Changelog • warbleR

warbleR 1.1.31

Changes and additions:

new vignette ‘Annotation data format’
confirm.extended argument in selection_table() has been deprecated.
song_param() alternative name for song_analysis() has been deprecated.

warbleR 1.1.30

CRAN release: 2024-01-23

Changes and additions:

gaps() now turns negative numbers (from overlapping annotations) into 0’s
error message added to simulate_songs() if negative numbers in ‘gaps’ are found

Bug fixes:

quer_xc() bug for searching on windows and macOS
spectro_analysis() bug when ‘harmonicity = TRUE’ due to changes in soundgen::analyze() output names
print.selection_table() now checks for possible errors in check_res() metadata
bug fixed in multi_DTW() when measuring contours other than dominant frequency

warbleR 1.1.29

CRAN release: 2023-09-05

Changes and additions:

full_spectrograms() new argument ‘only.annotated’ to only print pages that contain annotations.
New method (‘time.closest’) in test_coordination() which estimate coordination between more than 2 individuals
Default value of ‘confirm.extended’ argument in selection_table() set to FALSE. Will be deprecated in future versions.

warbleR 1.1.28

CRAN release: 2022-12-09

Changes and additions:

Warning messages in check_sels() and check_sound_files() when having sound files/wave objects with different sampling rates
Fix bug in file size estimation when ‘whole.recs = TRUE’ in selection_table()
Box and axis can be removed in phylo_spectro()

New functions:

by_element_est() convert a by-song extended selection table to by-element

warbleR 1.1.27

CRAN release: 2022-02-23

New functions:

sound_pressure_level() to measure, well, sound pressure level
find_clipping() to detect clipped selections
wav_2_flac() to convert ‘.wav’ files into flac compresed lossless format
gaps() for calculating time intervals (i.e. gaps) between selections
read_sound_files() is now use to read sound files
split_sound_files() now can also split associated selection tables

Changes and additions:

read_sound_files() and consequently most other functions in warbleR will look at the ‘channel’ column for deciding which channel to read
updated download URL in quer_xc()
selection_table and extended_selection_table subsetting ([) drop behavior switched to FALSE
overlapping_sels() has been updated to improve performance
unique.labs argument in overlapping_sels() has been deprecated
fix.selec argument added to check_sels() to fix ‘selec’ column labels
warbleR now supports ‘.wav’, ‘.flac’, ‘.wac’ and ‘.mp3’ formats
New argument ‘downsample’ to speed up processing in remove_silence()
New printing methods for ‘autodetec.output’, ‘find.peaks.output’ and ‘xcorr.output’ object classes
‘templates’ and ‘surveys’ arguments added to cross_correlation() to simplify signal detection with this function
auto_detec() output including envelopes is ~1/3 smaller to reduce memory usage

Bug fixes:

error when resampling wavs in resample_est_waves()
error when silences are not found in remove_silence()

warbleR 1.1.26

CRAN release: 2021-03-09

Changes and additions:

df_DTW() and ff_DTW() were merged in a new function freq_DTW()
sp.en.ts(), dfts() and ffts() were merged in a new function freq_ts()
sel_tailor() can undo deletions
button labels replaced by symbols in sel_tailor()
many functions renamed (see new_function_names)

warbleR 1.1.25

CRAN release: 2021-01-27

Bug fixes:

Negative gaps values in song_param()

New functions:

optimize_autodetec() for tunning detection parameters in autodetec()
envelope() a C-compiled version of seewave::env()
new function find_peaks() to detect signals on sound files using xcorr() output
read_sound_file() to read wav, wav and mp3 files as well as wave objects in extended selection tables

Changes and additions:

