Core competencies

Introduction

This WIO data training course is organised as a “self-paced” open learning model, with six modules covering the core skills required for standardising and visualising coral reef monitoring data. By the completion of this course, you should have developed an understanding/core skills for the following:

Context

• This module aims to provide a core understanding of the nexus between policy initiatives (e.g. UN Sustainable Development Goals) and global monitoring networks. This context is important for understanding how data collected on the status & trends of coral reefs can inform progress on broader policy goals for biodiversity and measures of sustainability.
• This module also explains background to the Global Coral Reef Monitoring Network (GCRMN) that provides standards and a framework for governance of global coral reef data
• General approaches for using code to address global environmental challenges
• Background to coral reef monitoring in the Western Indian Ocean (WIO) region
• Overview of the approach for this training course

Monitoring

• This module aims to provide a general background to the field data collection process and strategies for transferring the data into digital form. This may involve the transcription of information collected from a diving slate or underwater paper into a spreadsheet (e.g. Excel), database or data management platform (e.g. Mermaid).
• Without getting ahead of ourselves with the R skills training, this module aims to provide background information, GCRMN standards and strategies for simplifying the transcription process and ways that can minimise errors.

Data standards & Reproducible Research

• This module provides background to the GCRMN data standards which we will be using as part of this R training course. This includes aspects of knowledge management, how to use version control tools (e.g. git) and Rbasics.
• As part of this module, we will provide some examples of project workflow, excercise for coding, and some of the coding techniques we will use during the course.

Data formatting & Standardisation

• This module will describe more detail on the GCRMN data tier model and how it applies to formatting and standardisation of data for analysis. This is a key step for providing unified data sets that can be combined across locations, regions, countries and, ultimately, globally for reporting on the Status and Trends of coral reefs.
• Key skills will include strategies for the standardisation of taxonomic groups, dates, character strings and factors.
• This module also explains the use of intermediate data objects *.rda files for saving clean, standardised data sets to be used for visualisation and reporting.

Visualisation of Status & Trends

• This module provides basic techniques for visualising data of Status and trends for coral reefs, using the ggplot2 package. This includes strategies for creating data aggregations and summaries on-the-fly and the use of aesthetics and faceting to rapidly view data dimensions (e.g. years, reef types, taxa, et cetera).
• For this training, we provide common data type examples such as those from quadrat samples for quantifying benthic cover and coral reef fish size and abundance.

Mapping & Spatial Representation

• A common necessity for reporting on coral reef data is to visualise the distribution of sites on a map with reference to a coastline and other features. This module aims to provide the basic skills for plotting site positions and map production, building on techniques developed from the Visualisation module.
• We also provide some approaches for dealing with GPS data and how to harmonise coordinate data.

Linking Covariates & External Data

• A key competency for data standardisation and analysis is being able to link field data with other relevant information (e.g. taxonomic, IUCN Redlist classifications, functional triats). This module aims to provide the basic techniques for linking covariate information from local data sources (e.g. site characteristics) as well as information available on-line. These examples provide the basic skills that can be applied across a wide variety of data sources.

Project Documentation & Reporting

• A core skill for communicating the Status and Trends of coral reefs to stakeholders and decision makers is to combine the monitoring data into a reporting framework. The use of rmarkdown for creating standardised reports and presentations allows course participants to utilise the data standardisation, formatting, and visualisation workflow for facilitating the production and communication of results.