glatos: An R package for the Great Lakes Acoustic Telemetry Observation System

glatos is an R package with functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us. Functions may be generally useful for processing, analyzing, simulating, and visualizing acoustic telemetry data, but are not strictly limited to acoustic telemetry applications.

Package status

glatos is hosted by the Ocean Tracking Network on github.

• For recent changes, see NEWS.

• To report a bug, ask a question, or propose something new, submit an Issue or email the maintainer (Chris Holbrook): cholbrook@usgs.gov.

Installation

To install the latest release (0.8.0 'very-refreshing-lemonade'):

library(remotes) # for install_github
install_github('ocean-tracking-network/glatos', build_vignettes = TRUE)

To install the development version, an earlier version, or to see frequently asked questions about installation, see https://github.com/ocean-tracking-network/glatos/wiki/installation-instructions.

Contents

Data loading and processing

1. read_glatos_detections and read_otn_detections provide fast data loading from standard GLATOS and OTN data files to a single structure that is compatible with other glatos functions.

2. read_glatos_receivers and read_otn_deployments reads receiver location histories from standard GLATOS and OTN data files to a single structure that is compatible with other glatos functions.

3. read_glatos_workbook reads project-specific receiver history and fish taggging and release data from a standard glatos workbook file.

4. read_vemco_tag_specs reads transmitter (tag) specifications and operating schedule.

5. real_sensor_values converts 'raw' transmitter sensor (e.g., depth, temperature) to 'real'-scale values (e.g., depth in meters) using transmitter specification data (e.g., from read_vemco_tag_specs).

6. prepare_tag_sheet and prepare_deploy_sheet load OTN metadata sheets for Tagging and Deployment of Receivers and formats them for converting to ATT Data.

7. vue_convert and vdat_convert extracts data from proprietary receiver files (.vrl, .vdat) using Innovasea's VUE and VDAT software (packaged with Fathom Connect software).

8. read_vdat_csv reads data from a CSV file produced by Innovasea's Fathom Connect or VDAT software (or with vdat_convert()). Data from an "interleaved" (not "split") Fathom CSV format are read into R as a vdat_list object.

9. read_vue_detection_csv, and read_vue_event_csv read data from a CSV file exported from Innovasea's VUE software.

Filtering and summarizing

1. min_lag facilitates identification and removal of false positive detections by calculating the minimum time interval (min_lag) between successive detections.

2. false_detections removes potential false positive detections using "short interval" criteria (see min_lag).

3. detection_events distills detection data down to a much smaller number of discrete detection events, defined as a change in location or time gap that exceeds a threshold.

4. summarize_detections calculates number of fish detected, number of detections, first and last detection timestamps, and/or mean location of receivers or groups, depending on specific type of summary requested.

5. residence_index calculates the relative proportion of time spent at each location.

6. REI calculates the relative activity at each receiver based on number of unique species and individual animals.

7. detection_range_model for estimating detection range at which a certain detection efficiency is expected, using output from Innovasea's range testing software.

Simulation functions for system design and evaluation

1. calc_collision_prob estimates the probability of collisions for pulse-position-modulation type co-located telemetry transmitters. This is useful for determining the number of fish to release or tag specifications (e.g., delay).

2. receiver_line_det_sim simulates detection of acoustic-tagged fish crossing a receiver line (or single receiver). This is useful for determining optimal spacing of receviers in a line and tag specifications (e.g., delay).

3. crw_in_polygon, transmit_along_path, and detect_transmissions individually simulate random fish movement paths within a water body (crw_in_polygon: a random walk in a polygon), tag signal transmissions along those paths (transmit_along_path: time series and locations of transmissions based on tag specs), and detection of those transmittions by receivers in a user-defined receiver network (detect_transmissions: time series and locations of detections based on detection range curve). Collectively, these functions can be used to explore, compare, and contrast theoretical performance of a wide range of transmitter and receiver network designs.

Visualization and data exploration

1. abacus_plot is useful for exploring movement patterns of individual tagged animals through time.

2. detection_bubble_plot is useful for exploring distribution of tagged individuals among receivers.

3. interpolate_path, make_frames, and make_video Interpolate spatio-temporal movements, between detections, create video frames, and stitch frames together to create animated video file.

4. adjust_playback_time modify playback speed of videos and optionally convert between video file formats.

Data Exporting

1. convert_glatos_to_att converts the glatos detection and receiver objects to a format supported by VTrack/ATT.

2. convert_otn_erddap_to_att converts the OTN detection and ERDDAP csvs of OTN animals, tags and stations to a format supported by VTrack/ATT.

3. convert_otn_to_att converts the OTN detections and metadata sheets to the ATT format. Also accepts deployment metadata from the OTN website in CSV format.