Remove bioacoustics::resample() as it was deprecated (mp32wav() and fixwavs() affected)
Remove comment columns in lbh_selec_table
Selection table printing method uses huxtable package for text coloring
‘suffix’ argument added to lspec()
autodetec() does not create image files with spectrograms any more
new arguments added to autodetec(): ‘hold.time’ for merging selections, ‘thinning’ for decreasing envelope size
error when having “songs” across multiple files in song_param()

warbleR 1.1.24

CRAN release: 2020-07-01

Changes and additions:

lspec() allow to set resolution and custom dimensions of output image ifles
split_wavs() can now save selections in a data frame of selection table as sound files
read_wave() can now read .wav and .mp3 files from URLs
‘strength’ argument to control color in color_spectro()
‘method’ option to create spectrograms on the fly in xcorr()
‘img’ argument in autodetec() is being soft-deprecated
lspec() now takes output from xcorr(), find_peaks() and autodetec() and plots cross-correlation scores or envelopes along with spectrograms
‘download’ option available in find_annotations()
‘leaflet’ interactive maps in xc_maps()
‘split_wavs()’ new argument ‘only.sels’ to only return selection tables
‘color_spectro()’ frequency range is not restricted by the selection table top and bottom frequency

Bug fixes:

Negative gaps values in song_param()
Trivial bug when downloading files in quer_xc()
Fixed number of segments when using ‘sgmts’ argument in ‘split_wavs()’, it used to return ‘sgmts - 1’ segments.
Fix mismatch in specreator() spectrograms and oscillograms
Fix bug when no detections in x_corr()

warbleR 1.1.23

CRAN release: 2020-03-10

Changes and additions:

add ‘am.amps’ argument to add amplitude modulation in sim_songs()

Bug fixes:

fix ‘spectrograms()’ when plotting extended selection tables ‘by song’
fix ‘compare_methods()’ when less than 100 rows in ‘X’

warbleR 1.1.22

CRAN release: 2020-02-12

Bug fixes:

fix rbind in extended selection tables

warbleR 1.1.21

CRAN release: 2020-02-04

Changes and additions:

print information of extended selection table includes sampling rates, bit depths and warbleR version
warning message in ‘rbind.extended_selection_table()’ when some wave object names are found on both extended selection tables

warbleR 1.1.20

CRAN release: 2020-01-11

Changes and additions:

mfcc cross-correlation implemented in ‘xcorr()’ (argument ‘type’)
argument ‘cor.mat’ in ‘xcorr()’ has been deprecated
new argument ‘output’ in ‘xcorr()’
new example data ‘comp_matrix’ and ‘lbh_selec_table2’ for using on ‘find_peaks()’
‘xcorr()’ can run cross-correlation over entire sound files
‘seltailor()’ can take now extended selection tables

New functions:

new function ‘image_to_wave()’ to convert images into wave objects
new function ‘find_peaks()’ to detect signals on sound files using ‘xcorr()’ output

warbleR 1.1.19

CRAN release: 2019-12-17

Changes and additions:

remove duplicated sound file names in spectrogram() images when ‘by.song’
replace all class(.) == , by is(., *)
new argument ‘fill’ to control the fill color of boxes in ‘specreator()’

New functions:

new function rename_waves_est() to rename wave objects in extended selection tables

Bug fixes:

box/lines plotting when no frequency columns are supplied

warbleR 1.1.18

CRAN release: 2019-11-04

Changes and additions:

updates on specan() to improve harmonic detection
xcorr() performance has been largely improved (5X faster)
‘compare.matrix’ argument in xcorr() to let user defined the pairwise comparisons to be conducted
function xcorr.graph() has been deprecated (use corrplot package instead)
arguments ‘dens’ and ‘bp’ in xcorr() have been deprecated
jpeg and maps packages are not strong dependencies anymore

warbleR 1.1.17

CRAN release: 2019-09-29

Changes and additions:

arguments ‘custom1’ and ‘custom2’ in autodetec() to let users enter their own data
new vignette ‘Introduction to warbleR’

warbleR 1.1.16

CRAN release: 2019-09-02

New functions:

sort_colms: moves required colms to left side of data frame. Originally found in Rraven package
split_wavs: splits sound files in shorter segments

Changes and additions:

