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mid-project-update.Rmd
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---
title: 'EEB313 Mid-project update (12 marks)'
output:
html_document:
toc: false
---
*To submit this assignment, upload the full document on Quercus, including the
original questions, your code (if applicable), and the output. Submit your
assignment as a knitted `.pdf` or `.html` file.*
Prior to beginning this assignment, we suggest you take a look through [this
link](https://swcarpentry.github.io/r-novice-gapminder/02-project-intro/index.html)
on how to manage project in RStudio using Rprojects. While not a component of
this assignment, the tutorial may prove useful as you move forward with your
group projects.
These tasks seem like a lot of work. However, we will be doing these tasks
already during class and during project work. The purpose of the mid-project
update is for you to set up your repo and get something started on your final
project. While most of these tasks are group based, please fill out each as an
individual. In particular, the first question should be of *your* forked
repository, not one of your team members. The remainder of the questions each
involve a single pull request; make sure everyone in your group does at least
one. Each team member should submit their *own assignment*.
1. A new repository has been created for your project on the
`EEB313-2019` GitHub organization. Paste the URL of this forked
version below. (0.25 marks)
- URL of *your* fork:
2. On the main repo (you will be working on this from here on out, unless you
are doing the fork-based workflow) -- have one of your group members create
a new branch from `master` called `add-conduct`. Create a `CONDUCT.md` file in
this branch. Write down what you as a team decided on for acceptable
conduct/behaviour of team members to each other (e.g. "Must be considerate and
respectful"). You may reuse existing Codes of Conduct, such as the UofT Coders
Code of Conduct or the Contributor Covenant, but make sure to both a) credit
whichever you use and b) still expand upon it with project-specific items (i.e.
meeting frequency, PR approval policy, role rotations). The designated group
member needs to create a pull request of this new file to the `master` branch.
Copy and paste the link to the pull request below. Every team member must
approve this pull request via whatever means you as a team decide on ('all
members must 'thumbs up' the PR message', or 'all members must make a new
comment saying 'good to merge'). Make sure the expectations and behaviours are
explicit and clear. (1.0 marks)
- URL of team member's pull request for `CONDUCT.md`:
3. A `README.md` file should already exist in your project. Once the previous
PR has been merged into `master`, complete the following tasks in the
README, discussed and written up *as a team*. Decide who on your team will
create the branch, make these edits, and create a pull request of this file to
the main project repository. This person should *not* be the same person who
did task 2. Every team member must approve this pull request. (1.75 marks)
- Create the following headers (make sure to use Markdown headers
`#`): "Introduction to the project", "Description of the data",
"Team description".
- Fill out the "Introduction to the project" section, answering
these questions in a paragraph form (don't include these
questions in the section). What is your project about? What is
the goal? Why are you doing it?
- Fill out the "Description of the data" section, and briefly
write down what the data is about, what are the variables you
think you'll use, how the data was collected, and how it will
answer your research questions. Include a reference of the
dataset if one is available, for instance:
Forstmann BU, et al. (2014) Data from: Multi-modal ultra-high resolution
structural 7-Tesla MRI data repository. Dryad Digital Repository.
(https://dx.doi.org/10.5061/dryad.fb41s)
- Fill out the "Team description" section by writing down a brief
biography of each member (including what their skills are and
what their approximate responsibilities -- which can change later --
are for the project) as well as how team roles will be rotated.
- URL of team member's pull request for `README.md`:
4. Once the previous PR has been merged into `master`, have a different group member create a file called
`doc/objectives.md` in a new branch. Note that this will simultaneously create a new folder
called `doc` containing a file called `objectives.md` -- this is [how folders are created on GitHub repos](https://github.com/KirstieJane/STEMMRoleModels/wiki/Creating-new-folders-in-GitHub-repository-via-the-browser).
In `objectives.md`, create one header (`#` markdown header) called "Study
objectives". Create a list (`-` markdown syntax) of each of your research
questions that you *as a team* thought of. It doesn't matter what the questions
are, how simple, complicated or obvious they are. Just have something written
down, and make sure these are _explicitly_ framed as questions or
hypotheses. In this file, also list explicit predictions wherever possible;
i.e. what you think a given relationship might look like. Bear in mind that
these research questions *will* change as you do your analyses. The point is
for you to get started thinking about ideas. Decide on another (new) team
member to create this file, record it, and make a pull request of this new
file. Every team member must approve this pull request. (3 marks)
- URL of team member's pull request for `objectives.md`:
5. Once the previous PR has been merged, start up another branch and create a
file in the `doc/` folder called `analysis-plan.md`. Create three headers
(`#` markdown headers): "Possible analyses", "Possible results tables", and
"Possible results figures". As a team, discuss and record some possible
analyses on the data that you could do to answer the research questions.
Discuss and record possible ways to present your results (possible tables, some
visualizations). Moreover, discuss how you anticipate getting from the raw data
to whatever summary data you will use to generate a given plot (i.e. explain a
data cleaning/transformation plan). Moreover, discuss what kinds of statistical
approaches you anticipate employing. Once again, these do not have to be final,
but you need to show that your team has thought about how to approach this.
Decide on another (new) team member to create this file in a new branch, record
it, and make a pull request of this new file. Every team member must approve
this pull request. *Note:* this analysis and presentation plan does **not**
have to be accurate, nor do you have to use this later on. It could and will
(very likely) change. The point is to get you as a group thinking about how you
will answer the research questions. (3 marks)
- URL of team member's pull request for `analysis-plan.md`:
6. Finally, once the previous PR has been merged, have another group member
create a file called `plots/mock/README.md` in a new branch. This will also
create a folder called `plots` and a subfolder called `mock` within it. Add a
few mock figures into this folder showing your predictions. These do not have
to be 'publication-ready' plots, and can be made in any software of your
choosing (R, Excel, PowerPoint, etc) with or without simulated data points; the
important thing is that the predictions are clear and that your team can show
you have been thinking about how to present your data. In `README.md`, list
details about the mock figures in pseudo-figure caption format. Note that image
files (png, pdf, etc) can also be uploaded to GitHub via dragging and dropping
-- but make sure you are in a branch before you do this. The image files should
be part of the same PR as `README.md`. (3 marks)
- URL of team member's pull request for `plots/mock/README.md` and image files: