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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')

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Version

Install

install.packages('PAMpal')

Monthly Downloads

388

Version

1.2.1

License

GNU General Public License

Maintainer

Taiki Sakai

Last Published

July 11th, 2024

Functions in PAMpal (1.2.1)

addRecordings

Add Recordings to an AcousticStudy Object
addFunction

Add a Function to a PAMpalSettings Object
bindStudies

Combine AcousticStudy Objects
addMeasures

Add Measures
addWaveHeight

Add Wave Height Data to an AcousticStudy
addHydrophoneDepth

Add Hydrophone Depth Data to an AcousticStudy
addGps

Add GPS Locations to an AcousticStudy
filter.AcousticStudy

Filter an AcousticStudy or AcousticEvent Object
checkStudy

Check an AcousticStudy Object for Issues
getBinaryData

Get Raw Binary Data for Detections
calculateModuleData

Run Custom Calculations on Pamguard Module Data
exStudy

Example AcousticStudy Object
export_banter

Export Data for a BANTER Model
calculateEchoDepth

Calculate Depth from Echoes
matchTimeData

Match time-based data to PAMpal objects
is.PAMpalSettings

Check if an Object is a PAMpalSettings
calculateICI

Calculate Inter-Click Interval
loadPamguardXML

Load Pamguard XML Settings
plotDataExplorer

Explore Data in an Interactive Shiny Plot
is.AcousticEvent

Check if an Object is an AcousticEvent
is.AcousticStudy

Check if an Object is an AcousticStudy
matchEnvData,AcousticEvent-method

Match Environmental Data to an AcousticStudy Object
plotWaveform

Plot Graphical Representations of Waveforms
filterEchoDepths

Filter Candidate Echo Depths
removeCalibration

Remove a Calibration Function from a PAMpalSettings Object
markAnnotated

Mark Detections as Annotated
removeDatabase

Remove a Database from a PAMpalSettings Object
plotGram

Plot Spectrogram or Cepstrogram
setSpecies

Set the Species Classification of Events
getDetectorData

Extract and Combine Detector Data
getClipData

Get Wav Clips of Data
removeNote

removeNote
removeFunction

Remove a Function from a PAMpalSettings Object
testCeps

A fake cepstrum contour
testClick

A two-channel recording of a delphinid click
standardCepstrumCalcs

Calculate a Set of Measurements from a Cepstrum Contour
processPgDetections

Load and Process Detections from Pamguard
updateFiles

Update Location of Files in an AcousticStudy
getWarnings

Get Warning Messages
removeBinaries

Remove Binaries from a PAMpalSettings Object
updatePamObject

Update PAMpal S4 Object
standardClickCalcs

Calculate a Set of Measurements for Clicks
roccaWhistleCalcs

Calculate a Set of Measurements for Whistles
summariseDiveDepth

Summarise Dive Depth
testWhistle

A fake whistle contour
runDepthReview

Run Echo Depth Review App
removeSettings

Remove Settings from a PAMpalSettings Object
testGPL

A fake GPL detection
sampleDetector

Subsample Detectors in AcousticStudy
writeEventClips

Create Wav Clips of Data
writeWignerData

Write Wigner Transform Data of Click Detections to Disk
AcousticEvent-class

AcousticEvent Class
addBinaries

Add Binaries to a PAMpalSettings Object
addDatabase

Add a Database to a PAMpalSettings Object
AcousticStudy-class

AcousticStudy Class
addFPOD

Add FPOD Detector to an AcousticStudy
PAMpalSettings-class

PAMpalSettings Class
PAMpalSettings

Constructor for PAMpalSettings Object
addCalibration

Add a Calibration File to a PAMpalSettings Object
addAnnotation

Add Annotation Data to an AcousticStudy Object
PAMpal.accessors

AcousticEvent and AcousticStudy accessors
addSettings

Add Settingss to a PAMpalSettings Object
addNote

addNote
calculateAverageSpectra

Calculate Average Spectra of Clicks