Package: sonicscrewdriver 0.0.8.9000

Ed Baker

sonicscrewdriver: Bioacoustic Analysis and Publication Tools

Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.

Authors:Ed Baker [aut, cre], Quentin Geissman [ctb]

# Install 'sonicscrewdriver' in R:

install.packages('sonicscrewdriver', repos = c('https://edwbaker.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/edwbaker/sonicscrewdriver/issues

Datasets:

STP - STP: Standard Temperature and Pressure
sheepFrequencyStats - Sheep frequencyStats

On CRAN:

bioacoustics ecoacoustics

7.16 score 6 stars 24 scripts 3.2k downloads 116 exports 43 dependencies

Last updated 21 days agofrom:49d8c37856. Checks:OK: 1 ERROR: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-win	ERROR	Nov 01 2024
R-4.5-linux	ERROR	Nov 01 2024
R-4.4-win	ERROR	Nov 01 2024
R-4.4-mac	ERROR	Nov 01 2024
R-4.3-win	ERROR	Nov 01 2024
R-4.3-mac	ERROR	Nov 01 2024

Exports:ab_diel_traits addProcess addSpectra allChannels annotation audio_filesize audioblast audioblastDownload audiomothConfig audiomothWave autoBandPass bandpass beatComplexity beatSpectrum birdNetAnalyse channels_se circularise concat convert2bytes convert2Celsius convert2degrees convert2dyne_cm2 convert2Fahrenheit convert2Kelvin convert2Pascals convert2radians convert2seconds corWaveMC cutws data2Wave dayPhase daysPhases defaultCluster dielFraction dielHistogram dielLabels dielPlot dielPositions dielRings dolbear dutyCycle emptyDiel emptyYearly entropyStats filterWave frequencySound frequencyStats generateNoise generateTimeMask generateTimeShift getMaad gs_transcribe humanBytes humanTime jitter labelPadding labelReduction maad_acoustic_complexity_index maad_frequency_entropy maad_number_of_peaks maad_spectral_activity maad_spectrogram maad_spectrum maad_temporal_activity maad_temporal_entropy maad_temporal_events maad_temporal_median map2RGB merge_annotations naturalFrequency normalise ntd parseFilename pd_dietrich2004 pd_simple pseudoWave pulse pulseDetection pulseIntervals pythonInstall radarPower radarRange radialPolygon rainfallDetection readAudacityLabels readAudio readBirdNet readRespeaker6 referenceIntensity referencePressure region resonantFrequency sDuration shimmer sort_annotations soundSpeed specStats ste subtractSpectra sweptsine tagWave tSamples typicalVolume tzRot untagWave upsample validateIsWave windowing writeAnnotationWave writeAudacityLabels yearlyFraction yearlyLabels yearlyPlot yearlyPositions zerocross zeroSpectrum

Dependencies:cli colorspace cpp11 data.table fansi farver generics ggplot2 glue gtable hms isoband jsonlite labeling lattice lifecycle lubridate magrittr MASS Matrix mgcv mime munsell nlme pillar pkgconfig R6 rbibutils RColorBrewer Rdpack rlang scales seewave signal stringi suncalc tibble timechange tuneR utf8 vctrs viridisLite withr

Annotations: handling labelled audio data

Rendered fromannotations.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-11-01
Started: 2024-10-31

Managing audio in R

Rendered frommanage_audio.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-03-04
Started: 2024-02-11

SonicScrewdriveR

Rendered fromsonicscrewdriver.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-02-18
Started: 2020-11-18

