Skip to contents

Convert detections, tagging metadata, and deployment metadata to a format that ATT accepts.

Source: R/util-convert_otn_to_att.r
convert_otn_to_att.Rd

Convert glatos_detections, OTN tagging metadata and OTN deployment metadata 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_to_att(
  detectionObj,
  taggingSheet,
  deploymentObj = NULL,
  deploymentSheet = NULL,
  timeFilter = TRUE,
  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).

taggingSheet

a data frame from prepare_tag_sheet

deploymentObj

a data frame from read_otn_deployments

deploymentSheet

a data frame from prepare_deploy_sheet

timeFilter

Whether the data should be filtered using the deployment and recovery/last download times of receivers. Defaults to TRUE, if not all receiver metadata is available, this should be set to FALSE otherwise there will be data loss.

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.

Value

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

Details

This function takes 3 data frames containing detections, tagging metadata, and deployment metadata from either read_otn_deployments or prepare_deploy_sheet 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.

Author

Ryan Gosse

Examples

if (FALSE) { # \dontrun{
#--------------------------------------------------
# EXAMPLE #1 - loading from Deployment Object

library(glatos)

dets_path <- system.file("extdata", "blue_shark_detections.csv",
  package = "glatos"
)
deploy_path <- system.file("extdata", "hfx_deployments.csv",
  package = "glatos"
)
tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls",
  package = "glatos"
)

dets <- read_otn_detections(dets_path)
tags <- prepare_tag_sheet(tag_path, 5, 2)
deploy <- read_otn_deployments(deploy_path)

ATTdata <- convert_otn_to_att(dets, tags, deploymentObj = deploy)

#--------------------------------------------------
# EXAMPLE #2 - loading from Deployment Sheet

library(glatos)

dets_path <- system.file("extdata", "blue_shark_detections_old.csv",
  package = "glatos"
)
deploy_path <- system.file("extdata", "hfx_deploy_simplified.xlsx",
  package = "glatos"
)
tag_path <- system.file("extdata", "otn_nsbs_tag_metadata.xls",
  package = "glatos"
)

dets <- read_otn_detections(dets_path, format = "old")
tags <- prepare_tag_sheet(tag_path, 5, 2)
deploy <- prepare_deploy_sheet(deploy_path, 1, 1)

ATTdata <- convert_otn_to_att(dets, tags, deploymentSheet = deploy)
} # }