Package: PAMpal 1.4.2

Taiki Sakai

PAMpal: Load and Process Passive Acoustic Data

Tools for loading and processing passive acoustic data. Read in data that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite processing functions, and export data for reports or external modeling tools. Parameter calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>, Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010) <doi:10.1121/1.3479549>.

Authors:Taiki Sakai [aut, cre], Jay Barlow [ctb], Emily Griffiths [ctb], Michael Oswald [ctb], Simone Baumann-Pickering [ctb], Julie Oswald [ctb]

PAMpal_1.4.2.tar.gz
PAMpal_1.4.2.zip(r-4.5)PAMpal_1.4.2.zip(r-4.4)PAMpal_1.4.2.zip(r-4.3)
PAMpal_1.4.2.tgz(r-4.4-any)PAMpal_1.4.2.tgz(r-4.3-any)
PAMpal_1.4.2.tar.gz(r-4.5-noble)PAMpal_1.4.2.tar.gz(r-4.4-noble)
PAMpal_1.4.2.tgz(r-4.4-emscripten)PAMpal_1.4.2.tgz(r-4.3-emscripten)
PAMpal.pdf |PAMpal.html
PAMpal/json (API)
NEWS

# Install 'PAMpal' in R:
install.packages('PAMpal', repos = c('https://taikisan21.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/taikisan21/pampal/issues

Datasets:

On CRAN:

5.95 score 9 stars 80 scripts 308 downloads 102 exports 111 dependencies

Last updated 9 days agofrom:996359b788. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-winOKOct 28 2024
R-4.5-linuxOKOct 28 2024
R-4.4-winOKOct 28 2024
R-4.4-macOKOct 28 2024
R-4.3-winOKOct 28 2024
R-4.3-macOKOct 28 2024

Exports:addAnnotationaddBinariesaddCalibrationaddDatabaseaddFPODaddFunctionaddGpsaddHydrophoneDepthaddMeasuresaddNoteaddRecordingsaddSettingsaddWaveHeightancillaryancillary<-applyCalibrationbindStudiescalculateAverageSpectracalculateEchoDepthcalculateICIcheckAnnotationcheckStudydetectorsdetectors<-efforteffort<-eventsevents<-export_annomateexport_banterfilesfiles<-filterEchoDepthsgetAnnotationgetBinaryDatagetCepstrumDatagetClickDatagetClipDatagetDetectorDatagetFPODDatagetGPLDatagetICIgetMeasuresgetNotesgetWarningsgetWhistleDatagpsgps<-idid<-is.AcousticEventis.AcousticStudyis.PAMpalSettingsloadPamguardXMLlocalizationslocalizations<-mapWavFoldermarkAnnotatedmatchEnvDatamatchRecordingUrlmatchTimeDatamodelsmodels<-nCepstrumnClicksnDetectionsnGPLnWhistlesPAMpalSettingsparseEventClipNameplotDataExplorerplotGramplotSpectrogramplotWaveformplotWignerppspps<-prepAnnotationprocessPgDetectionsremoveBinariesremoveCalibrationremoveDatabaseremoveFunctionremoveNoteremoveSettingsroccaWhistleCalcsrunDepthReviewrunIciReviewsampleDetectorsetSpeciessettingssettings<-speciesspecies<-standardCepstrumCalcsstandardClickCalcssummariseDiveDepthtimeJoinupdateFilesupdatePamObjectwriteEventClipswriteWignerData

Dependencies:askpassbase64encbitbit64blobbslibcachemclicodetoolscolorspacecommonmarkcpp11crayoncrulcurldata.tableDBIdigestdplyrevaluatefansifarverfastmapfftwfontawesomeforeachfsfuturefuture.applygamgenericsgeosphereggplot2globalsgluegtableherehighrhoardrhtmltoolshttpcodehttpuvhttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelifecyclelistenvlubridatemagrittrMASSMatrixmemoisemgcvmimemunsellncdf4nlmeopensslPamBinariesPAMmiscparallellypillarpkgconfigplogrpngpromisespurrrR6rappdirsRColorBrewerRcppRcppRollRcppTOMLrerddapreticulaterjsonrlangrprojrootRSQLitesassscalesseewaveshinysignalsourcetoolsspstringistringrsuncalcsystibbletidyrtidyselecttimechangetriebeardtuneRurltoolsutf8vctrsviridisLitewithrxfunxml2xtableyaml

