Package: warbleR 1.1.32

warbleR: Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and qunatify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in diferent formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Authors:Marcelo Araya-Salas [aut, cre], Grace Smith-Vidaurre [aut]

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warbleR.pdf |warbleR.html✨
warbleR/json (API)
NEWS

# Install 'warbleR' in R:
install.packages('warbleR', repos = c('https://marce10.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/marce10/warbler/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • comp_matrix - Example matrix listing selections to be compared by 'cross_correlation'
  • lbh_selec_table - Example data frame of selections (i.e. selection table).
  • sim_coor_sing - Simulated coordinated singing events.
  • sth_annotations - Example data frame of annotations from a Scale-throated hermit song (i.e. selection table).

On CRAN:

animal-acoustic-signalsaudio-processingbioacousticsspectrogramstreamline-analysis

11.02 score 53 stars 4 packages 242 scripts 1.1k downloads 6 mentions 65 exports 50 dependencies

Last updated 1 months agofrom:1059c097ad. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-win-x86_64OKNov 14 2024
R-4.5-linux-x86_64OKNov 14 2024
R-4.4-win-x86_64OKNov 14 2024
R-4.4-mac-x86_64OKNov 14 2024
R-4.4-mac-aarch64OKNov 14 2024
R-4.3-win-x86_64OKNov 14 2024
R-4.3-mac-x86_64OKNov 14 2024
R-4.3-mac-aarch64OKNov 14 2024

Exports:by_element_estcatalogcatalog2pdfcheck_selscheck_sound_filescolor_spectrocompare_methodsconsolidatecross_correlationcut_selsduration_sound_filesenvelopeffDTWfilter_selsfind_clippingfix_extended_selection_tablefix_wavsfreq_DTWfreq_rangefreq_range_detecfreq_tsfull_spectrogram2pdffull_spectrogramsgapsimage_to_waveinflectionsinfo_sound_filesis_extended_selection_tableis_selection_tablemake.selection.tablemap_xcmfcc_statsmove_imagesmp32wavmulti_DTWopen_wdoverlapping_selsphylo_spectroplot_coordinationquerxcquery_xcread_sound_fileread_waveremove_channelsremove_silencerename_est_wavesresample_estselection_tablesig2noisesimulate_songssnr_spectrogramssong_analysissort_colmssound_pressure_levelspectro_analysisspectrogramssplit_sound_filestailor_selstest_coordinationtrack_freq_contourtrack_harmonictweak_spectrowarbleR_optionswav_2_flacwpd_features

Dependencies:base64encbioacousticsbitopsbriocallrclicrayondescdiffobjdigestdtwevaluatefastmapfftwfsgluehighrhtmltoolsjsonliteknitrlifecyclemagrittrMASSmomentsmonitoRNatureSoundspbapplypkgbuildpkgloadpraiseprocessxproxypsR6RcppRCurlrjsonrlangrprojrootseewavesignalstringistringrtestthattuneRvctrswaldowithrxfunyaml

Introduction to warbleR

Marcelo Araya-Salas, PhD & Grace Smith-Vidaurre

Rendered froma_warbleR.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-08-29
Started: 2024-08-29

Annotation data format

Marcelo Araya-Salas, PhD

Rendered fromb_annotation_data_format.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-08-29
Started: 2024-08-29

Import sound files and select signals

Marcelo Araya-Salas, PhD & Grace Smith-Vidaurre

Rendered fromc_warbleR_workflow_01.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-08-29
Started: 2024-08-29

Visual inspection and signal classification

Marcelo Araya-Salas, PhD & Grace Smith-Vidaurre

Rendered fromd_warbleR_workflow_02.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-08-29
Started: 2024-08-29

Acoustic (dis)similarity, coordinated singing and simulating songs

Marcelo Araya-Salas, PhD, Grace Smith-Vidaurre

Rendered frome_warbleR_workflow_03.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-08-29
Started: 2024-08-29

