Package: glatos 0.8.0

Christopher Holbrook

glatos: A package for the Great Lakes Acoustic Telemetry Observation System

Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.

Authors:Christopher Holbrook [cre, aut], Todd Hayden [aut], Thomas Binder [aut], Jon Pye [aut], Mike O'Brien [ctb], Alex Nunes [ctb], Benjamin Hlina [ctb], Angela Dini [ctb], Ryan Gosse [ctb]

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glatos.pdf |glatos.html✨
glatos/json (API)
NEWS

# Install 'glatos' in R:
install.packages('glatos', repos = c('https://benjaminhlina.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ocean-tracking-network/glatos/issues

Datasets:

On CRAN:

6.68 score 9 stars 113 scripts 70 exports 51 dependencies

Last updated 2 months agofrom:405a195fb5 (on dev). Checks:OK: 5 ERROR: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winNOTENov 06 2024
R-4.5-linuxERRORNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:abacus_plotadjust_playback_timeas_glatos_animalsas_glatos_detectionsas_glatos_receiverscalc_collision_probcheck_dependenciescheck_vdatcheck_vueconvert_glatos_to_attconvert_otn_erddap_to_attconvert_otn_to_attcrwcrw_in_polygondetect_transmissionsdetection_bubble_plotdetection_eventsdetection_range_modelfalse_detectionsformat_POSIXtget_local_vdat_templateget_local_vdat_versionget_local_vue_versionglatos_animalsglatos_check_col_classesglatos_check_col_namesglatos_detectionsglatos_receiversinstall_ffmpeginterpolate_pathis_glatos_animalsis_glatos_detectionsis_glatos_receiversjarasterizekml_to_csvkml_workbookmake_framesmake_transitionmake_videomake_video_ffmpegmin_lagpoint_offsetposition_heat_mapprepare_deploy_sheetprepare_tag_sheetread_glatos_detectionsread_glatos_receiversread_glatos_workbookread_otn_deploymentsread_otn_detectionsread_vdat_csvread_vemco_tag_specsread_vue_detection_csvread_vue_event_csvreal_sensor_valuesreceiver_line_det_simREIresidence_indexrotate_pointsscale_meters_to_degreessummarize_detectionstransmit_along_pathvalidate_glatos_animalsvalidate_glatos_detectionsvalidate_glatos_receiversvdat_convertvector_headingvrl2csvvue_convertwrite_vdat_csv

Dependencies:avcellrangerclassclassIntclicpp11crayondata.tableDBIdplyre1071fansigdistancegenericsgeodistgluehmsigraphjsonliteKernSmoothlatticelifecyclelubridatemagrittrMASSMatrixpillarpkgconfigplotrixprettyunitsprogressproxyR6rasterRcppreadxlrematchrlangs2sfspterratibbletidyselecttimechangeunitsutf8vctrswithrwkzip

Data loading methods for the R package glatos

Rendered fromdata_loading_vignette.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-09-20
Started: 2019-02-24

Data requirements of the R package glatos

Rendered fromdata_requirements_vignette.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-09-20
Started: 2019-02-24

Estimate Detection Range for Acoustic Telemetry Receivers

Benjamin L. Hlina

Rendered fromdetection_efficiency_vignette.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-09-20
Started: 2024-09-18

Supplemental documents & workshop handouts

Rendered fromsupplemental_docs.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-09-20
Started: 2019-02-23

