call.assign {callsync}

call.assign

Description

Assigns calls from a detection table. Or rather removes calls that are not the loudest and returns the cleaned detection table. Uses fine alignment and energy content.

Usage

call.assign(
  all_files = NULL,
  detections = NULL,
  save_files = TRUE,
  path_calls = NULL,
  ffilter_from = 1100,
  wing = 5,
  step_size = 0.01,
  assign_fraq = 0.05,
  save_wing = 0.1,
  quiet = FALSE
)

Arguments

all_files

character vector, should contain all the paths to the raw recordings that should be considered. If 'NULL' files are loaded from 'path_chunks'.

detections

data frame with start = start time in samples and end = end time in samples for each detection.

save_files

logical, if 'TRUE' the files are stored in the 'path_chunks' location. Results are also returned.

path_calls

character, path to where to store the results.

ffilter_from

numeric, frequency in Hz for the high-pass filter.

wing

numeric, the duration in seconds to load before and after each detection to improve alignment. This is not saved with the aligned call.

step_size

numeric, duration in seconds of the bins for signal compression before cross correlation. Default is '0.01'.

assign_fraq

numeric between 0 and 1, how much louder does the focal needs to be than the second loudest track to be accepted. Default is '0.05' and accepts if the focal is just 0.05 louder.

save_wing

numeric, how much extra to export before and after a detection to make sure the whole call is included in seconds. Default is '0.1'.

quiet

logical, if 'TRUE' no messages are printed.

Value

Returns a data frame with file = file name, start = start time in samples and end = end time in samples for each detection.

Examples

## Not run: 
require(callsync)
require(seewave)
require(tuneR)
path_git = 'https://raw.githubusercontent.com'
path_repo = '/simeonqs/callsync/master/tests/testthat/files'
file_1 = '/chunk@1@1@[e-mail]'
file_2 = '/chunk@2@1@[e-mail]'
url_1 = paste0(path_git, path_repo, file_1)
url_2 = paste0(path_git, path_repo, file_2)
local_file_1 = paste(tempdir(), file_1, sep = '/')
local_file_2 = paste(tempdir(), file_2, sep = '/')
if(!file.exists(local_file_1))
  download.file(url_1, destfile = local_file_1, mode = 'wb',)
if(!file.exists(local_file_2))
  download.file(url_2, destfile = local_file_2, mode = 'wb')
all_files = c(local_file_1, local_file_2)
detections = lapply(all_files, function(file){
  wave = load.wave(file, ffilter_from = 1100)
  detections = call.detect.multiple(wave, plot_it = FALSE)
  return(detections)
})
names(detections) = basename(all_files)
ca = call.assign(all_files = all_files,
                 detections = detections,
                 quiet = TRUE,
                 save_files = FALSE)

## End(Not run)