Package: PAMpal 1.4.2
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:
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')) |
Bug tracker:https://github.com/taikisan21/pampal/issues
- exStudy - Example AcousticStudy Object
- testCeps - A fake cepstrum contour
- testClick - A two-channel recording of a delphinid click
- testGPL - A fake GPL detection
- testWhistle - A fake whistle contour
Last updated 9 days agofrom:996359b788. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 28 2024 |
R-4.5-win | OK | Oct 28 2024 |
R-4.5-linux | OK | Oct 28 2024 |
R-4.4-win | OK | Oct 28 2024 |
R-4.4-mac | OK | Oct 28 2024 |
R-4.3-win | OK | Oct 28 2024 |
R-4.3-mac | OK | Oct 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 page | Topics |
---|---|
'AcousticEvent' Class | AcousticEvent-class |
'AcousticStudy' Class | AcousticStudy-class |
Add Annotation Data to an AcousticStudy Object | addAnnotation checkAnnotation export_annomate getAnnotation matchRecordingUrl prepAnnotation |
Add Binaries to a PAMpalSettings Object | addBinaries |
Add a Calibration File to a PAMpalSettings Object | addCalibration applyCalibration |
Add a Database to a PAMpalSettings Object | addDatabase |
Add FPOD Detector to an AcousticStudy | addFPOD |
Add a Function to a PAMpalSettings Object | addFunction |
Add GPS Locations to an AcousticStudy | addGps addGps,AcousticEvent-method addGps,AcousticStudy-method addGps,ANY-method addGps,data.frame-method addGps,list-method |
Add Hydrophone Depth Data to an AcousticStudy | addHydrophoneDepth |
Add Measures | addMeasures getMeasures |
addNote | addNote getNotes |
Add Recordings to an AcousticStudy Object | addRecordings mapWavFolder |
Add Settingss to a PAMpalSettings Object | addSettings |
Add Wave Height Data to an AcousticStudy | addWaveHeight |
Combine AcousticStudy Objects | bindStudies |
Calculate Average Spectra of Clicks | calculateAverageSpectra |
Calculate Depth from Echoes | calculateEchoDepth |
Calculate Inter-Click Interval | calculateICI calculateICI,AcousticEvent-method calculateICI,AcousticStudy-method getICI |
Run Custom Calculations on Pamguard Module Data | calculateModuleData |
Check an AcousticStudy Object for Issues | checkStudy |
Export Data for a BANTER Model | export_banter |
Example AcousticStudy Object | exStudy |
Filter an AcousticStudy or AcousticEvent Object | filter.AcousticStudy |
Filter Candidate Echo Depths | filterEchoDepths |
Get Raw Binary Data for Detections | getBinaryData |
Get Wav Clips of Data | getClipData |
Extract and Combine Detector Data | getCepstrumData getClickData getDetectorData getFPODData getGPLData getWhistleData nCepstrum nClicks nDetections nGPL nWhistles |
Get Warning Messages | getWarnings |
Check if an Object is an AcousticEvent | is.AcousticEvent |
Check if an Object is an AcousticStudy | is.AcousticStudy |
Check if an Object is a PAMpalSettings | is.PAMpalSettings |
Load Pamguard XML Settings | loadPamguardXML |
Mark Detections as Annotated | markAnnotated |
Match Environmental Data to an AcousticStudy Object | matchEnvData,AcousticEvent-method matchEnvData,AcousticStudy-method |
Match time-based data to PAMpal objects | matchTimeData 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 Object | PAMpalSettings |
'PAMpalSettings' Class | PAMpalSettings-class |
Explore Data in an Interactive Shiny Plot | plotDataExplorer |
Plot Spectrogram or Cepstrogram | plotGram |
Plot Graphical Representations of Waveforms | plotSpectrogram plotWaveform plotWigner |
Load and Process Detections from Pamguard | processPgDetections |
Remove Binaries from a PAMpalSettings Object | removeBinaries |
Remove a Calibration Function from a PAMpalSettings Object | removeCalibration |
Remove a Database from a PAMpalSettings Object | removeDatabase |
Remove a Function from a PAMpalSettings Object | removeFunction |
removeNote | removeNote |
Remove Settings from a PAMpalSettings Object | removeSettings |
Calculate a Set of Measurements for Whistles | roccaWhistleCalcs |
Run Echo Depth Review App | runDepthReview |
Run ICI Review App | runIciReview |
Subsample Detectors in AcousticStudy | sampleDetector |
Set the Species Classification of Events | setSpecies |
Calculate a Set of Measurements from a Cepstrum Contour | standardCepstrumCalcs |
Calculate a Set of Measurements for Clicks | standardClickCalcs |
Summarise Dive Depth | summariseDiveDepth |
A fake cepstrum contour | testCeps |
A two-channel recording of a delphinid click | testClick |
A fake GPL detection | testGPL |
A fake whistle contour | testWhistle |
Update Location of Files in an AcousticStudy | updateFiles |
Update PAMpal S4 Object | updatePamObject |
Create Wav Clips of Data | parseEventClipName writeEventClips |
Write Wigner Transform Data of Click Detections to Disk | writeWignerData |