Readme and manuals

Help Manual

Help pageTopics
'AcousticEvent' ClassAcousticEvent-class
'AcousticStudy' ClassAcousticStudy-class
Add Annotation Data to an AcousticStudy ObjectaddAnnotation checkAnnotation export_annomate getAnnotation matchRecordingUrl prepAnnotation
Add Binaries to a PAMpalSettings ObjectaddBinaries
Add a Calibration File to a PAMpalSettings ObjectaddCalibration applyCalibration
Add a Database to a PAMpalSettings ObjectaddDatabase
Add FPOD Detector to an AcousticStudyaddFPOD
Add a Function to a PAMpalSettings ObjectaddFunction
Add GPS Locations to an AcousticStudyaddGps addGps,AcousticEvent-method addGps,AcousticStudy-method addGps,ANY-method addGps,data.frame-method addGps,list-method
Add Hydrophone Depth Data to an AcousticStudyaddHydrophoneDepth
Add MeasuresaddMeasures getMeasures
addNoteaddNote getNotes
Add Recordings to an AcousticStudy ObjectaddRecordings mapWavFolder
Add Settingss to a PAMpalSettings ObjectaddSettings
Add Wave Height Data to an AcousticStudyaddWaveHeight
Combine AcousticStudy ObjectsbindStudies
Calculate Average Spectra of ClickscalculateAverageSpectra
Calculate Depth from EchoescalculateEchoDepth
Calculate Inter-Click IntervalcalculateICI calculateICI,AcousticEvent-method calculateICI,AcousticStudy-method getICI
Run Custom Calculations on Pamguard Module DatacalculateModuleData
Check an AcousticStudy Object for IssuescheckStudy
Export Data for a BANTER Modelexport_banter
Example AcousticStudy ObjectexStudy
Filter an AcousticStudy or AcousticEvent Objectfilter.AcousticStudy
Filter Candidate Echo DepthsfilterEchoDepths
Get Raw Binary Data for DetectionsgetBinaryData
Get Wav Clips of DatagetClipData
Extract and Combine Detector DatagetCepstrumData getClickData getDetectorData getFPODData getGPLData getWhistleData nCepstrum nClicks nDetections nGPL nWhistles
Get Warning MessagesgetWarnings
Check if an Object is an AcousticEventis.AcousticEvent
Check if an Object is an AcousticStudyis.AcousticStudy
Check if an Object is a PAMpalSettingsis.PAMpalSettings
Load Pamguard XML SettingsloadPamguardXML
Mark Detections as AnnotatedmarkAnnotated
Match Environmental Data to an AcousticStudy ObjectmatchEnvData,AcousticEvent-method matchEnvData,AcousticStudy-method
Match time-based data to PAMpal objectsmatchTimeData timeJoin
'AcousticEvent' and 'AcousticStudy' accessors$,AcousticEvent-method $,AcousticStudy-method $<-,AcousticEvent-method $<-,AcousticStudy-method ancillary ancillary,AcousticEvent-method ancillary,AcousticStudy-method ancillary<- ancillary<-,AcousticEvent-method ancillary<-,AcousticStudy-method detectors detectors,AcousticEvent-method detectors,AcousticStudy-method detectors<- detectors<-,AcousticEvent-method effort effort,AcousticStudy-method effort<- effort<-,AcousticStudy-method events events,AcousticStudy-method events<- events<-,AcousticStudy-method files files,AcousticEvent-method files,AcousticStudy-method files<- files<-,AcousticEvent-method files<-,AcousticStudy-method gps gps,AcousticStudy-method gps<- gps<-,AcousticStudy-method id id,AcousticEvent-method id,AcousticStudy-method id<- id<-,AcousticEvent-method id<-,AcousticStudy-method localizations localizations,AcousticEvent-method localizations<- localizations<-,AcousticEvent-method models models,AcousticStudy-method models<- models<-,AcousticStudy-method PAMpal.accessors pps pps,AcousticStudy-method pps<- pps<-,AcousticStudy-method settings settings,AcousticEvent-method settings,AcousticStudy-method settings<- settings<-,AcousticEvent-method settings<-,AcousticStudy-method species species,AcousticEvent-method species,AcousticStudy-method species<- species<-,AcousticEvent-method [,AcousticEvent,ANY,ANY,ANY-method [,AcousticStudy,ANY,ANY,ANY-method [<-,AcousticEvent,ANY,ANY,ANY-method [<-,AcousticStudy,ANY,ANY,ANY-method [[,AcousticEvent,ANY,ANY-method [[,AcousticStudy,ANY,ANY-method [[<-,AcousticEvent,ANY,ANY,ANY-method [[<-,AcousticStudy,ANY,ANY,ANY-method
Constructor for PAMpalSettings ObjectPAMpalSettings
'PAMpalSettings' ClassPAMpalSettings-class
Explore Data in an Interactive Shiny PlotplotDataExplorer
Plot Spectrogram or CepstrogramplotGram
Plot Graphical Representations of WaveformsplotSpectrogram plotWaveform plotWigner
Load and Process Detections from PamguardprocessPgDetections
Remove Binaries from a PAMpalSettings ObjectremoveBinaries
Remove a Calibration Function from a PAMpalSettings ObjectremoveCalibration
Remove a Database from a PAMpalSettings ObjectremoveDatabase
Remove a Function from a PAMpalSettings ObjectremoveFunction
removeNoteremoveNote
Remove Settings from a PAMpalSettings ObjectremoveSettings
Calculate a Set of Measurements for WhistlesroccaWhistleCalcs
Run Echo Depth Review ApprunDepthReview
Run ICI Review ApprunIciReview
Subsample Detectors in AcousticStudysampleDetector
Set the Species Classification of EventssetSpecies
Calculate a Set of Measurements from a Cepstrum ContourstandardCepstrumCalcs
Calculate a Set of Measurements for ClicksstandardClickCalcs
Summarise Dive DepthsummariseDiveDepth
A fake cepstrum contourtestCeps
A two-channel recording of a delphinid clicktestClick
A fake GPL detectiontestGPL
A fake whistle contourtestWhistle
Update Location of Files in an AcousticStudyupdateFiles
Update PAMpal S4 ObjectupdatePamObject
Create Wav Clips of DataparseEventClipName writeEventClips
Write Wigner Transform Data of Click Detections to DiskwriteWignerData