Package: glatos 0.7.3

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], Alex Nunes [ctb], Angela Dini [ctb], Ryan Gosse [ctb]

glatos_0.7.3.tar.gz


glatos_0.7.3.tar.gz(r-4.4-noble)
glatos_0.7.3.tgz(r-4.4-emscripten)glatos_0.7.3.tgz(r-4.3-emscripten)
glatos.pdf |glatos.html✨
glatos/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

43 exports 9 stars 1.85 score 79 dependencies

Last updated 4 months agofrom:f455938a81

Exports:abacus_plotadjust_playback_timecalc_collision_probcheck_dependenciesconvert_glatos_to_attconvert_otn_erddap_to_attconvert_otn_to_attcrwcrw_in_polygondetect_transmissionsdetection_bubble_plotdetection_eventsfalse_detectionsinstall_ffmpeginterpolate_pathkml_to_csvkml_workbookmake_framesmake_transitionmake_transition2make_transition3make_videomake_video_ffmpegmin_lagpoint_offsetposition_heat_mapprepare_deploy_sheetprepare_tag_sheetread_glatos_detectionsread_glatos_receiversread_glatos_workbookread_otn_deploymentsread_otn_detectionsread_vemco_tag_specsreal_sensor_valuesreceiver_line_det_simREIresidence_indexrotate_pointssummarize_detectionstransmit_along_pathvector_headingvrl2csv

Dependencies:avbase64encbslibcachemcellrangerclassclassIntclicpp11crayondata.tableDBIdigestdplyre1071evaluatefansifasterizefastmapfasttimefontawesomefsgdalUtilitiesgdistancegenericsgeodistgluehighrhmshtmltoolsigraphjquerylibjsonliteKernSmoothknitrlatticelifecyclelubridatemagrittrMASSMatrixmemoisemimepillarpkgconfigplotrixplyrprettyunitsprogressproxypurrrR6rappdirsrasterRcppRcppArmadilloreadxlrematchrlangrmarkdowns2sasssfspstringistringrterratibbletidyrtidyselecttimechangetinytexunitsutf8vctrswithrwkxfunyaml

Data loading methods for the R package glatos

Rendered fromdata_loading_vignette.Rmdusingknitr::rmarkdownon Jul 08 2024.

Last update: 2021-12-13
Started: 2019-02-24

Data requirements of the R package glatos

Rendered fromdata_requirements_vignette.Rmdusingknitr::rmarkdownon Jul 08 2024.

Last update: 2019-02-25
Started: 2019-02-24

Supplemental documents & workshop handouts

Rendered fromsupplemental_docs.Rmdusingknitr::rmarkdownon Jul 08 2024.

Last update: 2019-02-24
Started: 2019-02-23

Readme and manuals

Help Manual

Help pageTopics
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 if track crosses polygon boundarycheck_cross_boundary
Check if in polygoncheck_in_polygon
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
Plot number of tagged animals or detections on a mapdetection_bubble_plot
Classify discrete events in detection datadetection_events
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
Determines which calculation method to use for the residency index.get_days
An R package for the Great Lakes Acoustic Telemetry Observation System-package glatos
Constructor function for the class glatos_animalsglatos_animals
Constructor function for the class glatos_detectionsglatos_detections
Constructor function for the class glatos_receiversglatos_receivers
Defunct functions in glatoscheck_dependencies glatos-defunct install_ffmpeg make_video_ffmpeg
An sf POLYGON object with Great Lakes coastline and some major tributaries.great_lakes_polygon
Deprecated A SpatialPolygonDataFrame with Great Lakes coastline and some major tributaries.greatLakesPoly
A TransitionLayer object that only allows transitions to occur within water of the Great Lakes Basin.greatLakesTrLayer
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
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
Convert geographic positions to UTMlonlat_to_utm
Create an animated video of spatiotemporal path datamake_frames
Deprecated Create transition layer from polygon shapefilemake_transition
Deprecated Create transition layer from a spatial polygonmake_transition2
Create transition layer from polygon shapefilemake_transition3
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 telemetry transmitter (tag) specification data from a Vemco fileread_vemco_tag_specs
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
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 UTM positions to lonlatutm_to_lonlat
Calculate direction (heading) of a vector (in degrees)vector_heading
Video frames of walleye movements in Lake Huronvideo images
Convert Vemco VRL file(s) to CSV format (detection data only)vrl2csv