Using audioBlast with R

Rendered fromaudioblast.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2024-05-12
Started: 2024-02-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
PseudoWave scalar subtraction	-,PseudoWave,numeric-method
Check if two annotations overlap or are continuous	.annotation_check_overlap
Combine annotations helper function	.merge_annotations
Helper function to convert a Wave-like object to scikit-maad spectrogram	.spectrogram_maad_power
Helper function to convert a Wave-like object to scikit-maad spectrum	.spectrum_maad
Allow subsetting a Wave object with a TimeRegion	[,Wave,TimeRegion-method
Numeric multiplication by PseudoWave	*,numeric,PseudoWave-method
PseudoWave scalar manipulation	*,PseudoWave,numeric-method
PseudoWave scalar division	/,PseudoWave,numeric-method
Numeric addition by PseudoWave	+,numeric,PseudoWave-method
PseudoWave scalar addition	+,PseudoWave,numeric-method
Convert text times of day in audioblast traits to numeric values	ab_diel_traits
Add a process to a Tagged Wave or WaveMC object	addProcess addProcess,TaggedWave-method addProcess,TaggedWaveMC-method
Add two spectra from seewave	addSpectra
Apply a function to all channels of a Wave or WaveMC object	allChannels
Create a new Annotation object	annotation
A S4 class for annotations	Annotation-class
Calculated size of raw audio files	audio_filesize
Get data or analyses from audioBlast	audioblast
Download audio files from audioBlast	audioblastDownload
Read AudioMoth configuration file	audiomothConfig
Read AudioMoth metadata from a wave file	audiomothWave
Automatic Band Pass Filter	autoBandPass
Simple bandpass filter	bandpass
Beat spectrum complexity	beatComplexity
Computes a beat spectrum	beatSpectrum
Analyse sound files using BirdNET-Analyzer	birdNetAnalyse
Channels for sound ecology	channels_se
Circularise a dataset	circularise
Concatenate two or more Wave-like objects.	concat concat,TaggedWave-method concat,TaggedWaveMC-method concat,Wave-method concat,WaveMC-method
Convert bits to bytes	convert2bytes
Convert temperature to Celsius	convert2Celsius
Convert angle to degrees	convert2degrees
Convert pressure to dyne per square centimetre	convert2dyne_cm2
Convert temperature to Fahrenheit	convert2Fahrenheit
Convert temperature to Kelvin	convert2Kelvin
Convert pressure to Pascals	convert2Pascals
Convert angle to radians	convert2radians
Convert time to seconds	convert2seconds
Correlate channels in a WaveMC object	corWaveMC
Cut wave by samples	cutws
Convert data into a Wave object	data2Wave
Phase of day	dayPhase
Phases of day	dayPhases
Phases of days	daysPhases
Create Default Cluster for Windowing	defaultCluster
Calculate the fraction of a day given by a value	dielFraction
Diel Histogram	dielHistogram
Generate labels for a diel plot	dielLabels
Create a diel plot	dielPlot
Generate positions of labels for a diel plot	dielPositions
Plot rings on a diel plot	dielRings
Dolbear's law	dolbear
Calculate the duty cycle of a wave	dutyCycle
Create an empty diel plot	emptyDiel
Create an empty yearly plot	emptyYearly
Various measurements of frequency values for a Wave object	entropyStats
Apply a WaveFilter object to a Wave object	filterWave
Get the frequency from wavelength and speed of sound	frequencySound
Various measurements of frequency values for a Wave object	frequencyStats
Add noise to a Wave like object	generateNoise
Generate time masked Wave-like objects	generateTimeMask
Generated time-shifted versions of a Wave-like object	generateTimeShift
Import scikit-maad	getMaad
Google Speech API Transcribe	gs_transcribe
Converts bytes in human readable form	humanBytes
Converts time to human readable form	humanTime
Calculate the jitter in a Wave object	jitter
Pad labels with interval	labelPadding
Combines labels which overlap into single continuous regions	labelReduction
Compute the acoustic complexity index using scikit-maad	maad_acoustic_complexity_index
Compute the frequency entropy using scikit-maad	maad_frequency_entropy
Compute the number of peaks using scikit-maad	maad_number_of_peaks
Compute the spectral activity using scikit-maad	maad_spectral_activity
Compute the frequency entropy using scikit-maad	maad_spectral_entropy
Compute a spectrogram of a sound wave using scikit-maad	maad_spectrogram
Compute a spectrum of a sound wave using scikit-maad	maad_spectrum
Compute the acoustic activity index using scikit-maad	maad_temporal_activity
Compute the temporal entropy using scikit-maad	maad_temporal_entropy
Compute the acoustic event index using scikit-maad	maad_temporal_events
Compute the temporal envelope median using scikit-maad	maad_temporal_median
Map three vectors to RGB	map2RGB
Combine annotations	merge_annotations
Calculate the natural frequency	naturalFrequency
Normalise a Wave object	normalise
Natural Time Domain	ntd
Parse a filename	parseFilename
Pulse detection using Dietrich (2004)	pd_dietrich2004
Simplified pulse detection using Dietrich (2004)	pd_simple
Create a PseudoWave object	pseudoWave
An S4 class to represent a PseudoWave object that is converted to a Wave object when operated on.	PseudoWave-class
Generate a single pulse	pulse
Pulse detection	pulseDetection
Pulse intervals	pulseIntervals
Install sonicscrewdriver Python environment	pythonInstall
The radar equation	radarPower
Radar range	radarRange
Plot a radial polygon	radialPolygon
Rainfall detection	rainfallDetection
Read an Audacity label file	readAudacityLabels
Read an audio file	readAudio
Read output files from BirdNet Analyser	readBirdNet
Read a file from Seeed Studio Respeaker 6 mic array	readRespeaker6
Reference intensity	referenceIntensity
Reference pressure	referencePressure
Specify a region with a file to analyse	region
Calculate the resonant frequency	resonantFrequency
Sample duration	sDuration
Sheep frequencyStats	sheepFrequencyStats
Calculate the shimmer in a Wave object	shimmer
Sort annotations	sort_annotations
Calculate the speed of sound in a medium	soundSpeed
Calculate and plot statistics on a frequency spectrum	specStats
An S4 class to represent a spectrogram from scikit-maad.	spectrogram_maad-class
Short term energy	ste
STP: Standard Temperature and Pressure	STP
Subtract two spectra from seewave	subtractSpectra
Generate a sine sweep	sweptsine
A S4 class for tagged waves	TaggedWave-class
A S4 class for tagged multi-channel waves	TaggedWaveMC-class
Tag a Wave or WaveMC object	tagWave
An S4 class to represent a TimeRegion within a Wave object.	TimeRegion-class
Samples per time period	tSamples
Typical volumes	typicalVolume
Converts a timezone offset into a rotation	tzRot
Untag a TaggedWave or TaggedWaveMC object	untagWave
Upsample a wave	upsample
Check an object is a Wave object	validateIsWave
WaveFilter object for audio filters	WaveFilter-class
Windowing Function for Wave Objects	windowing
Save a time region defined by an Annotation object as a Wave file	writeAnnotationWave
Write an Audacity label file	writeAudacityLabels
Calculate the fraction of a year given by a value	yearlyFraction
Generate labels for a yearly plot	yearlyLabels
Create a yearly plot	yearlyPlot
Generate positions of labels for a yearly plot	yearlyPositions
Identify zero crossings in a Wave object	zerocross
Zero spectrum	zeroSpectrum