Package: PAMpal 1.5.2

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_1.5.2.tar.gz
PAMpal_1.5.2.zip(r-4.7)PAMpal_1.5.2.zip(r-4.6)PAMpal_1.5.2.zip(r-4.5)
PAMpal_1.5.2.tgz(r-4.6-any)PAMpal_1.5.2.tgz(r-4.5-any)
PAMpal_1.5.2.tar.gz(r-4.7-any)PAMpal_1.5.2.tar.gz(r-4.6-any)
PAMpal_1.5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

Datasets:

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

On CRAN:

5.97 score 11 stars 1 packages 94 scripts 216 downloads 102 exports 106 dependencies

Last updated from:8f800f35cf. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	273
source / vignettes	OK	254
linux-release-x86_64	OK	271
macos-release-arm64	OK	213
macos-oldrel-arm64	OK	204
windows-devel	OK	196
windows-release	OK	176
windows-oldrel	OK	226
wasm-release	OK	140

Exports:addAnnotation addBinaries addCalibration addDatabase addFPOD addFunction addGps addHydrophoneDepth addMeasures addNote addRecordings addSettings addWaveHeight ancillary ancillary<-applyCalibration bindStudies calculateAverageSpectra calculateEchoDepth calculateICI checkAnnotation checkStudy detectors detectors<-effort effort<-events events<-export_annomate export_banter files files<-filterEchoDepths getAnnotation getBinaryData getCepstrumData getClickData getClipData getDetectorData getFPODData getGPLData getICI getMeasures getNotes getWarnings getWhistleData gps gps<-id id<-is.AcousticEvent is.AcousticStudy is.PAMpalSettings loadPamguardXML localizations localizations<-mapWavFolder markAnnotated matchEnvData matchRecordingUrl matchTimeData models models<-nCepstrum nClicks nDetections nGPL nWhistles PAMpalSettings parseEventClipName plotDataExplorer plotGram plotSpectrogram plotWaveform plotWigner pps pps<-prepAnnotation processPgDetections removeBinaries removeCalibration removeDatabase removeFunction removeNote removeSettings roccaWhistleCalcs runDepthReview runIciReview sampleDetector setSpecies settings settings<-species species<-standardCepstrumCalcs standardClickCalcs summariseDiveDepth timeJoin updateFiles updatePamObject writeEventClips writeWignerData

Dependencies:askpass base64enc bit bit64 blob bslib cachem cli codetools commonmark cpp11 crul curl data.table DBI digest dplyr evaluate farver fastmap fftw fontawesome foreach fs future future.apply gam generics geosphere ggplot2 globals glue gtable here highr hoardr htmltools httpcode httpuv httr isoband iterators jquerylib jsonlite knitr labeling later lattice lifecycle listenv lubridate magrittr MASS Matrix memoise mime nanoparquet ncdf4 openssl otel PamBinaries PAMmisc parallelly pillar pkgconfig png promises purrr R6 rappdirs RColorBrewer Rcpp RcppRoll RcppTOML rerddap reticulate rjson rlang rprojroot RSQLite S7 sass scales seewave shiny signal sourcetools stringi stringr suncalc sys tibble tidyr tidyselect timechange triebeard tuneR urltools utf8 vctrs viridisLite withr xfun xml2 xtable yaml

Citation

Development and contributors

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,missing-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