‘to’ replaced by ‘dest.path’ argument removed in mp32wav()
read_wave() can also read regular .wav files
quer_ml() temporarily removed while ebird-macaulay API is updated
fix_wavs() now can use bioacoustics package or SOX for resampling
global options (from warbleR_options()) are now taken by wav_info()
‘coor.test()’ now returns 0 for coordination score when the ratio is undefined
‘dB.threshold’ argument in ‘frange()’ and ‘frange_detec()’ for detecting frequency range based on a dB scale
‘min_indx’ and ‘max_indx’ argument in ‘song_param()’ renamed as ‘min_colm’ and ‘max_colm’ and now take names instead of indexes
more accurate dominant frequency detection in ‘dfts()’, ‘trackfreqs()’ and ‘specan()’
‘elm_colm’ and ‘elm_fun’ argument to calculate element level parameters
‘unq.elemts’ and ‘mean.elemt.count’ parameters added to ‘song_param()’ output
more error messages in check_sels()
more info about file input in ‘auto_detec()’ documentation
add ‘frange’ for bp in ‘dfts()’
2 new methods available in ‘compare.methods()’
more error messages in check_sels()
more info about file input in ‘auto_detec()’ documentation
‘frange’ available as bandpass in ‘dfts()’ and ‘mfcc_stats()’
‘bioacoustics’ dependency changed to ‘suggested package’
‘mfcc_stats()’ return NAs instead of error when MFCC can’t be calculated

Bug fixes:

x_corr() on extended selection tables with extra column names generated and error
system() commands for windows in ‘fix_wavs()’ and ‘resample_est()’
normalization when downsampling in ‘mp32wav()’ was required
error when creating extended selection tables ‘by song’ and ‘song’ column tags are repeated across sound files (selection_table())

warbleR 1.1.15

CRAN release: 2018-10-16

New functions:

resample_est: resample wave objects in a extended selection table
phylo_spectro: add spectrograms to the tips of a phylogeny
wav_info: wrapper for ‘selection_table()’ that returns wave file information
multi_DTW: wrapper on dtw for comparing signals described by multiple contours
rm_channels: remove channels from wave files
melfcc_stats: calculate descriptive statistics on Mel-frequency cepstral coefficients

Changes and additions:

‘normalize’ argument in ‘mp32wav()’ renamed as ‘dip.depth’
‘frange’ and ‘dfrange’ arguments in ‘xcorr()’ function deprecated
’selection_table` now can take files found in different directories and create extended selection tables
new parameters measured by ‘specan()’
wav.size.MB column names is now wav.size in ‘check_sels()’ output
‘title.labels’ argument in ‘specreator()’ to customized title

Bug fixes:

Using ‘wav.path’ from ‘warbleR_options’ in ‘catalog()’
clipping.edges option in ‘dfts()’ and ‘ffts()’

warbleR 1.1.14

CRAN release: 2018-06-21

Changes and additions:

‘open_wd()’ example fixed (requested by CRAN)

warbleR 1.1.13

CRAN release: 2018-05-18

Changes and additions:

new function names (print(new_function_names))
object class ‘extended_selection_table’ to create self-contained acoustic data sets
‘before’ and ‘eq.dur’ arguments in ‘snrspec’ function
‘ts.df’ argument in ‘seltailor’ function to adjust frequency contours
‘ts.df’ argument in ‘seltailor’ function to adjust frequency contours
‘by.song’ argument in ‘specreator’ to create full song spectrograms with labeled elements

Bug fixes:

Change “http” to “https” protocol for accessing Xeno-Canto recordings in “querxc”

New functions:

selection_table: converts data frames into an object of classes ‘selection_table’ or ‘extended_selection_table’
generic S3 methods for and ‘print’, ‘cbind’ and ‘[’ for classes ‘selection_table’ or ‘extended_selection_table’
song_param: calculate acoustic parameters at the song (or other hierarchical) level
spec_param: plot catalog of a single selection with varying spectrogram (display) parameters
read_wave: wrapper for tuneR’s readWave that ignores extension file case mismatches
warbleR_options: function to set global parameters *open_wd: open current working directory in wave browser

warbleR 1.1.12

CRAN release: 2018-03-14

Changes and additions:

