IBEEM_workflow

Information related to reproducible workflow format for IBEEM

This repository contains code and workflows for research projects within IBEEM (MSU SPG-sponsored Institute for Biodiversity, Ecology, Evolution, and Macrosystems).

Location of data

These data are stored in a Google Shared Drive and the MSU HPCC IBEEM research space, accessible by collaborators. IBEEM research projects will publish open access data to accompany research papers.

Workflow

Repositories within the IBEEM GitHub Organization should include README files that include key information about the workflow within the repository, the contributors, and the funding. Here is a template README with filled-in examples for a NEON biodiversity project. The funding statement to include for IBEEM is included below in this README's "Funding" section.

All repositories should follow R packaging guidelines, even if they will not become official R packages. For questions, contact Pat Bills. If you work with other programming languages, include a separate directory structure for that (e.g., python/L0).

The workflow for this repository follows the guidelines set out by the Environmental Data Initiative (EDI). Briefly, this involves aligning with FAIR data practices, and employing a workflow that uses different levels for harmonization and derived data products. The overall workflow aligns with this EDI diagram:

Description of subdirectories in IBEEM-MSU GitHub Organization repositories (e.g., for R work).

• R: Main directory containing R scripts.
• /L0: Code & small text data files (includes R Markdown code & HTML/PDF output).
• /L1: Code to create L1 data products = cleaning & editing L0 data (includes R Markdown code & HTML/PDF output).
• /L2: Code to create derived products from L1 data (e.g., merging 2 or more L1 data products). Includes R Markdown code & HTML/PDF output.

Description of subdirectories in the project folders on the Google Shared Drive: IBEEM_Research

data

• L0: raw, L0 data files, & metadata.
• L1: L1 data products produced from scripts that clean & edit L0 data.
• L2: derived data products from L1 data (e.g., merging 2 or more L1 data products, creating a summary variables from L1 data; e.g., diversity of species in L1 data product).

docs

• documents supporting the data and analysis, such as manuscript outline, manuscript draft.

meetings

• meeting notes on the IBEEM research.

Funding

Funding is provided by Michigan State University through a Strategic Partnership Grant for The Institute for Biodiversity, Ecology, Evolution, and Macrosystems (IBEEM).

Authors of this repository

• Phoebe L. Zarnetske
• Pat Bills