We are often interested in getting the frequency range of acoustic signals, either because we have specific predictions about its variation or simply because we want to measure other stuff within that range. Measuring frequency range is typically done by drawing boxes in Raven/Avisoft/Syrinx. An alternative way, and potentially less subjective, is to infer the range from the energy distribution in the frequency domain applying amplitude thresholds on spectrums. I have added two new functions to warbleR that do exactly that:

  • freq_range_detec: detects the frequency range of signals in wave objects (like a seewave function). Can produce images n the graphic device if plot = TRUE.

  • freq_range: applies freq_range_detec iteratively on signals listed in a selection table (like most warbleR functions). If img = TRUE image files including a spectrogram and a frequency spectrum are produced for each selection.

This post shows how these functions work.

Let’s first Load/install warbleR:

if(!require(githubinstall)) install.packages("githubinstall")

githubinstall("warbleR", ask = FALSE)

library("warbleR")

We will run the functions on signals detected on a recording from a male Striped-throated Hermit (Phaethornis striigularis) from Xeno-Canto. We can download the sound file and convert it into wave format as follows:

# set temporary working directory
 setwd(tempdir())

# Query and download  Xeno-Canto for metadata using genus and species as keywords
Phae.stri <- quer_xc(qword = "nr:154074", download = TRUE, pb = FALSE)

# Convert mp3 to wav format
# Simultaneously lower sampling rate to speed up down stream analyses
mp32wav(samp.rate = 22.05, pb = FALSE)

Now, we need to detect the time “coordinates” of the signals in the sound file using auto_detec:

ad <- auto_detec(wl = 200, threshold = 3.5, ssmooth = 1200, bp = c(4, 9.6), 
                 pb = FALSE,  mindur = 0.1, maxdur = 0.25, img = FALSE)

And selec the highest signal-to-noise ratio signals (just for the sake of the example):

snr <- sig2noise(ad, pb = FALSE, mar = 0.05)

ad <- snr[rank(-snr$SNR) < 60, ]

Let’s take a look at the subset of signals that we will analyze (the output of catalog will be found in your working directory):

catalog(ad, nrow = 5, ncol = 4, mar = 0.01, flim = c(3.5, 10.5), 
        labels = "selec", pal = reverse.heat.colors, pb = FALSE)

open_wd()

frange1

freq_range_detec

Now we are ready to run the new functions. freq_range_detec works on wave objects. In this example we use it to detect the frequency range of the first selection in “ad”. But first the selection has to be read as a wave object into R:

w2 <- readWave(as.character(ad$sound.files[2]), from = ad$start[2], 
               to = ad$end[2], units = "seconds")

freq_range_detec(w2, bp = c(2, 9.6), fsmooth = 1, ovlp = 95, 
                 wl = 200, threshold = 8)

frange2

We can look at the detection for each selection in the ‘ad’ data frame using a loop as follows:

for(i in 1:nrow(ad))
{
  wv <- readWave(as.character(ad$sound.files[i]), from = ad$start[i], 
                 to = ad$end[i], units = "seconds")

freq_range_detec(wv, bp = c(2, 12), fsmooth = 1, ovlp = 95, wl = 200, 
                 threshold = 8, flim = c(0, 13), 
                 main = paste("selection", i))

Sys.sleep(0.8)
}

frange_gif

In most cases the detection is good. However, there are some issues with highly amplitude-modulated signals (e.g. high variation in amplitude across the signal). Some parameter tweeking will be required to improve those detections.

freq_range

As mentioned above, the frequency range can be calculated for all selection in a selection table using freq_range:

fr_ad <- freq_range(X = ad, bp = c(2, 12), fsmooth = 0.001, ovlp = 95, 
                          wl = 200, threshold = 10, img = FALSE)

