Learn R Programming

PAMpal

Welcome! The tutorial has moved to here.

Please reach out if you have any issues taiki.sakai@noaa.gov.

Installation Guide

PAMpal is available on CRAN and can be installed with

install.packages('PAMpal')

A more recent development version may be available on GitHub, and can be installed with

devtools::install_github('TaikiSan21/PAMpal')

Copy Link

Version

Install

install.packages('PAMpal')

Monthly Downloads

373

Version

1.4.4

License

GNU General Public License

Maintainer

Taiki Sakai

Last Published

March 4th, 2025

Functions in PAMpal (1.4.4)

addGps

Add GPS Locations to an AcousticStudy
getBinaryData

Get Raw Binary Data for Detections
calculateAverageSpectra

Calculate Average Spectra of Clicks
addWaveHeight

Add Wave Height Data to an AcousticStudy
addNote

addNote
calculateModuleData

Run Custom Calculations on Pamguard Module Data
calculateICI

Calculate Inter-Click Interval
is.AcousticEvent

Check if an Object is an AcousticEvent
filter.AcousticStudy

Filter an AcousticStudy or AcousticEvent Object
getClipData

Get Wav Clips of Data
matchTimeData

Match time-based data to PAMpal objects
matchEnvData,AcousticEvent-method

Match Environmental Data to an AcousticStudy Object
checkStudy

Check an AcousticStudy Object for Issues
markAnnotated

Mark Detections as Annotated
filterEchoDepths

Filter Candidate Echo Depths
export_banter

Export Data for a BANTER Model
runDepthReview

Run Echo Depth Review App
is.AcousticStudy

Check if an Object is an AcousticStudy
plotDataExplorer

Explore Data in an Interactive Shiny Plot
calculateEchoDepth

Calculate Depth from Echoes
standardClickCalcs

Calculate a Set of Measurements for Clicks
plotGram

Plot Spectrogram or Cepstrogram
removeSettings

Remove Settings from a PAMpalSettings Object
removeCalibration

Remove a Calibration Function from a PAMpalSettings Object
roccaWhistleCalcs

Calculate a Set of Measurements for Whistles
exStudy

Example AcousticStudy Object
removeDatabase

Remove a Database from a PAMpalSettings Object
standardCepstrumCalcs

Calculate a Set of Measurements from a Cepstrum Contour
removeFunction

Remove a Function from a PAMpalSettings Object
removeNote

removeNote
is.PAMpalSettings

Check if an Object is a PAMpalSettings
loadPamguardXML

Load Pamguard XML Settings
getDetectorData

Extract and Combine Detector Data
addRecordings

Add Recordings to an AcousticStudy Object
getWarnings

Get Warning Messages
writeWignerData

Write Wigner Transform Data of Click Detections to Disk
updatePamObject

Update PAMpal S4 Object
writeEventClips

Create Wav Clips of Data
processPgDetections

Load and Process Detections from Pamguard
runIciReview

Run ICI Review App
setSpecies

Set the Species Classification of Events
summariseDiveDepth

Summarise Dive Depth
removeBinaries

Remove Binaries from a PAMpalSettings Object
sampleDetector

Subsample Detectors in AcousticStudy
testCeps

A fake cepstrum contour
testClick

A two-channel recording of a delphinid click
plotWaveform

Plot Graphical Representations of Waveforms
updateFiles

Update Location of Files in an AcousticStudy
testWhistle

A fake whistle contour
testGPL

A fake GPL detection
AcousticEvent-class

AcousticEvent Class
PAMpal.accessors

AcousticEvent and AcousticStudy accessors
PAMpalSettings-class

PAMpalSettings Class
AcousticStudy-class

AcousticStudy Class
addBinaries

Add Binaries to a PAMpalSettings Object
PAMpalSettings

Constructor for PAMpalSettings Object
addAnnotation

Add Annotation Data to an AcousticStudy Object
addDatabase

Add a Database to a PAMpalSettings Object
addFPOD

Add FPOD Detector to an AcousticStudy
addCalibration

Add a Calibration File to a PAMpalSettings Object
addSettings

Add Settingss to a PAMpalSettings Object
bindStudies

Combine AcousticStudy Objects
addFunction

Add a Function to a PAMpalSettings Object
addMeasures

Add Measures
addHydrophoneDepth

Add Hydrophone Depth Data to an AcousticStudy