Chapter 1 Overview

This guide is a resource for calculating the annual Ocean Health Index global assessments. It is intended for use by OHI fellows and anyone interested in the process of how scores are calculated, but only those with access to the internal server (Mazu) are able to actually perform the assessment.

By conducting a yearly assessment, the OHI delivers information about a suite of goals important to humans and our use of the oceans. The OHI methods are reproducible and ever-evolving, so updates to this guide are welcomed as improvements and upgrades are incorporated.

Content covered in the following chapters includes:

  • How to initialize a new assessment
  • Thorough instructions for data prep, including how to:
    • Access and organize files
    • Structure data prep scripts
    • Gapfill data
    • Check results
  • Update data layers to OHI global and recalculate scores
  • Finalize the assessment, including how to:
    • Review scores
    • Create bibliography
    • Update metadata
    • Create methods and results documents
    • Upload to repository

1.1 Repositories used to calculate the global assessment

The OHI uses GitHub repositories (repos) to organize all of the associated data prep scripts, functions/packages, and score calculation materials for each assessment year. There are separate repositories for different parts of the project, which are detailed here. Practicioners of the assessment will clone all repositories to their RStudio workspace, but mainly work in the ohiprep_v20?? repository.

OHI github page

1.1.1 ohiprep_v20??

Scripts and intermediate files used to prepare the data layers used by the OHI model are included in this repo. Each year a new version of this repository is created by copying over the previous assessment’s repository contents and deleting the history (more on that later). The suffix of the repo name indicates the year of the assessment (e.g. for 2019, the repo name was ohiprep_v2019)


folder description
globalprep Contains R markdown (Rmd) scripts used to prepare all goal, pressure, and resilience data layers. Files are organized by individual data layer, and contain all data, prep scripts, and any other files from previous assessment years in addition to the current assessment year.
Reference handy reference materials used throughout the global assessmeent
workflow Rmd templates, sourced files, and functions used throughout data preparation

1.1.2 ohi-global

This repo contains data layers, supplementary information, models, and scripts used to calculate the global scores. The contents of this repository are updated each time a data layer in ohiprep_v20?? is completed.


folder description
eez global models and data
eez/layers data layers used in the models (data are copied from ohiprep using paths from metadata_documentation/layers_eez_base.csv)
eez/conf models and supplementary data used to calculate scores
eez/calculate_scores.R master script used to calculate scores
eez/scores.csv score output from calculate_scores.R (includes all score dimensions for each goal and country)
metadata_documentation csv files describing data layers
yearly_results reporting on results of each year’s OHI assessment
documents files used to create OHI methods document

1.1.3 ohicore

This is an R package that includes the core functions used in all assessments. See package description for more information.

1.1.4 globalfellows-issues

This repository was created in 2018 for the first cohort of Global Fellows, and is used to communicate about the data prep process for each layer, document reference information, share ideas, and keep track of progress on tasks. This repository is used just for writing issues, and is separate from the other repositories where data prep occurs. More information about communicating via issues is found throughout this guide.