View(fr_ad)
sound.files selec start end SNR bottom.freq top.freq
Phaethornis-striigularis-154074.wav 1 4.489751 4.638935 20.90457 6.50475 8.48925
Phaethornis-striigularis-154074.wav 3 5.008890 5.173992 18.34097 2.97675 9.59175
Phaethornis-striigularis-154074.wav 4 5.515987 5.648255 20.36164 7.16625 8.70975
Phaethornis-striigularis-154074.wav 5 6.026758 6.148005 19.19053 5.84325 8.26875
Phaethornis-striigularis-154074.wav 6 6.465987 6.688504 20.75168 4.96125 8.48925
Phaethornis-striigularis-154074.wav 7 6.751951 6.921702 24.45381 6.94575 8.48925
Phaethornis-striigularis-154074.wav 8 7.232495 7.362042 22.34749 6.50475 8.70975
Phaethornis-striigularis-154074.wav 9 7.733947 7.902042 21.29256 4.52025 8.93025
Phaethornis-striigularis-154074.wav 10 8.260749 8.381226 22.84151 6.94575 8.70975
Phaethornis-striigularis-154074.wav 11 8.831634 8.993493 20.23309 3.41775 9.59175
Phaethornis-striigularis-154074.wav 12 9.436532 9.559366 24.22708 6.28425 8.26875
Phaethornis-striigularis-154074.wav 13 10.009502 10.171838 21.27714 4.52025 8.93025
Phaethornis-striigularis-154074.wav 14 10.634196 10.756079 21.71106 6.94575 8.70975
Phaethornis-striigularis-154074.wav 15 11.125671 11.245172 20.07081 5.84325 7.82775
Phaethornis-striigularis-154074.wav 16 11.658051 11.780795 21.47064 3.41775 8.70975
Phaethornis-striigularis-154074.wav 17 12.033539 12.257553 20.78009 5.18175 8.48925
Phaethornis-striigularis-154074.wav 18 12.306600 12.505330 18.45269 6.94575 8.48925
Phaethornis-striigularis-154074.wav 19 12.648097 12.783539 22.10976 6.50475 8.70975
Phaethornis-striigularis-154074.wav 20 12.952428 13.122383 18.94679 2.97675 9.59175
Phaethornis-striigularis-154074.wav 21 13.421272 13.588845 19.06837 4.07925 7.82775
Phaethornis-striigularis-154074.wav 22 13.820070 13.942904 25.49960 5.40225 9.15075
Phaethornis-striigularis-154074.wav 23 14.245467 14.402179 21.68081 2.97675 9.81225
Phaethornis-striigularis-154074.wav 24 14.681113 14.892746 22.28803 4.96125 8.48925
Phaethornis-striigularis-154074.wav 25 14.952995 15.108936 25.53068 7.16625 8.48925
Phaethornis-striigularis-154074.wav 26 15.367939 15.479209 26.28637 6.50475 8.70975
Phaethornis-striigularis-154074.wav 27 15.759118 15.911431 23.86172 4.52025 9.59175
Phaethornis-striigularis-154074.wav 28 16.321249 16.428211 25.17833 6.94575 8.70975
Phaethornis-striigularis-154074.wav 29 17.303608 17.412905 25.80084 5.40225 8.70975
Phaethornis-striigularis-154074.wav 30 18.262293 18.368415 27.95617 7.16625 8.70975
