# Streamline Bioacoustic Analysis

## Documentation for package ‘warbleR’ version 1.1.28

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

auto_detec | 'auto_detec' automatically detects the start and end of vocalizations in sound files based on amplitude, duration, and frequency range attributes.
by_element_est | Convert a by-song extended selection table to by-element
catalog | Create catalogs of vocal signals
catalog2pdf | Combine 'catalog' images into pdfs 'catalog2pdf' combines 'catalog' jpeg images into pdfs
check_sound_files | Check sound files
color_spectro | Highlight spectrogram regions
compare_methods | Assessing the performance of acoustic distance measurements
comp_matrix | Example matrix listing selections to be compared by 'cross_correlation'
consolidate | Consolidate (sound) files into a single directory
cross_correlation | Time-frequency cross-correlation
duration_sound_files | Measure the duration of sound files
envelope | Calculates the absolute amplitude envelope
filter_sels | Subset selection data frames based on manually filtered image files
find_annotations | Obtain annotations from audioblast.org data base
find_clipping | Find clipped selections
find_peaks | Find cross-correlation peaks
fix_extended_selection_table | Fix extended selection tables
fix_wavs | Fix .wav files to allow importing them into R
freq_DTW | Acoustic dissimilarity using dynamic time warping on dominant frequency contours
freq_range | Detect frequency range iteratively
freq_range_detec | Detect frequency range on wave objects
freq_ts | Extract frequency contours as time series
full_spectrogram2pdf | 'full_spectrogram2pdf' combines 'full_spectrograms' images in .jpeg format to a single pdf file.
full_spectrograms | Create long spectrograms of whole sound files
gaps | Gap duration
image_to_wave | Convert images into wave objects
inflections | Count number of inflections in a frequency contour
info_sound_files | Get sound file parameter information
is_extended_selection_table | Class 'extended_selection_table': selection table containing wave objects
is_selection_table | Class 'selection_table': double-checked frequency/time coordinates of selections
lbh_selec_table | Example data frame of selections (i.e. selection table).
lbh_selec_table2 | Example data frame of selections (i.e. selection table).
map_xc | Maps of 'Xeno-Canto' recordings by species
mfcc_stats | Calculate descriptive statistics on Mel-frequency cepstral coefficients
move_imgs | Move/copy image files between directories
mp32wav | Convert .mp3 files to .wav
multi_DTW | A wrapper on 'dtwDist' for comparing multivariate contours
new_function_names | Data frame detailing function name changes
open_wd | Open working directory
optimize_auto_detec | Optimize the detection of signals based on a-priori detections
overlapping_sels | Find overlapping selections
phylo_spectro | Add spectrograms onto phylogenetic trees
plot_coordination | Coordinated singing graphs
query_xc | Access 'Xeno-Canto' recordings and metadata
read_sound_file | An extended version of read_wave that reads several sound file formats and files from selection tables
read_wave | A wrapper for tuneR's readWave that read sound files listed within selection tables
remove_channels | Remove channels in wave files
remove_silence | Remove silence in wave files
rename_est_waves | Rename wave objects and associated metadata in extended selection tables
resample_est | Resample wave objects in a extended selection table
selec.table | Alternative name for 'lbh_selec_table'
selection_table | Create 'selection_table' and 'extended_selection_table' objects
sig2noise | Measure signal-to-noise ratio
simulate_songs | Simulate animal vocalizations
sim_coor_sing | Simulated coordinated singing events.
snr_spectrograms | Spectrograms with background noise margins
song_analysis | Calculates acoustic parameters at the song level
sort_colms | Sort columns in a more intuitive order
sound_pressure_level | Measure relative sound pressure level
spectrograms | Spectrograms of selected signals
spectro_analysis | Measure acoustic parameters in batches of sound files
split_sound_files | Splits sound files
tailor_sels | Interactive view of spectrograms to tailor selections
test_coordination | Randomization test for singing coordination
track_freq_contour | Spectrograms with frequency measurements
try_na | Wrapper for "try" function
tweak_spectro | Plot a mosaic of spectrograms with varying display parameters
warbleR | warbleR: A package to streamline bioacoustic analysis
warbleR_options | Setting warbleR options
wav_2_flac | Convert .wav files to .flac
wpd_features | Measure wavelet packet decomposition features (EXPERIMENTAL)