157 lines
5.1 KiB
R
157 lines
5.1 KiB
R
library(warbleR)
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##
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# This is an examle that shows how to:
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# 1. choose bird call samples from xeno-canto by different selection types
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# 2. download the files
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# 3. turn the mp3 files into wavs for further processing
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# 4. fine tune the spectrogram creator and create spectrograms of each wav file
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# 5. fine tune the auto_detection of warbleR and create detections
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# 6. mash it all together and print spectrograms with detections
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##
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# Create a new folder inside a new tempdir and set it to your working dir
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wd <- file.path(tempdir(), "xeno-canto_example")
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dir.create(wd)
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setwd(wd)
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##
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# Do the queries
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##
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# Query xeno-canto for all Phaethornis recordings (e.g., by genus)
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Phae <- query_xc(qword = "Phaethornis", download = FALSE)
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# Check out the structure of resulting the data frame
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str(Phae)
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# Query xeno-canto for all Phaethornis longirostris recordings
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Phae.lon <- query_xc(qword = "Phaethornis longirostris", download = FALSE)
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# Check out the structure of resulting the data frame
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str(Phae.lon)
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##
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# filter xeno-canto recordings by quality, signal type and locality
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##
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# How many recordings are available for Phaethornis longirostris?
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nrow(Phae.lon)
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# How many signal types exist in the xeno-canto metadata?
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unique(Phae.lon$Vocalization_type)
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# How many recordings per signal type?
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table(Phae.lon$Vocalization_type)
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##
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# Filter the metadata to select the signals we want to retain
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##
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# First by quality
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Phae.lon <- Phae.lon[Phae.lon$Quality == "A", ]
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nrow(Phae.lon)
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# Then by signal type
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Phae.lon.song <- Phae.lon[grep("song", Phae.lon$Vocalization_type, ignore.case = TRUE), ]
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nrow(Phae.lon.song)
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# Finally by locality
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Phae.lon.LS <- Phae.lon.song[grep("La Selva Biological Station, Sarapiqui, Heredia", Phae.lon.song$Locality, ignore.case = FALSE), ]
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nrow(Phae.lon.LS)
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# Check resulting data frame, 3 recordings remain
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str(Phae.lon.LS)
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# check the location
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map_xc(Phae.lon.LS, img = FALSE)
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##
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# Once we're sure the recordings fit, it's time to download the files, also save
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# the metadata as .csv file
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##
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# Download sound files
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query_xc(X = Phae.lon.LS)
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# Save the metadata object as a .csv file
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write.csv(Phae.lon.LS, "Phae_lon.LS.csv", row.names = FALSE)
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##
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# xeno-canto maintains recordings in mp3 format due to file size restrictions.
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# However, we require wav format for all downstream analyses
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##
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# here we are downsampling the original sampling rate of 44.1 kHz
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# to speed up downstream analyses in the vignette series
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mp32wav(samp.rate = 22.05)
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# Use checkwavs to see if wav files can be read
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check_wavs()
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##
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# Make long spectrograms of whole recordings
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##
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# Create a vector of all the recordings in the directory
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wavs <- list.files(pattern = "wav$")
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# Print this object to see all sound files
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wavs
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# How long are these files? this will determine number of pages returned by full_spectrograms
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duration_wavs(wavs)
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# ovlp = 10 to speed up function
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# tiff image files are better quality and are faster to produce
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full_spectrograms(flist = wavs, ovlp = 10, it = "tiff")
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# We can zoom in on the frequency axis by changing flim,
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# the number of seconds per row, and number of rows
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full_spectrograms(flist = wavs, flim = c(2, 10), sxrow = 6, rows = 15, ovlp = 10, it = "tiff")
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##
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# Once satisfied with the argument settings we can make long spectrograms for all the sound files.
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##
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# Make long spectrograms for the xeno-canto sound files
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full_spectrograms(flim = c(2, 10), ovlp = 10, sxrow = 6, rows = 15, it = "jpeg", flist = wavs)
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# Concatenate full_spectrograms image files into a single PDF per recording
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# full_spectrograms images must be jpegs to do this
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full_spectrogram2pdf(keep.img = FALSE, overwrite = TRUE)
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##
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# Automatically detect signals with auto_detect
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##
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# Select a subset of sound files
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# Reinitialize the wav object
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wavs <- list.files(pattern = ".wav$", ignore.case = TRUE)
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# Set a seed so we all have the same results
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set.seed(1)
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sub <- wavs[sample(1:length(wavs), 3)]
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##
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# Run auto_detec() on subset of recordings
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##
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# play around with the auto detection, setting the values accordingly.
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# Phaethornis longirostris songs have frequencies between 2 and 10 kHz and durations between 0.05 and 0.5 s.
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Phae.ad <- auto_detec(
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path = wd,
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threshold = 20, # amplitude threshold in %
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ssmooth = 900, # amplitude envelope with sum smooth
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bp = c(2, 10), # bandpass filter (between 2 and 10 kHz)
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wl = 300, # window for ffilter bandpass
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parallel = 6*2 # how many cores shall be used in parallel (*2 due to hyper threading)
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)
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# Let's look at the number of selections per sound file
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table(Phae.ad$sound.files)
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# When we're done, create an image with all detections using full spectrograms
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full_spectrograms(
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flim = c(2, 10),
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ovlp = 10,
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sxrow = 6,
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rows = 15,
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it = "jpeg",
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flist = wavs,
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X = auto_detec(
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path = wd,
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threshold = 20,
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ssmooth = 900,
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bp = c(2, 10),
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wl = 300,
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parallel = 6*2)
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)
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# combine the image into a single pdf per species like before
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full_spectrogram2pdf(keep.img = FALSE, overwrite = TRUE)
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