Phaethornis-striigularis-154074.wav 31 20.295694 20.400161 24.66168 6.94575 8.93025
Phaethornis-striigularis-154074.wav 32 21.410978 21.519051 23.77559 5.62275 8.48925
Phaethornis-striigularis-154074.wav 33 21.833019 22.039572 20.78263 4.74075 8.48925
Phaethornis-striigularis-154074.wav 34 22.103654 22.258121 24.28746 6.94575 8.48925
Phaethornis-striigularis-154074.wav 35 22.463654 22.572906 19.35437 6.50475 8.70975
Phaethornis-striigularis-154074.wav 36 23.326307 23.433563 16.89860 5.18175 8.48925
Phaethornis-striigularis-154074.wav 37 23.732679 23.846375 21.67463 5.40225 8.48925
Phaethornis-striigularis-154074.wav 38 25.414629 25.534357 14.28221 7.38675 8.48925
Phaethornis-striigularis-154074.wav 39 27.724970 27.836784 22.53570 5.40225 8.70975
Phaethornis-striigularis-154074.wav 40 29.991206 30.140140 16.33969 5.40225 8.48925
Phaethornis-striigularis-154074.wav 41 36.950889 37.054041 15.93673 2.75625 8.70975
Phaethornis-striigularis-154074.wav 43 42.691548 42.792818 23.03548 6.94575 8.70975
Phaethornis-striigularis-154074.wav 44 44.947807 45.055176 14.97918 7.38675 8.48925
Phaethornis-striigularis-154074.wav 47 55.080257 55.197989 14.60428 7.38675 8.48925
Phaethornis-striigularis-154074.wav 48 57.503908 57.607672 16.81580 3.85875 8.48925
Phaethornis-striigularis-154074.wav 50 58.645473 58.760031 15.19377 7.38675 8.48925
Phaethornis-striigularis-154074.wav 51 61.539351 61.650349 15.68119 7.38675 8.48925
Phaethornis-striigularis-154074.wav 54 66.936200 67.039170 17.64989 7.16625 8.93025
Phaethornis-striigularis-154074.wav 75 80.315567 80.475068 13.71808 2.75625 9.59175
Phaethornis-striigularis-154074.wav 77 81.066723 81.179580 13.69326 7.16625 8.93025
Phaethornis-striigularis-154074.wav 86 84.856429 84.967336 14.32599 3.85875 8.70975
Phaethornis-striigularis-154074.wav 88 85.438107 85.552211 13.87818 2.97675 8.48925
Phaethornis-striigularis-154074.wav 90 86.451735 86.559264 14.22499 3.41775 8.70975
Phaethornis-striigularis-154074.wav 92 87.433572 87.545341 13.07171 2.75625 8.48925
Phaethornis-striigularis-154074.wav 95 88.701803 88.856792 13.27620 2.75625 9.15075
Phaethornis-striigularis-154074.wav 97 89.906566 90.013414 13.40520 2.97675 8.26875
Phaethornis-striigularis-154074.wav 100 91.123459 91.281441 13.01602 3.63825 8.70975
Phaethornis-striigularis-154074.wav 106 93.240942 93.404752 14.42909 4.29975 8.48925
Phaethornis-striigularis-154074.wav 110 94.960058 95.075546 14.95041 2.97675 8.70975
Phaethornis-striigularis-154074.wav 111 95.955614 96.172258 13.14609 3.19725 8.48925

