# Load and Process Passive Acoustic Data

## Documentation for package ‘PAMpal’ version 0.9.14

- DESCRIPTION file.

## Help Pages

A C D E F G I L M P R S T U W misc

## -- A --

AcousticEvent-class | 'AcousticEvent' Class
AcousticStudy-class | 'AcousticStudy' Class
addBinaries | Add Binaries to a PAMpalSettings Object
addCalibration | Add a Calibration File to a PAMpalSettings Object
addDatabase | Add a Database to a PAMpalSettings Object
addFunction | Add a Function to a PAMpalSettings Object
addGps | Add GPS Locations to an AcousticStudy
addGps-method | Add GPS Locations to an AcousticStudy
addRecordings | Add Recordings to an AcousticStudy Object
ancillary | 'AcousticEvent' and 'AcousticStudy' accessors
ancillary-method | 'AcousticEvent' and 'AcousticStudy' accessors
ancillary<- | 'AcousticEvent' and 'AcousticStudy' accessors
ancillary<--method | 'AcousticEvent' and 'AcousticStudy' accessors
applyCalibration | Add a Calibration File to a PAMpalSettings Object

## -- C --

calculateAverageSpectra | Calculate Average Spectra of Clicks
calculateICI | Calculate Inter-Click Interval
calculateICI-method | Calculate Inter-Click Interval
calculateModuleData | Run Custom Calculations on Pamguard Module Data
checkStudy | Check an AcousticStudy Object for Issues

## -- D --

detectors | 'AcousticEvent' and 'AcousticStudy' accessors
detectors-method | 'AcousticEvent' and 'AcousticStudy' accessors
detectors<- | 'AcousticEvent' and 'AcousticStudy' accessors
detectors<--method | 'AcousticEvent' and 'AcousticStudy' accessors

## -- E --

effort | 'AcousticEvent' and 'AcousticStudy' accessors
effort-method | 'AcousticEvent' and 'AcousticStudy' accessors
effort<- | 'AcousticEvent' and 'AcousticStudy' accessors
effort<--method | 'AcousticEvent' and 'AcousticStudy' accessors
events | 'AcousticEvent' and 'AcousticStudy' accessors
events-method | 'AcousticEvent' and 'AcousticStudy' accessors
events<- | 'AcousticEvent' and 'AcousticStudy' accessors
events<--method | 'AcousticEvent' and 'AcousticStudy' accessors
export_banter | Export Data for a BANTER Model
exStudy | Example AcousticStudy Object

## -- F --

files | 'AcousticEvent' and 'AcousticStudy' accessors
files-method | 'AcousticEvent' and 'AcousticStudy' accessors
files<- | 'AcousticEvent' and 'AcousticStudy' accessors
files<--method | 'AcousticEvent' and 'AcousticStudy' accessors
filter.AcousticStudy | Filter an AcousticStudy or AcousticEvent Object

## -- G --

getBinaryData | Get Raw Binary Data for Detections
getCepstrumData | Extract and Combine Detector Data
getClickData | Extract and Combine Detector Data
getDetectorData | Extract and Combine Detector Data
getICI | Calculate Inter-Click Interval
getWhistleData | Extract and Combine Detector Data
gps | 'AcousticEvent' and 'AcousticStudy' accessors
gps-method | 'AcousticEvent' and 'AcousticStudy' accessors
gps<- | 'AcousticEvent' and 'AcousticStudy' accessors
gps<--method | 'AcousticEvent' and 'AcousticStudy' accessors

## -- I --

id | 'AcousticEvent' and 'AcousticStudy' accessors
id-method | 'AcousticEvent' and 'AcousticStudy' accessors
id<- | 'AcousticEvent' and 'AcousticStudy' accessors
id<--method | 'AcousticEvent' and 'AcousticStudy' accessors
is.AcousticEvent | Check if an Object is an AcousticEvent
is.AcousticStudy | Check if an Object is an AcousticStudy
is.PAMpalSettings | Check if an Object is a PAMpalSettings

## -- L --

localizations | 'AcousticEvent' and 'AcousticStudy' accessors
localizations-method | 'AcousticEvent' and 'AcousticStudy' accessors
localizations<- | 'AcousticEvent' and 'AcousticStudy' accessors
localizations<--method | 'AcousticEvent' and 'AcousticStudy' accessors

## -- M --

matchEnvData-method | Match Environmental Data to an AcousticStudy Object
models | 'AcousticEvent' and 'AcousticStudy' accessors
models-method | 'AcousticEvent' and 'AcousticStudy' accessors
models<- | 'AcousticEvent' and 'AcousticStudy' accessors
models<--method | 'AcousticEvent' and 'AcousticStudy' accessors

## -- P --

PAMpal.accessors | 'AcousticEvent' and 'AcousticStudy' accessors
PAMpalSettings | Constructor for PAMpalSettings Object
PAMpalSettings-class | 'PAMpalSettings' Class
plotDataExplorer | Explore Data in an Interactive Plot
plotSpectrogram | Plot Graphical Representations of Waveforms
plotWaveform | Plot Graphical Representations of Waveforms
plotWigner | Plot Graphical Representations of Waveforms
pps | 'AcousticEvent' and 'AcousticStudy' accessors
pps-method | 'AcousticEvent' and 'AcousticStudy' accessors
pps<- | 'AcousticEvent' and 'AcousticStudy' accessors
pps<--method | 'AcousticEvent' and 'AcousticStudy' accessors
processPgDetections | Load and Process Detections from Pamguard

## -- R --

removeBinaries | Remove Binaries from a PAMpalSettings Object
removeCalibration | Remove a Calibration Function from a PAMpalSettings Object
removeDatabase | Remove a Database from a PAMpalSettings Object
removeFunction | Remove a Function from a PAMpalSettings Object
roccaWhistleCalcs | Calculate a Set of Measurements for Whistles

## -- S --

setSpecies | Set the Species Classification of Events
settings | 'AcousticEvent' and 'AcousticStudy' accessors
settings-method | 'AcousticEvent' and 'AcousticStudy' accessors
settings<- | 'AcousticEvent' and 'AcousticStudy' accessors
settings<--method | 'AcousticEvent' and 'AcousticStudy' accessors
species | 'AcousticEvent' and 'AcousticStudy' accessors
species-method | 'AcousticEvent' and 'AcousticStudy' accessors
species<- | 'AcousticEvent' and 'AcousticStudy' accessors
species<--method | 'AcousticEvent' and 'AcousticStudy' accessors
standardCepstrumCalcs | Calculate a Set of Measurements from a Cepstrum Contour
standardClickCalcs | Calculate a Set of Measurements for Clicks

## -- T --

testCeps | A fake cepstrum contour
testClick | A two-channel recording of a delphinid click
testWhistle | A fake whistle contour

## -- U --

updateFiles | Update Location of Files in an AcousticStudy

## -- W --

writeEventClips | Create Wav Clips of Data
writeWignerData | Write Wigner Transform Data of Click Detections to Disk

## -- misc --

$-method | 'AcousticEvent' and 'AcousticStudy' accessors
$<--method | 'AcousticEvent' and 'AcousticStudy' accessors
[-method | 'AcousticEvent' and 'AcousticStudy' accessors
[<--method | 'AcousticEvent' and 'AcousticStudy' accessors
[[-method | 'AcousticEvent' and 'AcousticStudy' accessors
[[<--method | 'AcousticEvent' and 'AcousticStudy' accessors