Readme and manuals

Help Manual

Help pageTopics
Convert a by-song extended selection table to by-elementby_element_est
Create catalogs of vocal signalscatalog
Combine 'catalog' images into pdfscatalog2pdf
Check selection data framescheck_sels
Check sound filescheck_sound_files
Highlight spectrogram regionscolor_spectro
Example matrix listing selections to be compared by 'cross_correlation'comp_matrix
Assessing the performance of acoustic distance measurementscompare_methods
Consolidate (sound) files into a single directoryconsolidate
Time-frequency cross-correlationcross_correlation
Cut selections into individual sound filescut_sels
Measure the duration of sound filesduration_sound_files
Calculates the absolute amplitude envelopeenvelope
Subset selection data frames based on manually filtered image filesfilter_sels
Find clipped selectionsfind_clipping
Fix extended selection tablesfix_extended_selection_table
Fix .wav files to allow importing them into Rfix_wavs
Acoustic dissimilarity using dynamic time warping on dominant frequency contoursfreq_DTW
Detect frequency range iterativelyfreq_range
Detect frequency range on wave objectsfreq_range_detec
Extract frequency contours as time seriesfreq_ts
'full_spectrogram2pdf' combines 'full_spectrograms' images in .jpeg format to a single pdf file.full_spectrogram2pdf
Create long spectrograms of entire sound filesfull_spectrograms
Gap durationgaps
Convert images into wave objectsimage_to_wave
Count number of inflections in a frequency contourinflections
Get sound file parameter informationinfo_sound_files
Class 'extended_selection_table': selection table containing wave objectsis_extended_selection_table
Class 'selection_table': double-checked frequency/time coordinates of selectionsis_selection_table
Example data frame of selections (i.e. selection table).lbh_selec_table
Maps of 'Xeno-Canto' recordings by speciesmap_xc
Calculate descriptive statistics on Mel-frequency cepstral coefficientsmfcc_stats
Move/copy image files between directoriesmove_images
Convert .mp3 files to .wavmp32wav
A wrapper on 'dtwDist' for comparing multivariate contoursmulti_DTW
Open working directoryopen_wd
Find overlapping selectionsoverlapping_sels
Add spectrograms onto phylogenetic treesphylo_spectro
Coordinated singing graphsplot_coordination
Access 'Xeno-Canto' recordings and metadataquery_xc
An extended version of read_wave that reads several sound file formats and files from selection tablesread_sound_file
A wrapper for tuneR's readWave that read sound files listed within selection tablesread_wave
Remove channels in wave filesremove_channels
Remove silence in wave filesremove_silence
Rename wave objects and associated metadata in extended selection tablesrename_est_waves
Resample wave objects in a extended selection tableresample_est
Create 'selection_table' and 'extended_selection_table' objectsselection_table
Measure signal-to-noise ratiosig2noise
Simulated coordinated singing events.sim_coor_sing
Simulate animal vocalizationssimulate_songs
Spectrograms with background noise marginssnr_spectrograms
Calculates acoustic parameters at the song levelsong_analysis
Sort columns in a more intuitive ordersort_colms
Measure relative sound pressure levelsound_pressure_level
Measure acoustic parameters in batches of sound filesspectro_analysis
Spectrograms of selected signalsspectrograms
Splits sound filessplit_sound_files
Example data frame of annotations from a Scale-throated hermit song (i.e. selection table).sth_annotations
Interactive view of spectrograms to tailor selectionstailor_sels
Randomization test for singing coordinationtest_coordination
Spectrograms with frequency measurementstrack_freq_contour
Track harmonic frequency contourtrack_harmonic
Plot a mosaic of spectrograms with varying display parameterstweak_spectro
Setting warbleR optionswarbleR_options
Convert .wav files to .flacwav_2_flac
Measure wavelet packet decomposition features (EXPERIMENTAL)wpd_features