The range can then be used as a band pass filter in other warbleR functions like trackfreqs, dfts or specan:

sp <- specan(X = fr_ad, wl = 200, bp = "frange", ovlp = 90, pb = FALSE, 
             threshold = 15)

View(sp)
sound.files selec duration meanfreq sd freq.median freq.Q25 freq.Q75 freq.IQR time.median time.Q25 time.Q75 time.IQR skew kurt sp.ent time.ent entropy sfm meanfun minfun maxfun meandom mindom maxdom dfrange modindx startdom enddom dfslope meanpeakf bottom.freq top.freq
Phaethornis-striigularis-154074.wav 1 0.1491837 7.595923 0.5151054 7.731654 7.161780 8.019943 0.8581622 0.0680240 0.0389379 0.0905423 0.0516044 0.5476544 2.704384 0.9597727 0.8880751 0.8523502 0.6989461 5.951745 1.3781250 7.35 7.444951 6.6150 8.1585 1.5435 3.428571 7.0560 7.9380 5.912174 7.38675 6.50475 8.48925
Phaethornis-striigularis-154074.wav 3 0.1651021 7.392857 1.4663635 7.816846 6.417519 8.495308 2.0777885 0.0624963 0.0391768 0.1035386 0.0643618 1.6768368 5.677156 0.9366713 0.8868538 0.8306906 0.5640262 5.247411 0.1743083 8.82 6.865568 3.0870 9.4815 6.3945 8.931035 3.3075 3.0870 -1.335538 8.04825 2.97675 9.59175
Phaethornis-striigularis-154074.wav 4 0.1322676 7.892218 0.3212360 7.862338 7.597522 8.157419 0.5598971 0.0597793 0.0395391 0.0828437 0.0433047 0.5337817 2.517482 0.9283590 0.8907942 0.8269768 0.4810346 5.032002 0.3150000 7.35 7.948601 7.2765 8.5995 1.3230 6.666667 7.2765 8.1585 6.668300 8.26875 7.16625 8.70975
Phaethornis-striigularis-154074.wav 5 0.1212472 7.108289 0.4080179 7.196250 6.891000 7.386000 0.4950000 0.0580288 0.0410448 0.0745411 0.0334963 1.5882154 4.702673 0.8871230 0.8932471 0.7924201 0.4093291 5.486558 0.1743083 7.35 6.971113 5.9535 7.9380 1.9845 5.222222 6.1740 7.7175 12.730193 7.38675 5.84325 8.26875
Phaethornis-striigularis-154074.wav 6 0.2225170 7.080586 0.8983189 7.337250 6.387750 7.895250 1.5075000 0.0941062 0.0695366 0.1543712 0.0848346 2.3159439 9.899743 0.9512709 0.8842104 0.8411236 0.6635994 5.642261 0.1743083 7.35 6.689686 5.0715 8.1585 3.0870 4.571429 7.2765 7.2765 0.000000 8.04825 4.96125 8.48925
Phaethornis-striigularis-154074.wav 7 0.1697506 7.871154 0.3172318 7.941366 7.705718 8.129886 0.4241679 0.0708849 0.0452357 0.0983994 0.0531636 1.6622037 5.545733 0.9229465 0.8861465 0.8178659 0.5776405 5.143396 0.1743083 7.35 7.816544 7.0560 8.1585 1.1025 5.800000 8.1585 7.9380 -1.298965 8.04825 6.94575 8.48925
Phaethornis-striigularis-154074.wav 8 0.1295465 7.662273 0.5731449 7.742645 7.185592 8.168171 0.9825789 0.0701906 0.0395706 0.0895048 0.0499343 0.4835166 2.427618 0.9612345 0.8918360 0.8572635 0.7310556 6.045615 1.6961538 7.35 7.460250 6.6150 8.3790 1.7640 3.250000 7.9380 7.9380 0.000000 7.38675 6.50475 8.70975
Phaethornis-striigularis-154074.wav 9 0.1680953 7.508169 1.1319577 7.900655 6.877011 8.436282 1.5592713 0.0578995 0.0378214 0.0882500 0.0504286 2.6782343 11.774223 0.9311766 0.8861346 0.8251479 0.5943380 5.157648 0.1743083 8.82 6.776193 4.6305 8.5995 3.9690 7.111111 6.8355 7.2765 2.623512 8.48925 4.52025 8.93025
Phaethornis-striigularis-154074.wav 10 0.1204762 7.775408 0.3414647 7.752863 7.503241 8.035769 0.5325283 0.0585845 0.0373240 0.0831522 0.0458282 0.4209429 1.985766 0.9214282 0.8943691 0.8240969 0.4235481 5.129286 0.2505682 7.35 7.849388 7.0560 8.3790 1.3230 5.166667 7.2765 8.3790 9.151184 8.26875 6.94575 8.70975
