# SORTEE Code Club: Hacky Hour Tuesday May 21 8-9h UTC

###### tags: `sortee` `open-code` `reproducibility`

:::warning
Link to this document: https://hackmd.io/@8fJ_d1O7Thq_0GNEZ0O-MA/H19cC3Nm0
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> 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](https://sortee.org/join)
> [Code Club Agenda](https://docs.google.com/spreadsheets/d/1rOOOE7ghPduwtFftG0DJJf0DXVigAdcmQ0xdEwbKQXo/edit?usp=sharing)
> [More information and debriefs of previous montly Code Club meetings](https://www.sortee.org/code_club/)

:::danger
:exclamation: Make sure you are familiar with [SORTEE's Code of Conduct](https://www.sortee.org/codeofconduct/) so this can be a safe and fun place to learn and discuss.
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:::info
:bulb: **Hint:** HackMD is great for sharing information in this kind of online set up, as the code formatting is nice & easy with [MarkDown](https://www.markdownguide.org/basic-syntax/)! Just add 3 ticks (``` ` ```) for the``` code blocks ```.
Otherwise, it's like a Google doc: it allows simultaneous editing. There's a section for practice down there ⬇️
:::

[ToC]

## 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](https://www.sortee.org/blog/2024/05/03/202404_code_club/), and **kick off the [Find an ORTEE Code Reviewer list](https://docs.google.com/spreadsheets/d/1eHdU8o0psUj6Y4dPxqA-uW8Fc8SQVwzY1BnEbXM5k54/edit?usp=sharing)**.

For the exercise, you can bring a piece of your own code (old or new, published or unpublished), for example code using the base R ```mean()```function (read about why [here](https://www.sortee.org/blog/2024/04/04/202403_code_club/)). Don’t have your own code? No worries:hugging_face:, you can do the exercise choosing one of the pieces of code below ⬇️

:::danger
:exclamation: 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](https://sortee.org/join).
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## 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 :pencil2: :desktop_computer: :eye: (a pencil, a two-column window, and an eye). You can add your answer by clicking the edit button :pencil2: (the pencil).

**Q: If you could be another organism for one day, what would you like to be?**
:lizard::monkey::unicorn_face::tropical_fish::snake::penguin::spider::blowfish::turtle::seedling::dolphin::octopus::bee::rabbit::scorpion::panda_face::deciduous_tree::bat::fish::sunflower::fox_face:

_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](https://github.com/SORTEE/peer-code-review) Team:
* NEvanDis
* StefanVriend
* avrodrigues
* kumar-a
*

:::warning
**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](https://github.com/SORTEE/peer-code-review) (we will do a live demonstration before starting the code review exercise) ***OR*** choose one of the papers to review below ⬇️
- :exclamation: **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](https://forms.gle/7bmDwTg7DiFGZqPt5) 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 :heart:
- **Want to contribute to code peer review in the future? Add your details to the [Find an ORTEE Code Reviewer list](https://docs.google.com/spreadsheets/d/1eHdU8o0psUj6Y4dPxqA-uW8Fc8SQVwzY1BnEbXM5k54/edit?usp=sharing)**
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**Don’t have your own code?** No worries:hugging_face:, 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](https://osf.io/5ykhq/wiki/home/) by Stefan Vriend and Joey Burant_

**Option 1:** Woodman et al. (2022), Journal of Animal Ecology
[paper](https://doi.org/10.1111/1365-2656.13851)
[data and readme on Dryad](https://doi.org/10.5061/dryad.m63xsj44s)
[code on Zenodo](https://doi.org/10.5281/zenodo.7327335)

**Option 2:** Pollierer et al. (2023), Ecology Letters
[paper](https://doi.org/10.1111/ele.14276)
[data and readme on Dryad](https://doi.org/10.5061/dryad.2280gb5xv)
[code on Zenodo](https://doi.org/10.5281/zenodo.7993642) (Note: there are multiple scripts available; focus on the main script "Pollierer_FoodWebReconstruction.Rmd")

**Option 3:** Govaert et al. (2023), Ecology
[paper](https://doi.org/10.1002/ecy.4199)
[data and readme on Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.r4xgxd2jf)
[code on Zenodo](https://zenodo.org/records/7827593)

:::warning
:raised_hands: If you feel comfortable, please add coding mistakes you find (and potentially how to recognize them) to the [SORTEE Library of Code Mistakes](https://docs.google.com/presentation/d/12QN3WUc5v1Df7OArEox2U7l_N_qnHHuwzjCYiI4idC8/edit?usp=sharing). 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._
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:::info
:bulb: Want to request a more extensive code review? Scroll down to fill in your details ⬇️
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## 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.
:::info
:bulb: Want to propose a Code Club topic or host a session? See **[the Code Club page](https://www.sortee.org/code_club/)**.
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**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.

:::warning
**Would you like your code to be checked by peers?** You are very welcome to request it here!
:::
:::info
:bulb:**Tip** You can use SORTEE's [Code Club github](https://github.com/SORTEE/peer-code-review) to do the code review by adding your code review request and the code review as an issue (how-to explained on the page).
:::

- [ ] **Put your name here and add the following details below:**
- **Research topic:** briefly describe what the code is about/does so people can judge whether they have the right expertise to help
- **Coding language:** e.g. R, python, shell...
- **Code status (pick one):** in-process / pre-publication / post-publication
- **Code review goal:** briefly describe what you would like to get out of a code review session
- **Preferred type of code review (pick one):** group / 1-on-1
- **Code reviewer:** :exclamation:_put your name here to volunteer to review this code!_

- [ ] **Put your name here and add the following details below:**
- **Research topic:** briefly describe what the code is about/does so people can judge whether they have the right expertise to help
- **Coding language:** e.g. R, python, shell...
- **Code status (pick one):** in-process / pre-publication / post-publication
- **Code review goal:** briefly describe what you would like to get out of a code review session
- **Preferred type of code review (pick one):** group / 1-on-1
- **Code reviewer:** :exclamation:_put your name here to volunteer to review this code!_

- [ ] **Put your name here and add the following details below:**
- **Research topic:** briefly describe what the code is about/does so people can judge whether they have the right expertise to help
- **Coding language:** e.g. R, python, shell...
- **Code status (pick one):** in-process / pre-publication / post-publication
- **Code review goal:** briefly describe what you would like to get out of a code review session
- **Preferred type of code review (pick one):** group / 1-on-1
- **Code reviewer:** :exclamation:_put your name here to volunteer to review this code!_