Readme and manuals

Help Manual

Help pageTopics
Subset method for vdat_list that retains attributes[.vdat_list
Plot detection locations of acoustic transmitters over timeabacus_plot
Modify playback time of videoadjust_playback_time
The function below aggregates timedelta of first_detection and last_detection, excluding overlap between detections. Any overlap between two detections is converted to a new detection using the earlier first_detection and the latest last_detection. If the first_detection and last_detection are the same, a timedelta of one second is assumed.aggregate_total_no_overlap
The function below aggregates timedelta of first_detection and last_detection of each detection into a final timedelta then returns a float of the number of days. If the first_detection and last_detection are the same, a timedelta of one second is assumed.aggregate_total_with_overlap
Estimate probability of collision for telemetry transmitterscalc_collision_prob
Check path to Innovasea program VDAT.execheck_vdat
Check path to Innovasea program VUE.execheck_vue
Convert detections and receiver metadata to a format that ATT accepts.convert_glatos_to_att
Convert detections, transmitter, receiver, and animal metadata to a format that ATT accepts.convert_otn_erddap_to_att
Convert detections, tagging metadata, and deployment metadata to a format that ATT accepts.convert_otn_to_att
Simulate a correlated random walkcrw
Simulate a correlated random walk inside a polygoncrw_in_polygon
Simulate detection of transmitter signals in a receiver networkdetect_transmissions
Make bubble plots showing the number of fish detected across a defined set of receiver locations.detection_bubble_plot
Classify discrete events in detection datadetection_events
Detection Range Probability Modeldetection_range_model
False detection filterfalse_detections
An sf POLYGON object with coastline of Flynn Islandflynn_island_polygon
A transition object for Flynn Island for testing make_transitionflynn_island_transition
Round timestamp by fractional second and coerce to characterformat_POSIXt
Determines which calculation method to use for the residency index.get_days
Get schema from local installation of Innovasea program VDAT.exeget_local_vdat_template
Get version of local installation of Innovasea program VDAT.exeget_local_vdat_version
Get version of local installation of Innovasea program VUE.exeget_local_vue_version
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): [email protected]. 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.glatos-package glatos
Construct, check, and validate a glatos_animals objectas_glatos_animals glatos_animals is_glatos_animals validate_glatos_animals
Check column names and classes of a list or data.frame against requirementsglatos_check_col_classes glatos_check_col_names
Construct, check, and validate a glatos_detections objectas_glatos_detections glatos_detections is_glatos_detections validate_glatos_detections
Construct, check, and validate a glatos_receivers objectas_glatos_receivers glatos_receivers is_glatos_receivers validate_glatos_receivers
Defunct functions in glatoscheck_dependencies glatos-defunct install_ffmpeg make_video_ffmpeg
Deprecated functions in package 'glatos'.glatos-deprecated vrl2csv
An sf POLYGON object with Great Lakes coastlinegreat_lakes_polygon
Deprecated A SpatialPolygonDataFrame with Great Lakes coastline and some major tributaries.greatLakesPoly
A 'TransitionLayer' of the Great Lakes that only prevents transition over landgreatLakesTrLayer
An sf POLYGON object with coastline of Higgins Lakehiggins_lake_polygon
A transition object for Higgins Lake for testing make_transitionhiggins_lake_transition
Interpolate new positions within a spatiotemporal path datainterpolate_path
The function below takes a detection events data frame and determines the number of time bins in which detections were observed and returns the cumulative time covered by all bins, in days. Interval (bin) size is determined by the 'time_interval_size' argument.interval_count
Just another rasterizerjarasterize
KML To CSV Conversionkml_to_csv
Make a KML or KMZ file of receiver and animal release locationskml_workbook
Sea Lamprey positions from Lake George, St. Marys River, 2012lamprey_tracks
Create an animated video of spatiotemporal path datamake_frames
Create transition layer from spatial object.make_transition
Create video from sequence of still imagesmake_video
Calculate 'min_lag' for identifying potential false positive detectionsmin_lag
Example animal data from the OTN ERDDAPotn_aat_animals
Example station data from the OTN ERDDAPotn_aat_receivers
Example tag release data from the OTN ERDDAPotn_aat_tag_releases
Identify new location based on distance and bearing from anotherpoint_offset
Position Heat Mapsposition_heat_map
Loads the OTN receiver deployment metadata sheet to prepare it for use in 'convert_otn_to_att'prepare_deploy_sheet
Loads the OTN tagging metadata sheet to prepare it for use in 'convert_otn_to_att'prepare_tag_sheet
Detection range data setrange_detection
Raw GLATOS Workbook from St. Marys River Sea Lamprey projectraw_lamprey_workbook
Zipped GLATOS detection file from Huron Erie Corridor Walleye projectraw_walleye_detections
Read data from a GLATOS detection fileread_glatos_detections
Read data from a GLATOS receiver location fileread_glatos_receivers
Read data from a GLATOS project workbookread_glatos_workbook
Read data from a OTN deployment fileread_otn_deployments
Read data from a OTN detection fileread_otn_detections
Read data from an Innovasea Fathom VDAT CSV fileread_vdat_csv
Read telemetry transmitter (tag) specification data from a Vemco fileread_vemco_tag_specs
Read detection data exported from Innovasea VUE softwareread_vue_detection_csv
Read receiver event data exported from Innovasea VUE softwareread_vue_event_csv
Add 'real'-scale sensor values to glatos detetectionsreal_sensor_values
Simulate detection of acoustic-tagged fish crossing a receiver linereceiver_line_det_sim
Calculates a returns a list of each station and the REI (defined here)REI
Generate the residence index from a set of detectionsresidence_index
Rotate points in a 2-d planerotate_points
Detection Efficiency data setsample_detection_efficiency
Get degree-scale equivalent of meter-scale distance on a spatial objectscale_meters_to_degrees
zipped polygon shapefile of Great Lakesshoreline
Summarize detections by animal, location, or bothsummarize_detections
The function below determines the total days difference.total_diff_days
Simulate telemetry transmitter signals along a pathtransmit_along_path
Convert an Innovasea VRL or VDAT file to a Fathom CSV filevdat_convert
A schema for Innovasea Fathom (VDAT) CSV filesvdat_csv_schema
Calculate direction (heading) of a vector (in degrees)vector_heading
Video frames of walleye movements in Lake Huronvideo-images
Convert an Innovasea Vemco VRL file to a VUE CSV filevue_convert
Write a vdat_list object to disk in Innovasea Fathom VDAT CSV formatwrite_vdat_csv