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REI()
Calculates a returns a list of each station and the REI (defined here)
abacus_plot()
Plot detection locations of acoustic transmitters over time
adjust_playback_time()
Modify playback time of video
aggregate_total_no_overlap()
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_with_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.
calc_collision_prob()
Estimate probability of collision for telemetry transmitters
cast()
Cast a list of scalars to a new class
check_vdat()
Check path to Innovasea program vdat.exe
check_vue()
Check path to Innovasea program VUE.exe
convert_glatos_to_att()
Convert detections and receiver metadata to a format that ATT accepts.
convert_otn_erddap_to_att()
Convert detections, transmitter, receiver, and animal metadata to a format that ATT accepts.
convert_otn_to_att()
Convert detections, tagging metadata, and deployment metadata to a format that ATT accepts.
crw()
Simulate a correlated random walk
crw_in_polygon()
Simulate a correlated random walk inside a polygon
detect_transmissions()
Simulate detection of transmitter signals in a receiver network
detection_bubble_plot()
Make bubble plots showing the number of fish detected across a defined set of receiver locations.
detection_events()
Classify discrete events in detection data
detection_range_model()
Detection Range Probability Model
false_detections()
False detection filter
flynn_island_polygon
An sf POLYGON object with coastline of Flynn Island
flynn_island_transition
A transition object for Flynn Island for testing make_transition
format_POSIXt()
Round timestamp by fractional second and coerce to character
get_days()
Determines which calculation method to use for the residency index.
get_local_vdat_template()
Get schema from local installation of Innovasea program vdat.exe
get_local_vdat_version()
Get version of local installation of Innovasea program vdat.exe
get_local_vue_version()
Get version of local installation of Innovasea program VUE.exe
glatos-defunct check_dependencies make_video_ffmpeg install_ffmpeg
Defunct functions in glatos
vrl2csv()
Deprecated functions in package glatos .
glatos-package glatos
glatos: A package for the Great Lakes Acoustic Telemetry Observation System
glatos_animals() as_glatos_animals() is_glatos_animals() validate_glatos_animals()
Construct, check, and validate a glatos_animals object
glatos_check_col_names() glatos_check_col_classes()
Check column names and classes of a list or data.frame against requirements
glatos_detections() as_glatos_detections() is_glatos_detections() validate_glatos_detections()
Construct, check, and validate a glatos_detections object
glatos_receivers() as_glatos_receivers() is_glatos_receivers() validate_glatos_receivers()
Construct, check, and validate a glatos_receivers object
greatLakesPoly
Deprecated A SpatialPolygonDataFrame with Great Lakes coastline and some major tributaries.
greatLakesTrLayer
A TransitionLayer of the Great Lakes that only prevents transition over land
great_lakes_polygon
An sf POLYGON object with Great Lakes coastline
higgins_lake_polygon
An sf POLYGON object with coastline of Higgins Lake
higgins_lake_transition
A transition object for Higgins Lake for testing make_transition
identify_workbook_version()
Identify and check GLATOS workbook file version
interpolate_path()
Interpolate new positions within a spatiotemporal path data
interval_count()
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.
jarasterize()
Just another rasterizer
kml_to_csv()
KML To CSV Conversion
kml_workbook()
Make a KML or KMZ file of receiver and animal release locations
lamprey_tracks
Sea Lamprey positions from Lake George, St. Marys River, 2012
make_frames()
Create an animated video of spatiotemporal path data
make_transition()
Create transition layer from spatial object.
make_video()
Create video from sequence of still images
min_lag()
Calculate 'min_lag' for identifying potential false positive detections
otn_aat_animals
Example animal data from the OTN ERDDAP
otn_aat_receivers
Example station data from the OTN ERDDAP
otn_aat_tag_releases
Example tag release data from the OTN ERDDAP
point_offset()
Identify new location based on distance and bearing from another
position_heat_map()
Position Heat Maps
prepare_deploy_sheet()
Loads the OTN receiver deployment metadata sheet to prepare it for use in convert_otn_to_att
prepare_tag_sheet()
Loads the OTN tagging metadata sheet to prepare it for use in convert_otn_to_att
range_detection
Detection range data set
raw_lamprey_workbook
Raw GLATOS Workbook from St. Marys River Sea Lamprey project
raw_walleye_detections
Zipped GLATOS detection file from Huron Erie Corridor Walleye project
read_glatos_detections()
Read data from a GLATOS detection file
read_glatos_receivers()
Read data from a GLATOS receiver location file
read_glatos_workbook()
Read data from a GLATOS project workbook
read_otn_deployments()
Read data from a OTN deployment file
read_otn_detections()
Read data from a OTN detection file
read_vdat_csv()
Read data from an Innovasea Fathom VDAT CSV file
read_vemco_tag_specs()
Read telemetry transmitter (tag) specification data from a Vemco file
read_vue_detection_csv()
Read detection data exported from Innovasea VUE software
read_vue_event_csv()
Read receiver event data exported from Innovasea VUE software
read_workbook_project()
Read Project sheet from GLATOS workbook file
real_sensor_values()
Add 'real'-scale sensor values to glatos detetections
receiver_line_det_sim()
Simulate detection of acoustic-tagged fish crossing a receiver line
residence_index()
Generate the residence index from a set of detections
rotate_points()
Rotate points in a 2-d plane
sample_detection_efficiency
Detection Efficiency data set
scale_meters_to_degrees()
Get degree-scale equivalent of meter-scale distance on a spatial object
shoreline
zipped polygon shapefile of Great Lakes
`[`(<vdat_list> )
Subset method for vdat_list that retains attributes
summarize_detections()
Summarize detections by animal, location, or both
total_diff_days()
The function below determines the total days difference.
transmit_along_path()
Simulate telemetry transmitter signals along a path
vdat_convert()
Convert an Innovasea VRL or VDAT file to a Fathom CSV file
vdat_csv_schema
A schema for Innovasea Fathom (VDAT) CSV files
vector_heading()
Calculate direction (heading) of a vector (in degrees)
video-images
Video frames of walleye movements in Lake Huron
vue_convert()
Convert an Innovasea Vemco VRL file to a VUE CSV file
write_vdat_csv()
Write a vdat_list object to disk in Innovasea Fathom VDAT CSV format