Parallel computing available in ‘querxc’ function when getting metadata
Parallel computing available in ‘checksels’ function
New arguments in ‘seltailor’ to allow tailoring frequency contours
Parallel computing with and without progress bar in all iterative functions
Parallel computing in windows OS with and without progress bar
New arguments in ‘specreator’ to customize control lines/box around selections
Replace internal “message” functions by “cat” (so warnings are printed in black, no red)

New functions:

track_harm: track harmonic frequency contour
sim_song: simulate songs

warbleR 1.1.10

CRAN release: 2018-02-11

Changes and additions:

Example sound files have been moved to the new R package ‘NatureSounds’ (which is now a dependency)

Bug fixes:

Problem with multiple tags in ‘catalog’

New functions:

rm_sil: removes silence segments (i.e. segments with very low amplitude values) from wave files
consolidate: copies (sound) files scattered in several directories into a single folder

warbleR 1.1.9

CRAN release: 2017-11-18

Changes and additions:

“low.freq” and “high.freq” column names in default table format are now “bottom.freq” and “top.freq” respectively
Moved ‘imp.syrinx’ and ‘imp.raven’ functions to new R package Rraven
Added a new object class ‘selection.table’
Split vignette into a series of three with new functions added to the workflow
New arguments “title”, “by.row”, “prop.mar”, “box” and “rm.axes” in “catalog” function to further customize catalog setup
New arguments “spec.mar”, “lab.mar” and “group.tag” in “catalog” function to color groups of selections
“trackfreqs”, “dfts”, and “dfDTW” functions can use “frange.detec” internally to set bandpass limits (see “frange.detec” argument)
New argument “index” in “seltailor” function to indicate which selection should be tailored
New argument “wl.freq” in “specan” function to set windows length independently for time and frequency domain measurements
New measurement “meanpeakf” in specan
“imp.raven” and “imp.syrinx” now import low and high frequency in kHz (if all.data == FALSE)
Mew argument “bp” (bandpass) and “wl” in “sig2noise” function to calculate signal-to-noise ratio within a frequency range

New functions:

is.selection.table: checks if an object is of class ‘selection.table’
make.selection.table: creates an object of class ‘selection.table’
frange.detec: detects the frequency range of signals in wave objects
frange: applies ‘frange.detec’ function iteratively on signals listed in a selection table
move.imgs: copy/cut image files to folders
ovlp_sels: find overlapping/duplicated selections
cut_sels: generates individual sound files (.wav) for each selection in a selection table
color_spectro: produces spectrograms in which signals are highlighted with colors
exp.raven: exports selection tables to a .txt file that can be opened in Raven

Bug fixes:

Reading wave files with no stereo slot in “specan” and “checksels”

warbleR 1.1.8

CRAN release: 2017-04-27

Bug fixes:

installation in some linux distributions

warbleR 1.1.7

CRAN release: 2017-04-24

Changes and additions:

“seltailor” function now can use external graphic devices (X11 or quartz)

Bug fixes:

installation in windows OS fixed (pbmcapply conflict in previous version)

warbleR 1.1.6

CRAN release: 2017-04-05

New functions:

catalog: create song catalogs (i.e. images with multiple spectrograms in several rows/columns that can be color-labeled)
catalog2pdf: convert several catalog jpeg’s images into single pdf files
fixwavs: convert corrupted files to a format that can be imported into R