Phaethornis-striigularis-154074.wav 11 0.1618594 7.566993 1.3964559 7.923101 6.742687 8.627642 1.8849550 0.0561362 0.0355529 0.0916891 0.0561362 1.5298547 5.331965 0.9437879 0.8868838 0.8370302 0.6037433 5.602845 0.2383784 8.82 6.896937 3.5280 9.2610 5.7330 4.500000 4.1895 7.0560 17.709811 8.48925 3.41775 9.59175
Phaethornis-striigularis-154074.wav 12 0.1228345 7.444825 0.4232132 7.492917 7.133583 7.819583 0.6860000 0.0477165 0.0321259 0.0680314 0.0359055 0.3452488 2.400311 0.9426623 0.8926454 0.8414632 0.5437088 5.971276 2.3210526 7.35 7.360500 6.3945 7.9380 1.5435 3.571429 7.2765 6.6150 -5.385296 8.04825 6.28425 8.26875
Phaethornis-striigularis-154074.wav 13 0.1623356 7.494048 1.1762380 7.943397 6.820851 8.467663 1.6468112 0.0552035 0.0374261 0.0837408 0.0463148 3.2779647 15.376351 0.9269290 0.8866527 0.8218641 0.6108722 5.852994 0.2090047 8.82 6.901476 4.6305 8.5995 3.9690 3.166667 7.2765 7.0560 -1.358297 8.48925 4.52025 8.93025
Phaethornis-striigularis-154074.wav 14 0.1218821 7.812830 0.3321780 7.737077 7.539245 8.083283 0.5440374 0.0557445 0.0359033 0.0784203 0.0425170 0.8583218 2.881642 0.9110010 0.8936527 0.8141185 0.4017141 6.299054 2.3210526 7.35 7.874087 7.0560 8.3790 1.3230 5.166667 7.9380 8.1585 1.809125 7.60725 6.94575 8.70975
Phaethornis-striigularis-154074.wav 15 0.1195012 7.216396 0.4136238 7.367212 7.074142 7.484440 0.4102975 0.0585697 0.0401486 0.0736845 0.0335359 1.9959573 6.841179 0.8995461 0.8938433 0.8040533 0.5380238 5.642966 0.1968750 7.35 7.028437 5.9535 7.7175 1.7640 7.625000 6.6150 7.7175 9.225853 7.38675 5.84325 7.82775
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Phaethornis-striigularis-154074.wav 19 0.1354422 7.710930 0.5897865 7.821830 7.200287 8.250992 1.0507047 0.0710131 0.0413851 0.0912354 0.0498502 0.8279834 3.538390 0.9597460 0.8905087 0.8546622 0.7176440 5.994420 0.5582278 7.35 7.512542 6.6150 8.3790 1.7640 5.000000 6.8355 7.2765 3.256002 7.38675 6.50475 8.70975
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Phaethornis-striigularis-154074.wav 23 0.1567120 7.691524 1.4693448 8.025191 6.914662 8.925103 2.0104412 0.0533289 0.0322780 0.0870103 0.0547323 1.6620349 5.941476 0.9332716 0.8876544 0.8284226 0.5326246 5.620870 0.1771084 8.82 7.002048 3.0870 9.4815 6.3945 7.793103 4.6305 7.2765 16.884472 8.04825 2.97675 9.81225
Phaethornis-striigularis-154074.wav 24 0.2116327 7.057101 0.9391337 7.221818 6.285432 7.917014 1.6315818 0.0844674 0.0570851 0.1429449 0.0858597 1.6674539 7.015124 0.9664641 0.8846288 0.8549619 0.7426098 5.855529 1.4225806 7.35 6.738036 5.0715 8.1585 3.0870 3.214286 7.4970 6.8355 -3.125699 7.16625 4.96125 8.48925
Phaethornis-striigularis-154074.wav 25 0.1559411 7.900825 0.2360337 7.962619 7.776371 8.084643 0.3082718 0.0627511 0.0351219 0.0875705 0.0524486 2.5004748 11.100437 0.8942239 0.8874681 0.7935952 0.4647881 5.930598 1.8375000 7.35 7.891297 7.2765 8.1585 0.8820 5.750000 7.2765 7.4970 1.413996 8.04825 7.16625 8.48925
Phaethornis-striigularis-154074.wav 26 0.1112699 7.536154 0.5574551 7.431750 7.035750 8.061750 1.0260000 0.0629740 0.0340912 0.0833340 0.0492428 0.6504043 2.947743 0.9514919 0.8978629 0.8543093 0.6058308 6.289384 1.7640000 7.35 7.422813 6.6150 8.3790 1.7640 2.500000 6.8355 7.2765 3.963338 7.38675 6.50475 8.70975
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That’s it!