# Load and Process Passive Acoustic Data

## Documentation for package ‘PAMpal’ version 1.4.4

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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

## -- A --

AcousticEvent-class | 'AcousticEvent' Class
AcousticStudy-class | 'AcousticStudy' Class
addAnnotation | Add Annotation Data to an AcousticStudy Object
addBinaries | Add Binaries to a PAMpalSettings Object
addCalibration | Add a Calibration File to a PAMpalSettings Object
addDatabase | Add a Database to a PAMpalSettings Object
addFPOD | Add FPOD Detector to an AcousticStudy
addFunction | Add a Function to a PAMpalSettings Object
addGps | Add GPS Locations to an AcousticStudy
addGps-method | Add GPS Locations to an AcousticStudy
addHydrophoneDepth | Add Hydrophone Depth Data to an AcousticStudy
addMeasures | Add Measures
addNote | addNote
addRecordings | Add Recordings to an AcousticStudy Object
addSettings | Add Settingss to a PAMpalSettings Object
addWaveHeight | Add Wave Height Data to an AcousticStudy
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

## -- B --

bindStudies | Combine AcousticStudy Objects

## -- C --

calculateAverageSpectra | Calculate Average Spectra of Clicks
calculateEchoDepth | Calculate Depth from Echoes
calculateICI | Calculate Inter-Click Interval
calculateICI-method | Calculate Inter-Click Interval
calculateModuleData | Run Custom Calculations on Pamguard Module Data
checkAnnotation | Add Annotation Data to an AcousticStudy Object
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_annomate | Add Annotation Data to an AcousticStudy Object
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
filterEchoDepths | Filter Candidate Echo Depths

## -- G --

getAnnotation | Add Annotation Data to an AcousticStudy Object
getBinaryData | Get Raw Binary Data for Detections
getCepstrumData | Extract and Combine Detector Data
getClickData | Extract and Combine Detector Data
getClipData | Get Wav Clips of Data
getDetectorData | Extract and Combine Detector Data
getFPODData | Extract and Combine Detector Data
getGPLData | Extract and Combine Detector Data
getICI | Calculate Inter-Click Interval
getMeasures | Add Measures
getNotes | addNote
getWarnings | Get Warning Messages
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 --

loadPamguardXML | Load Pamguard XML Settings
localizations | 'AcousticEvent' and 'AcousticStudy' accessors
localizations-method | 'AcousticEvent' and 'AcousticStudy' accessors
localizations<- | 'AcousticEvent' and 'AcousticStudy' accessors
localizations<--method | 'AcousticEvent' and 'AcousticStudy' accessors

## -- M --

mapWavFolder | Add Recordings to an AcousticStudy Object
markAnnotated | Mark Detections as Annotated
matchEnvData-method | Match Environmental Data to an AcousticStudy Object
matchRecordingUrl | Add Annotation Data to an AcousticStudy Object
matchTimeData | Match time-based data to PAMpal objects
models | 'AcousticEvent' and 'AcousticStudy' accessors
models-method | 'AcousticEvent' and 'AcousticStudy' accessors
models<- | 'AcousticEvent' and 'AcousticStudy' accessors
models<--method | 'AcousticEvent' and 'AcousticStudy' accessors

## -- N --

nCepstrum | Extract and Combine Detector Data
nClicks | Extract and Combine Detector Data
nDetections | Extract and Combine Detector Data
nGPL | Extract and Combine Detector Data
nWhistles | Extract and Combine Detector Data

## -- P --

PAMpal.accessors | 'AcousticEvent' and 'AcousticStudy' accessors
PAMpalSettings | Constructor for PAMpalSettings Object
PAMpalSettings-class | 'PAMpalSettings' Class
parseEventClipName | Create Wav Clips of Data
plotDataExplorer | Explore Data in an Interactive Shiny Plot
plotGram | Plot Spectrogram or Cepstrogram
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
prepAnnotation | Add Annotation Data to an AcousticStudy Object
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
removeNote | removeNote
removeSettings | Remove Settings from a PAMpalSettings Object
roccaWhistleCalcs | Calculate a Set of Measurements for Whistles
runDepthReview | Run Echo Depth Review App
runIciReview | Run ICI Review App

## -- S --

sampleDetector | Subsample Detectors in AcousticStudy
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
summariseDiveDepth | Summarise Dive Depth

## -- T --

testCeps | A fake cepstrum contour
testClick | A two-channel recording of a delphinid click
testGPL | A fake GPL detection
testWhistle | A fake whistle contour
timeJoin | Match time-based data to PAMpal objects

## -- U --

updateFiles | Update Location of Files in an AcousticStudy
updatePamObject | Update PAMpal S4 Object

## -- 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