like this anywhere in your .Rmd file:

![](./images/picwithfish.jpg)

Resources for quant ecologists and marine scientists

Seminar Series

Here’s a list of seminar series I mostly learned about while I was a Knauss fellow, but that I still now attend as a PhD student. Sometimes it’s nice to get out of your PhD bubble and see some research going on at different institutions or outside your field entirely.

  1. UBC Institute for the Oceans and Fisheries Quant Seminar
  2. NOAA Central Library Seminar Series - I love the stock assessment seminar and the Knauss lunch and learn series!
  3. UW School of Aquatic and Fishery Science Quant Seminar
  4. UW SAFS Fisheries Think Tank
  5. NWFSC Monster Jam seminar
  6. International Pacific Halibut Commission Seminar Series
  7. Alaska Groundfish seminar series
  8. ALL NOAA science seminars - you can also add these to your calendar and sign up for a weekly email digest!