calibrate_tdr: Calibrate CEFAS data

In mczapanskiy-usgs/pfsh.dive: Analysis of Pink-footed Shearwater Diving Behavior

Description

calibrate_tdr is a wrapper for calibrateDepth. CEFAS tags record depth in bursts, so this function uses a split-apply-combine approach to calibrate each FastLog individually. Tags have an error of +/-1m, so for shallow diving birds the error may be greater than the depth of the dive. To avoid losing these dives, the "surface" is assumed to be at the shallowest point in each FastLog, not at 0. For tags with a 1m threshold, this may bias dive depths shallower.

Usage

calibrate_tdr(tdr, deployid, rate = 0.1, surface_thr = 0.1,
  depth_thr = 0.2, dur_thr = 0.5)

Arguments

tdr	data.frame. Use read_cefas to parse CEFAS file.
deployid	character. Deployment identifier.
rate	numeric. Sampling rate for FastLog events.
surface_thr	numeric. Threshold for surface noise.
depth_thr	numeric. Minimum depth to qualify as a dive.
dur_thr	numeric. Minimum duration to qualify as a dive.

Value

data.frame with columns

• Row (Row number in original CEFAS file)

• UTC (Datetime of record in UTC timezone)

• Pressure

• EventID (FastLog identifier)

• CalibPressure (Pressure after surface offset)

• Surface (Surface offset)

• DivePhase (From diveMove)

• duration

• depth

• DiveID

• DeployID

Examples

# Load metadata
metadata_path <- system.file('extdata',
                             'MOC2015PFSHmetadata.csv',
                             package = 'pfsh.dive')
metadata <- readr::read_csv(metadata_path)

# Read CEFAS output
tdr_path <- system.file('extdata',
                         paste0(metadata$TDR_filename[1], '.CSV'),
                         package = 'pfsh.dive')
tdr <- read_cefas(tdr_path,
                  metadata$Deployed[1],
                  metadata$Recovered[1])

# Calibrate TDR data
calib_tdr <- calibrate_tdr(tdr, metadata$DeployID[1])

mczapanskiy-usgs/pfsh.dive documentation built on May 26, 2019, 5:42 p.m.