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
Prior to beginning this assignment, we suggest you take a look through this link 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.
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)
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
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)
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
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. 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)
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)
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)
plots/mock/README.mdand image files:
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