NatureSounds contains a collection of animal sounds for bioacoustic analysis. The main goal is to provide example acoustic data to faciliate the development of bioacoustic tools in the R environment. At the same time, this data can be used as case studies for showing the functionality of tools already available in R. This tutorial offers a quick glance over the acoustic data sets included in the package.
Most data sets are provided as extended selection tables. These are R objects that contains both the annotations (locations of signals in time and frequency) and the corresponding acoustic data as wave objects. Therefore, these are self-contained objects since the original sound files are no longer needed to perform acoustic analyses. These objects are created by the function
selection_table() from warbleR. Take a look at the intro to warbleR vignette for more details and check out the packages warbleR, tuneR and seewave for sound file manipulation and analysis in R.
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)