Background
Overview
Teaching: 5 min
Exercises: 0 minQuestions
What is the Ocean Tracking Network?
How does your local telemetry network interact with OTN?
What methods of data analysis will be covered?
Objectives
Intro to OTN
The Ocean Tracking Network (OTN) supports global telemetry research by providing training, equipment, and data infrastructure to our large network of partners.
OTN and affiliated networks provide automated cross-referencing of your detection data with other tags in the system to help resolve “mystery detections” and provide detection data to taggers in other regions. OTN’s Data Managers will also extensively quality-control your submitted metadata for errors to ensure the most accurate records possible are stored in the database. OTN’s database and Data Portal website are excellent places to archive your datasets for future use and sharing with collaborators. We offer pathways to publish your datasets with OBIS, and via open data portals like ERDDAP, GeoServer etc. The data-product format returned by OTN is directly ingestible by analysis packages such as glatos and resonATe for ease of analysis. OTN offers support for the use of these packages and tools.
Learn more about OTN and our partners here https://members.oceantrack.org/. Please contact OTNDC@DAL.CA if you are interested in connecting with your regional network and learning about their affiliation with OTN.
Intended Audience
This set of workshop material is directed at researchers who are ready to begin the work of acoustic telemetry data analysis. The first few lessons will begin with introductory R - no previous coding experince required. The workshop material progresses into more advanced techniques as we move along, beginning around lesson 8 “Introduction to Glatos”.
If you’d like to refresh your R coding skills outside of this workshop curriculum, we recommend Data Analysis and Visualization in R for Ecologists as a good starting point. Much of this content is included in the first two lessons of this workshop.
Getting Started
Please follow the instrucions in the “Setup” tab along the top menu to install all required software, packages and data files. If you have questions or are running into errors please reach out to OTNDC@DAL.CA for support.
Intro to Telemetry Data Analysis
OTN-affiliated telemetry networks all provide researchers with pre-formatted datasets, which are easily ingested into these data analysis tools.
Before diving in to a lot of analysis, it is important to take the time to clean and sort your dataset, taking the pre-formatted files and combining them in different ways, allowing you to analyse the data with different questions in mind.
There are multiple R packages necessary for efficient and thorough telemetry data analysis. General packages that allow for data cleaning and arrangement, dataset manipulation and visualization, pairing with oceanographic data and temporo-spatial locating are used in conjuction with the telemetry analysis tool packages remora, actel and glatos.
There are many more useful packages covered in this workshop, but here are some highlights:
Intro to the glatos Package
glatos is an R package with functions useful to members of the Great Lakes Acoustic Telemetry Observation System (http://glatos.glos.us). Developed by Chris Holbrook of GLATOS, OTN helps to maintain and keep relevant. Functions may be generally useful for processing, analyzing, simulating, and visualizing acoustic telemetry data, but are not strictly limited to acoustic telemetry applications. Tools included in this package facilitate false filtering of detections due to time between pings and disstance between pings. There are tools to summarise and plot, including mapping of animal movement. Learn more here.
Maintainer: Dr. Chris Holbrook, ( cholbrook@usgs.gov )
Intro to the actel Package
This package is designed for studies where animals tagged with acoustic tags are expected to move through receiver arrays. actel combines the advantages of automatic sorting and checking of animal movements with the possibility for user intervention on tags that deviate from expected behaviour. The three analysis functions: explore, migration and residency, allow the users to analyse their data in a systematic way, making it easy to compare results from different studies.
Author: Dr. Hugo Flavio, ( hflavio@wlu.ca )
Intro to the remora Package
This package is designed for the Rapid Extraction of Marine Observations for Roving Animals (remora). This is an R package that enables the integration of animal acoustic telemetry data with oceanographic observations collected by ocean observing programs. It includes functions for:
- Interactively exploring animal movements in space and time from acoustic telemetry data
- Performing robust quality-control of acoustic telemetry data as described in Hoenner et al. 2018
- Identifying available satellite-derived and sub-surface in situ oceanographic datasets coincident and collocated with the animal movement data, based on regional Ocean Observing Systems
- Extracting and appending these environmental data to animal movement data
Whilst the functions in remora were primarily developed to work with acoustic telemetry data, the environmental data extraction and integration functionalities will work with other spatio-temporal ecological datasets (eg. satellite telemetry, species sightings records, fisheries catch records).
Maintainer: Created by a team from IMOS Animal Tracking Facility, adapted to work on OTN-formatted data by Bruce Delo ( bruce.delo@dal.ca )
Intro to the pathroutr Package
The goal of pathroutr is to provide functions for re-routing paths that cross land around barrier polygons. The use-case in mind is movement paths derived from location estimates of marine animals. Due to error associated with these locations it is not uncommon for these tracks to cross land. The pathroutr package aims to provide a pragmatic and fast solution for re-routing these paths around land and along an efficient path. You can learn more here
Author: Dr. Josh M London ( josh.london@noaa.gov )
Key Points