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Reassemble annotations from clips

Source: R/reassemble_detection.R
reassemble_detection.Rd

reassemble_detection reassembles detections made on clips so they refer to the original sound files

Usage

reassemble_detection(detection, Y, cores = 1, pb = TRUE)

Arguments

detection

Data frame or selection table (using the warbleR package's format, see selection_table) containing the start and end of the signals. Must contained at least the following columns: "sound.files", "selec", "start" and "end".

Y

Data frame with the start and end of clips in the orignal sound files. Must contain the column "original.sound.files", "sound.files" (clip files), "start" and "end".

cores

Numeric. Controls whether parallel computing is applied. It specifies the number of cores to be used. Default is 1 (i.e. no parallel computing).

pb

Logical argument to control progress bar. Default is TRUE.

Value

A data frame with annotations refering to the position of the detections in the original sound files.

Details

When working with large sound files, it can be convenient to split files into smaller clips to speed up the detection process (this can be done with the function split_acoustic_data). However, this can make it difficult to interpret the results, as the detections will refer to the clips rather than the original sound files. The function will take detections made on clips created with split_acoustic_data, and format their information so they refer back to the original (unsplit) sound files.

References

Araya-Salas, M., Smith-Vidaurre, G., Chaverri, G., Brenes, J. C., Chirino, F., Elizondo-Calvo, J., & Rico-Guevara, A. (2023). ohun: An R package for diagnosing and optimizing automatic sound event detection. Methods in Ecology and Evolution, 14, 2259–2271. https://doi.org/10.1111/2041-210X.14170

See also

label_detection, split_acoustic_data

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr).

Examples

{
# load example data
data("lbh1", "lbh2", "lbh_reference")
tuneR::writeWave(lbh1, file.path(tempdir(), "lbh1.wav"))
tuneR::writeWave(lbh2, file.path(tempdir(), "lbh2.wav"))
 
## if X is a data frame #####
df_ref <- as.data.frame(lbh_reference)
  
# get split annotations
split_df_ref <- split_acoustic_data(X = df_ref,
 only.sels = TRUE, sgmt.dur = 1.5, 
 path = tempdir(), pb = FALSE, 
 files = c("lbh1.wav", "lbh2.wav"))
   
# get clip information
Y <- split_acoustic_data(sgmt.dur = 1.5, 
 path = tempdir(), pb = FALSE,
 output.path = tempdir(), files = c("lbh1.wav", "lbh2.wav"))
   
# reassemble annotations
tc <- reassemble_detection(detection = split_df_ref,  
Y = Y, pb = FALSE)

# start and end are the same as in the original unsplit data
df_ref <- df_ref[order(df_ref$sound.files, df_ref$start), ]
all(tc$end == df_ref$end)
all(tc$start == df_ref$start)
 
### if X is a selection table ##
# split annotations and files
split_lbh_reference <- split_acoustic_data(X = lbh_reference, 
 sgmt.dur = 1.5, path = tempdir(),
 output.path = tempdir(),
 files = c("lbh1.wav", "lbh2.wav"))

# reassemble annotations
tc <- reassemble_detection(detection = split_lbh_reference, 
  Y = attributes(split_lbh_reference)$clip.info)
  
# start and end are the same as in the original unsplit data
lbh_reference <- lbh_reference[order(lbh_reference$sound.files, lbh_reference$start), ]
all(tc$end == lbh_reference$end)
all(tc$start == lbh_reference$start)
}
#> [1] TRUE