This lesson is being piloted (Beta version)

Combined Acoustic Telemetry Tool Training: Glossary

Key Points

Introduction to Acoustic Telemetry Data Analysis

  • Techniques covered will include cleaning and sorting of data.

  • Various packages will be used for summarising and plotting data.
Data Manipulation Basics

  • read.csv() can be used to load data.

  • head, tail, and str() can be used to inspect data.
The GLATOS Package

  • The GLATOS package is a collection of data analysis and visualization tools.

  • False detections are produced by tag collisions.

  • The Pincock algorithm filters out false detections by comparing pings across nearby stations.
Data Analysis Using GLATOS

  • Multiple tools agregated to allow for data ingestion and filtering.

  • Provides functionality for creating basic plots from GLATOS formatted data.
Network Analysis

  • Network analysis is the interpretation of connections between individual movements and receivers.

  • A data frame is created and cleaned to facilitate network analysis.
Matching Detections to Times

  • Time matching links station deployment information to verify that all detections fall within the deployment period.

  • Generate a dataset for the station info in order to group detections.
Summarising and Plotting Data

  • Data can be summarised by fish ID, station or detection.

  • Data can be plotted into an abacus plot by day, or can be mapped based on the station information.
Advanced Plotting

  • Plotly can be used to create an interactive map.

  • gganimate can be used to create an animated plot.
Additional Interpolation and Plotting with VTrack

  • VTrack provides robust options for more advanced visualization.
Animating animal movements

  • ggmap can be used to create an interactive map.

  • gganimate can be used to create an animated plot.
Working with Spatial data

  • st_as_sf() can easily convert data frame to a spatial object.

  • mapview() is a quick and simple way to visualise spatial data.

Glossary

abacus plot
A dot-plot, often with time as the X axis, station as the Y axis, and individual ID as the color-code, popular in telemetry studies to show patterns of animal/spatial use over time.
acoustic telemetry
The practice of affixing animals with uniquely-coded acoustic pingers and deploying listening stations to identify and locate them over time.
ATT
A set of metadata formats implemented as an object in R. Devised by Vinay Udyawer of AIMS for use in the VTrack analysis package, standardizing the reporting of listening device deployment and recovery, tagging efforts, and detection events into one uniform data format.
Brownian bridges
A conditional probability distribution that pins the process at both origin and a second time (t), a paradigm that is very useful for estimating path probability between two known events (i.e.: the location of an animal at two points in time and space).
COA/Centers of Activity
An estimate of relative spatial activity given input data about animal positions in time. Based on technique described in: Simpfendorfer, C. A., M. R. Heupel, and R. E. Hueter. 2002. Estimation of short-term centers of activity from an array of omnidirectional hydrophones and its use in studying animal movements. Canadian Journal of Fisheries and Aquatic Sciences 59:23-32.
data cleaning
The process of removing irregularities in formatting, errors, and typos from data to ensure uniform operation in analysis and visualization.
dplyr
An R package focused on manipulating, subsetting, and summarising data frames (square matrices of data). Very useful for working with our tabular datasets. Part of the ‘Tidyverse’ family of R packages.
FishID
A unique identifier for an individual animal observed at a location and time, regardless of the method of location. Often synonymous with catalognumber and animalID.
fork length
A common measurement for fish length, the length from nose to tail fork.
glatos
A package maintained by the telemetry network of the same name to ingest, standardize, and operate on acoustic telemetry datasets.
Lubridate
Date manipulator package. Part of the ‘Tidyverse’ family of R packages.
MapBox
A geospatial visualization library, an open source mapping platform for custom-designed maps.
package
In R, a package is a collection of R functions, data and compiled code. The location where the packages are stored is called the library. If there is a particular functionality that you require, you can download the package from the appropriate site and it will be stored in your library.
ping
A series of transmissions made by an acoustic tag for the purposes of relaying its unique code to a listening instrument.
POSIX
A set of IEEE standards that are meant to guarantee interoperability. In most common R parlance, it’s a shorthand for the functions that standardize the format for a date and time.
R
A statistical programming language.
residence index
Any of a few ratios that can be calculated to determine the relative spatial use of an animal across an observatory of listening devices.
station
A geographical location where listening equipment is deployed and recovered regularly.
stringr
Character string manipulator package. Part of the ‘Tidyverse’ family of R packages.
tagging date
The date an animal was affixed with an electronic tag (acoustic or otherwise).
Time series
A dataset that takes measurements regularly over a period of time.
Tx receivers
Listening devices that also transmit their own coded pings, for the purposes of synchronizing clocks or for being heard by mobile listening stations.