SORTEE Code Club: Hacky Hour Tuesday May 21 8-9h UTC
This is the collaborative "notebook" for Code Club Hacky Hour Tuesday May 21 08:00-09:00 UTC +00:00, run by the Member Engagement Committee of the Society for Open, Reproducible and Transparent Ecology & Evolution (SORTEE).
Become a SORTEE member
Code Club Agenda
More information and debriefs of previous montly Code Club meetings
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Make sure you are familiar with SORTEE's Code of Conduct so this can be a safe and fun place to learn and discuss.
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Hint: HackMD is great for sharing information in this kind of online set up, as the code formatting is nice & easy with MarkDown! Just add 3 ticks (`
) for thecode blocks
.
Otherwise, it's like a Google doc: it allows simultaneous editing. There's a section for practice down there β¬οΈ
Topic of today's Hacky Hour and how to join
In today's Hacky Hour we will do a code review exercise using the 17-step checklist for Ecology and Evolution, and kick off the Find an ORTEE Code Reviewer list.
For the exercise, you can bring a piece of your own code (old or new, published or unpublished), for example code using the base R mean()
function (read about why here). Donβt have your own code? No worries
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
, you can do the exercise choosing one of the pieces of code below β¬οΈ
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
You can find the zoom link for today's Code Club on SORTEE's Slack which you will get access to by becoming a SORTEE member.
ICE BREAKER (practice HackMD editing)
Let's learn how to use this HackMD document by answering an ice breaker question!
Somewhere on the screen (probably at the top), you should see three icons
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
(a pencil, a two-column window, and an eye). You can add your answer by clicking the edit button
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
(the pencil).Q: If you could be another organism for one day, what would you like to be?
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Answers:
- Jelly fish
- Ant eater
- Any bird that flies
- Any tree
Code review exercise
Code Club can play an important role in promoting code review during development to normalize sharing code and making coding errors. To practice code sharing and code review, we will do a code review exercise today!
Did you bring your own code? Please add either your GitHub username, full name, or email below, so that you will be added as a member to SORTEE's Code Club github Team:
- NEvanDis
- StefanVriend
- avrodrigues
- kumar-a
Steps:
- You will be randomly split into pairs for the exercise
- Submit your code review request as an issue on SORTEE's Code Club github (we will do a live demonstration before starting the code review exercise) OR choose one of the papers to review below β¬οΈ
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Formulate a goal for your code review request, also if you plan to review one of the provided papers. For example, you can pick one of the 7 sections in the 17-step checklist to focus on (see next step).
- Start reviewing the code of the person you have paired up with! Open the the 17-step checklist for Ecology and Evolution and fill in the parts that are relevant for the goal of the code review request
- Please also answer the last question on the form: giving feedback to the makers of the checklist! Stefan Vriend, Freddy Hillemann and Joey Burant
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
- Want to contribute to code peer review in the future? Add your details to the Find an ORTEE Code Reviewer list
Donβt have your own code? No worries
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
, you can do the exercise as follows:Select one of the following publications and download the corresponding data and R code. As we won't have time to do a complete code review, make sure to formulate a goal for the code review exercise (i.e. focusing on one of the 7 sections in the checklist).
**NB: From code review workshop by Stefan Vriend and Joey Burant
Option 1: Woodman et al. (2022), Journal of Animal Ecology
paper
data and readme on Dryad
code on Zenodo
Option 2: Pollierer et al. (2023), Ecology Letters
paper
data and readme on Dryad
code on Zenodo (Note: there are multiple scripts available; focus on the main script "Pollierer_FoodWebReconstruction.Rmd")
Option 3: Govaert et al. (2023), Ecology
paper
data and readme on Dryad
code on Zenodo
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
If you feel comfortable, please add coding mistakes you find (and potentially how to recognize them) to the SORTEE Library of Code Mistakes. This way we can build a resource of (common) code mistakes that people can use during code review.
NB: You can make your mistake as anonymous as you like.
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Want to request a more extensive code review? Scroll down to fill in your details β¬οΈ
Give feedback
Any feedback on Code Club is welcome! Things you liked, things which could be improved, topics you would like to see in upcoming Code Clubs etc.
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Want to propose a Code Club topic or host a session? See the Code Club page.
Feedback:
Request a code review
Code Club can play an important role in promoting code review during development to normalize sharing code and making coding errors. Code Club can also provide code review immediately pre-publication through a code pre-check.
Would you like your code to be checked by peers? You are very welcome to request it here!
Image Not Showing
Possible Reasons
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More β
Tip You can use SORTEE's Code Club github to do the code review by adding your code review request and the code review as an issue (how-to explained on the page).