Changes and additions:

added new acoustic parameters to “specan” function related to distribution of energy in the time axis. Also time entropy (“time.ent”) and overall entropy (“entropy”) were added
“centroid” and “mode” parameters were removed from “specan” function
sig2noise function can return signal-to-noise ratio in dB (“in.dB” argument). It can also measure noise at both sides of the signal or just right before (“before” argument)
scale argument in dfDTW and ffDTW to allow to focus dynamic time warping comparisons on the frequency contours while ignoring differences in pitch
NAs can be removed from xcorr function output. They can also be ignored when using XCORR in compare.methods function
filtersels can return selections with or without image files (“missing” argument). It can also return a data frame or the row index of the selections (“index” argument)
imp.raven function can import raven selections from files that do not share all the columns and extract the sound file name from the selection table name
FF function (from tuneR package) now can be used for measuring fundamental frequency (in trackfreqs, specan, ffts and ffDTW functions). Seems to be more accurate and faster than fund function from seewave
window overlap can now be defined by users for fundamental and dominant frequency measures in specan function
More arguments to control dynamic time warping settings in dfDTW and ffDTW
Progress bar is available for parallel computing (when parallel > 1) in Linux and for some functions also in iOS. It works using the function mcpbapply::pbmclapply *Spectrogram creating functions (manualoc, specreator, trackfreqs, dfts, ffts, dfDTW, ffDTW, lspec, catalog) can perform faster (4-10 times) using a different image algorithm. This can be called with the argument “fast.spec”. Note that not all spectrogram options are available when fast.spec = TRUE
selections longer than 20 s can be analyzed with specan function (previously it returned an error, this is going to be slow anyways)
“clip.edges” argument in compare.methods function to set removing missing values at the start and end of signals when using dfDTW and ffDTW methods
“threshold” argument in compare.methods function to set the amplitude detection threshold for ffDTW, dfDTW and SP methods
“exclude” argument in imp.syrinx function to exclude selection files that cannot be read
“rm.imcomp” argument in coor.test function to exclude singing events that only have one individual
“cutoff” argument in coor.test function to determine the minimum number of signals per individual needed for a singing event to be included
“rm.solo” argument in coor.test to control if signals that are not intercalated at the start or end of the sequence are removed. For instances the sequence of signals A-A-A-B-A-B-A-B-B-B (in which A and B represent different individuals) would be subset to A-B-A-B-A-B
“incl.wav” argument in filtersels function to indicate if the sound file extension is included in the image files
3 different options (formulas) for calculating signal-to-noise ratio are now available (sig2noise function). In addition the “eq.dur” argument allows to measure a noise segment of the same duration than the signal
grid can be removed from spectrograms in compare.methods function

Bug fixes:

error produced when calculating frequency limits based on dominant frequency contours in xcorr (when frange is not provided)
error for identifying readable sound files in some specific .wav formats in checkwavs function
error when comparing signals with a high duration difference in xcorr

warbleR 1.1.5

CRAN release: 2017-01-21

Changes and additions:

“frange” argument in seltailor to define also the frequency range (low.f and high.f)
trackfreqs, specan now can use low.f and high.f as bandpass limits
trackfreqs and specreator can plot boxes around signals if low.f and high.f are provided
manualoc.df data frame example replaced by selec.table (which includes low.f and high.f columns)
complex searches are now allowed in querxc() following xeno-canto advance query syntax
added ‘clip.edges’ argument to dfts/ ffts/ dfDTW/ ffDTW/sp.en.ts functions to remove missing values at the start or end of signals
more detailed checksels output (now including, sampling rate, duration, number of samples and bits)

New functions:

sp.en.ts: extracts the spectral entropy across signals as a time series iteratively

warbleR 1.1.4

CRAN release: 2016-11-16

Changes and additions:

“pb” argument to allow users to knock down progress bars and messages (in looping functions)
modification to (slightly) improve ‘lspec’ performance
new “sp” argument in compare.methods to allow users to input their own spectral parameters
new “custom.contour” argument in trackfreqs to allow users to input their own frequency contours

Bug fixes:

bug fix for setting ‘path’ argument in several functions
bug fix to due to missing values (undetected) in amplitude detection in trackfreqs, ffts, dfts, ffDTW, and dfDTW

New functions:

filtersels: subsets selection data frames based on manually filtered image files
lspec2pdf: combines lspec images to single pdf files iteratively