ubc-mds/taracyc_ocean_virus_analysis

DSCI 522 Data Science Workflows Project

taracyc_ocean_virus_analysis's Issues

Alert: Master branch getting updated without pull requests

Hi,

Follow the following steps in order to work with fork-pull request.

• Clone the forked repository locally

• Follow the steps here to set an upstream as your master branch
  https://help.github.com/articles/configuring-a-remote-for-a-fork/

• Now when you makes changes to your "forked repository", push them, make a pull request, the other team member will critique it and accept it

• For updating your forked repository, so that it's up to date with the master branch, follow the following steps:
  https://help.github.com/articles/syncing-a-fork/

Feedback on Proposal

@HarjyotKaur and @heathervant , you have chosen an interesting question and I look forward to reading more on your analysis. This analysis will be very useful for me personally as I have such little knowledge on biology topics and I want to change that :) Here are some improvement points and minor suggestions for your project.

Reasoning

• Keep in mind that your readme is the landing page for someone examining your analysis. Therefore, you can do some additions that would make the readme more informative and intriguing for a visitor. In particular, you can include a brief introduction about the context and your motivation to do such analysis. Then, you can introduce your question and explain the data as you have done already.

Mechanics

• Your names should not be a part of the project repository name. The name should be more descriptive of the project. For example, simply "taracyc_analysis" can be a great name for your project. I would also recommend taking "DSCI_522" out of the name of your project. But if you like it this way, no problem. You should also update your readme title based on the changes you make in the repository title.

• Always include a link when you point your readers to a specific file and/or folder in your repository. For example, include the link to the file within the sentence "For further information, the steps followed for downloading this data have been outlined in the same repository."

• The screenshot of the data import is useful, but I would suggest using a code chunk for the code and printing output as a table. I believe it might look more professional that way. You can do this easily by creating the README file as an R markdown and knitting as github_document.

• I see that you have found a solution within Github to store the large data set needed for your analysis. The data repository is well-organized and explains the data extraction steps quite well. Just don't forget to add a link to your analysis repository in the readme of the data repository.

Minor Suggestions:

• It is great you mention the authors in the readme. However, my recommendation is to include your github.com profile names and links instead of your UBC cwl profiles. These repositories are public, so your public github profiles would be more meaningful to those looking at your project.

• My recommendation is to store only raw data or metadata files in the data/ folder. Your explanations and instructions about the data source and the data, data_load.md file, can be in doc/ folder rather than the data/ folder. However, in the end, it is up to you.

• Your commit messages are meaningful in general. Although I spot some commit messages that are version statements. Try to eliminate such messages and instead state the change you made. I would recommend checking out the post here to improve your committing habits.

I hope this feedback is helpful in improving your project. Please let me know if you have any questions. Good luck!

Feedback from peers on milestone 1

1. For people with no biological background add some links to help explain what is going with why we want to collect this biological data would be helpful.
2. relevel the depth factor to include the description on what the depth actually means, or add a descriptive legend so you don't have to cross-reference it to the table in the introduction of the report.
   Good job otherwise!

Resources for understanding One Way and Two Way Anova

Video Links:

Video 1: https://www.youtube.com/watch?v=-yQb_ZJnFXw
Video 2: https://www.youtube.com/watch?v=lZFmFuZGQTk
Video 3: https://www.youtube.com/watch?v=cNIIn9bConY

Paper: http://oak.ucc.nau.edu/rh232/courses/EPS625/Handouts/Two-way%20ANOVA/Understanding%20the%20Two-way%20ANOVA.pdf

Feedback on Milestone 2

@heathervant and @HarjyotKaur great job on Milestone 2! There is not much I can add. I will only suggest taking a look at http://swcarpentry.github.io/make-novice/reference. This would help make your Make code more practical. For example, you can use automatic variables and avoid some repetition.

Feedback on milestone 1

@heathervant @HarjyotKaur
Your readme, final report and scripts are very informative and organized. You have done a great job!
Here are some remaining issues:

• Add a link to your report on your main readme
• Add version information to your dependencies

Suggestions:

• In your report, alongside a snapshot, you can add summary statistics table for the variables used.
• You can include a flow chart/dependency diagram on your readme.