Load and Process Passive Acoustic Data
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Documentation for package ‘PAMpal’ version 1.4.4
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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 |