convert_otn_erddap_to_att: Convert detections, transmitter, receiver, and animal...

In ocean-tracking-network/glatos: A package for the Great Lakes Acoustic Telemetry Observation System

Convert detections, transmitter, receiver, and animal metadata to a format that ATT accepts.

Description

Convert glatos_detections and transmitter, receiver, and animal metadata from the OTN ERDDAP to ATT format for use in the Animal Tracking Toolbox https://github.com/vinayudyawer/ATT, now part of VTrack https://github.com/RossDwyer/VTrack.

Usage

convert_otn_erddap_to_att(
  detectionObj,
  erdTags,
  erdRcv,
  erdAni,
  crs = sf::st_crs(4326)
)

Arguments

detectionObj	A glatos_detections object (e.g., created by read_otn_detections or read_glatos_detections) or a data.frame containing required columns (see glatos_detections).
erdTags	a data frame with tag release data from the OTN ERDDAP
erdRcv	a data frame with receiver station data from the OTN ERDDAP
erdAni	a data frame with animal data from the OTN ERDDAP
crs	an object of class crs (see sf::st_crs) with geographic coordinate system for all spatial information (latitude/longitude). If none provided or crs is not recognized, defaults to WGS84.

Details

This function takes 4 data frames containing detection, and ERDDAP data from the tags, receivers, and animals tables, and transforms them into 3 tibble objects inside of a list. The input that AAT uses to get this data product is located here: https://github.com/vinayudyawer/ATT/blob/master/README.md and our mappings are found here: https://github.com/ocean-tracking-network/glatos/issues/75#issuecomment-982822886 in a comment by Ryan Gosse. The OTN ERDDAP instance is here: https://members.oceantrack.org/erddap/tabledap/index.html but please note that this only contains public data.

Value

a list of 3 tibbles containing tag detections, tag metadata, and station metadata, to be ingested by VTrack/ATT

Author(s)

Ryan Gosse

Examples

#--------------------------------------------------
# EXAMPLE #1 - loading from the OTN ERDDAP + vignettes

library(glatos)

# get path to example files from OTN ERDDAP
ani_erd_file <- system.file("extdata", "otn_aat_animals.csv",
  package = "glatos"
)
animals <- read.csv(ani_erd_file) # load the CSVs from ERDDAP

tags_erd_file <- system.file("extdata", "otn_aat_tag_releases.csv",
  package = "glatos"
)
tags <- read.csv(tags_erd_file)

rcv_erd_file <- system.file("extdata", "otn_aat_receivers.csv",
  package = "glatos"
)
stations <- read.csv(rcv_erd_file)

# Remove first row; (blank or metadata about the column)
animals <- animals[-1, ]
tags <- tags[-1, ]
stations <- stations[-1, ]

# get blue shark example data
shrk_det_file <- system.file("extdata", "blue_shark_detections.csv",
  package = "glatos"
)
blue_shark_detections <- read_otn_detections(shrk_det_file) # load shark data

ATTdata <- convert_otn_erddap_to_att(
  detectionObj = blue_shark_detections,
  erdTags = tags,
  erdRcv = stations,
  erdAni = animals
)

ocean-tracking-network/glatos documentation built on April 17, 2025, 10:38 p.m.