PAMpal (version 1.4.4)

addCalibration: Add a Calibration File to a PAMpalSettings Object

Description

Adds a new calibration function to the "calibration" slot of a PAMpalSettings object. Interactively asks user to supply file and other parameters if not supplied.

Usage

addCalibration(
  pps,
  calFile = NULL,
  module = "ClickDetector",
  calName = NULL,
  all = FALSE,
  units = NULL
)
applyCalibration(pps, module = "ClickDetector", all = FALSE)

Value

the same PAMpalSettings object as pps, with the calibration function added to the calibration slot.

Arguments

pps

a PAMpalSettings object to add a database to

calFile

a calibration file name. Must be csv format with two columns. The first column must be the frequency (in Hz), and the second column must be the sensitivity (in dB), and the columns should be labeled Frequency and Sensitivity. Can also be supplied as a dataframe in which case the calName argument should also be set

module

the Pamguard module type this calibration should be applied to, for now this is only for ClickDetector modules. This is left as an option for future-proofing purposes but should not be needed.

calName

the name to assign to the calibration function, defaults to the file name and only needs to be set if supplying a dataframe instead of a csv file

all

logical flag whether or not to apply calibration to all functions without asking individually, recommended to stay as FALSE

units

a number from 1 to 3 specifying the units of the calibration file, number corresponds to dB re V/uPa, uPa/Counts, or uPa/FullScale respectively. A NULL (default) or other value will prompt user to select units.

Author

Taiki Sakai

Details

When adding a calibration, you will be asked what units your calibration value is in. The wave clips stored by Pamguard are values from -1 to 1, so if your calibration is expecting different units then this needs to be accounted for in order to get an accurate SPL value. For V / uPa you must know the voltage range of your recording equipment, and for calibrations expecting Count data you must know the bit rate of your recordings. If your calibration is already relative to full-scale, then nothing needs to be adjusted. If you don't know the units of your calibration and you are only interested in relative dB levels, then you can select the Full-Scale options.

The calibration function created takes frequency (in Hz) as input and outputs the associated dB value that needs to be added to correct the power spectrum of a signal. If the input is a matrix or dataframe, the first column is assumed to be frequency.

Examples

pps <- new('PAMpalSettings')
calFile <- system.file('extdata', 'calibration.csv', package='PAMpal')
pps <- addCalibration(pps, calFile, all = TRUE, units=3)
calClick <- function(data, calibration=NULL) {
    standardClickCalcs(data, calibration=calibration, filterfrom_khz = 0)
}
pps <- addFunction(pps, calClick, module = 'ClickDetector')
pps <- applyCalibration(pps, all=TRUE)
pps