Acoustic data sets in NatureSounds

Long billed hermit songs

The example data ‘lbh.est’ is an extended selection table containing long-billed hermit (Phaethornis longirostris) songs. The data contains the annotations and wave objects of 50 long-billed hermit songs from 10 different song types (5 per song type, ‘lek.song.type’ column) recorded at 8 leks (‘lek’ column) in the Caribbean slope of Costa Rica. This data set was used in Araya-Salas et al 2019 to show lek (social group) level signatures in song structure. See this blog post for details on statistical analysis.

The spectrograms of the song types can be displayed using the catalog() function from warbleR:

library(warbleR)

# create a color palette
trc <- function(n) terrain.colors(n = n, alpha = 0.3)

# set global options for catalogs
warbleR_options(same.time.scale = TRUE, mar = 0.001, res = 100, spec.mar = 1, max.group.cols = 5, ovlp = 95,
 width = 23, height = 12.5, tag.pal = list(trc), hatching = 0, cex = 1.3, rm.axes = TRUE, path = "~/Dropbox/R_package_testing/NatureSounds/", box = FALSE)

# load data
data("lbh.est")

# plot catalog
catalog(X = lbh.est, flim = c(1.5, 10.5), nrow = 10, ncol = 5, group.tag = "lek.song.type", height = 25, cex = 2,
        title = "Long billed hermits", img.prefix = "lbh.est", wl = 100)

Song types are labeled by color groups of consecutive spectrograms.

Monk parakeet contact calls

‘monk.parakeet.est’ contains annotations and wave objects of 52 monk parakeet calls from four different social scales (individual, flock, pair, site; ‘scale’ column). The ‘ID’ column refers to selections belonging to the same individual when scale == "Individual. See Smith-Vidaurre, Araya-Salas & Wright (2019) for more details.

# load data
data("monk.parakeet.est")

# monk parakeets
catalog(X = monk.parakeet.est, flim = c(1, 11), nrow = 7, ncol = 8,  group.tag = "scale", 
        title = "Monk parakeets", img.prefix = "monk.parakeet.est", wl = 300)

In this case color groups refer to the different social scales in the data.

Spix’s disc-winged bat social calls

‘thyroptera.est’ is an extended selection table of Spix’s disc-winged bats (Thyroptera tricolor) social calls. The data contains the annotations and wave objects of social from 8 individual Spix’s disc-winged bats (‘id’ column) belonging to 4 social groups (‘group’ column). See Araya-Salas et al (2020) for more details. Can be used (among other things) to test for individual acoustic signatures.

# load data
data("thyroptera.est")

# thyroptera
catalog(X = thyroptera.est, flim = c(2, 60), nrow = 5, ncol = 8, group.tag = "group", title = "Spix's disc-winged bats", img.prefix = "thyroptera.est", wl = 300)

Color groups refer to calls from individuals belonging to the same social group.

Additional acoustic data

The package also includes 5 wave objects that were originally included as example data in warbleR. These are 4 wave objects with long-billed hermit song bouts and 1 with 2 songs from a little tinamou (Crypturellus soui).

# load data
data("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "Cryp.soui")

# spectrogram
seewave::spectro(Phae.long1, wl = 100, scale = FALSE, ovlp = 90, grid = FALSE, palette = seewave::reverse.gray.colors.1, collevels = seq(-50, 0, 5))

# spectrogram
seewave::spectro(Phae.long2, wl = 100, scale = FALSE, ovlp = 90, grid = FALSE, palette = seewave::reverse.gray.colors.1, collevels = seq(-50, 0, 5))

# spectrogram
seewave::spectro(Phae.long3, wl = 100, scale = FALSE, ovlp = 90, grid = FALSE, palette = seewave::reverse.gray.colors.1, collevels = seq(-50, 0, 5))

# spectrogram
seewave::spectro(Phae.long4, wl = 100, scale = FALSE, ovlp = 90, grid = FALSE, palette = seewave::reverse.gray.colors.1, collevels = seq(-50, 0, 5))

# spectrogram
seewave::spectro(Cryp.soui, wl = 1200, scale = FALSE, ovlp = 90, grid = FALSE, palette = seewave::reverse.gray.colors.1, collevels = seq(-35, 0, 2), flim = c(1.4, 2.4))

References

1. Araya-Salas M, G Smith-Vidaurre. 2017. warbleR: An R package to streamline analysis of animal acoustic signals. Methods Ecol Evol 8:184–191.

2. Araya-Salas M, G Smith-vidaurre, D Mennill, P Gonzalez-Gomez, J Cahill & T Wright. 2019. Social group signatures in hummingbird displays provide evidence of co-occurrence of vocal and visual learning. Proceedings of the Royal Society B. 286: 20190666

3. Smith-Vidaurre G, M Araya-Salas, & T Wright. 2019. Individual signatures outweigh social group identity in contact calls of a communally nesting parrot. Behavioral Ecology.

4. Araya-Salas M, A Hernandez-Pinson, N Rojas & G Chaverri. 2020. Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. Animal Behaviour.

Session information

## R version 4.4.2 (2024-10-31)
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