One key to open reproducible science is to provide rigorous organization of all workflow code. Not just for when you send your project to someone else. A future version of yourself will also benefit when you return to an organized workflow after some time away.
I created a GitHub repository (with accompanying video tutorial) that provides a Python script and Jupyter Notebook each containing an example workflow. I use this structure for all of my computational projects. The workflow contains the following stages:
How many times have you returned to a programming project after time away and the analysis failed? Broken file paths. Missing data. Code execution errors. I know what you are thinking: this sounds familiar. I have also experienced computational heartbreak. Let’s avoid that going forward. I’ll start.
One aspect of open reproducible science is to provide a rigorous workflow structure. Not just for when you send your project to someone else though. Adding structure will set a future version of yourself up for success. Imagine how thrilled you will be upon returning to a well-managed, reproducible project.
Using Object-Based Image Analysis to Extract Alpine Tundra Features on Vermont’s Highest Mountain
Editor’s Preface: Cale is back, this time with a look at the alpine tundra of Mount Mansfield. Download and check out the data from this work at the VT Open Geodata Portal here (metadata here). It makes a nice compliment to lower-resolution NLCD land cover datasets, and an even better one to the high-resolution (0.5m) 2016 statewide land cover set soon available from VCGI:
Editor’s Preface: Obtaining, digitizing, georeferencing and publishing historical Vermont orthoimagery are some of the many things we at VCGI wish there were more time and resources to do. Fortunately, we’ve been lucky to have met Cale Kochenour, a Vermonter and current graduate student in GIS and remote sensing at Penn State. Cale has graciously volunteered not only to georeference some of the digitized old black and white VT orthoimagery we’ve collected over the years, but also document for others the process and lessons learned. …
Scientific programmer. Interested in all things remote sensing.