Reproducibility

Image from wikipedia

The goal of this assignment it to continue to ensure the reproducability of the project by making individual instructions that can be used to generate project figures. All figures you generate as part of your project should follow these guidelines in your final deliverables. This milestone is for you to complete at least one figure and demonstrate your understanding of what is expected in your final project.

1. Deliverables

Generate an instruction file (typically a Jupyter notebook file is ideal because it can include code, however a markdown file may also be appropriate) with complete instructions that describe how you created each of your figures for your project. Basically any figure you generate should have complete instructions about how that figure was generated.

More than one file is acceptable as ALL of your figures will need an associated instruction file in your final deliverables.

2. What to include

Typical instructions should include the following:

Description of the figure(s) the instructions for and where the figure is used (In your presentation, in your reports, etc.)
Link to instructions to install the raw data, software and dependencies (ex your INSTALL.md file).
Code to generate the required data used in the figure and instructions for any munging or analysis.
Links to intermediate data that takes a while to generate.
Code to generate the figure or visualizations.
Code to add formatting such as axes labels, titles, etc.
Code to export a file.

As much as possible try to automate the instructions. The best instructions will just allow the reader to run the notebook and produce the figure. However, that may not be possible. Instead you need to include steps that include any manual steps.

If a step requires a lot of time, it is expected that intermediate results are stored so that the instructor could complete the time consuming step or skip over it. If the data is still under the NDA please put the intermediate results in the Teams director or contact the instructor before this assignment is due to agree on a work around.

It is also acceptable for a single notebook to generate multiple related figures.

Submission

Although you will need instructions for all of your figures the goal of this project is to commit at least one figure instruction file to your project git repository on or before the due date. Make sure it is clear where the file is located (i.e. update your README.md file). Your instructor will download your repository and check your instructions and try to reproduce your results.

Evaluation

Instructors will follow your instructions and try to reproduce your results. Points will be taken off for any missing or confusing steps.

Written by Dr. Dirk Colbry, Michigan State University
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.