warbleR (version 1.0.1)

manualoc: Interactive view of spectrograms

Description

manualoc produce an interactive spectrographic view to measure start and end times of acoustic signals.

Usage

manualoc(wl = 512, flim = c(0,12), seltime = 1, tdisp = NULL, reccomm =
  FALSE, wn = "hanning", title = TRUE, selcomm = FALSE, osci = FALSE, player =
  NULL, pal = reverse.gray.colors.2)

Arguments

wl

a number specifying the spectrogram window length, default is 512.

flim

a numeric vector of length two for the frequency limit in kHz of the spectrogram, as in the function spectro() in the seewave package. Default is c(0,12).

seltime

time interval in seconds at which the spectrograms are produce with higher "resolution" (ovlp = 70) and oscilograms (if "osci=TRUE"). Default is 1 s.

tdisp

length in seconds of the total sound file to be displayed. Default is NULL which displays the full sound file.

reccomm

if TRUE pops up a comment window at the end of each sound file. The comment needs to be quoted. Default is FALSE.

wn

window function (by default "hanning"). See function ftwindow() in seewave package.

title

if TRUE the name of the sound file will be printed as the main title of the spectrogram window. Default is TRUE.

selcomm

if TRUE pops up a comment window after each selection. The comment is printed as a label on the selected unit. The comment needs to be quoted. Default is FALSE.

osci

if TRUE adds a oscillogram whenever the spectrograms are produce with higher "resolution" (see seltime). Default is FALSE.

player

path to or name of a program capable of playing a wave file by invocation from the command line. If under Windows and no player is given, windows player will be chosen as the default. The external program must be closed before resuming analysis. Default i

pal

a color palette function to be used to assign colors in the plot, as in spectro (seewave package). Default is reverse.gray.colors.2. See Details.

Value

• .csv file saved in the working directory with start and end of selections.

Details

Users can zoom-in a specific sound file segment by clicking at the start and end (left side and right side) of the segment. To select the start and end of a vocalization unit the users need to click at the end and then at the start (right side and left side) of the unit. In addition, 6 "buttons" are provided at the upper right side of the spectrogram that allow to display a full view of the spectrogram ("Full view"), go back to the previous view ("Previous view"), stop the analysis ("Stop"), go to the next sound file ("Next rec"), play the current view using external software ("Play", see "player" argument), or delete the last manual selection in the current sound file ("Del-sel"). When a unit has been selected the function plots a red circle with the selection number in the middle point of the selection in the spectrogram. It also plots vertical dotted lines at the start and end of the selection. The circle and lines "disappear" when the selection is deleted ("Del-sel" button).

The function produces and .csv file (manualoc_output.csv) with information about the .wav file name, selection number, start and end time, selection comment (selcomm), and sound file comment (reccomm). The file is saved in the working directory and is updated every time the user moves into the next sound file (Next rec "button") or stop the process (Stop "button"). When resuming the process (after "stop" and re-running the function in the same working directory), the function will keep the previous selections and will only pick up .wav files that are not present in the .csv file (not previously analyzed).

When users go to the next sound file (Next rec "button") without making any selection the file is still included in the .csv file, with NA's in the "end", "time" and "selec" field. Windows length (wl) control the temporal and frequency precision of the spectrogram. A high "wl" value increases the frequency resolution but reduces the temporal one, and vice versa. Any color palette that comes with the seewave package can be used: temp.colors, reverse.gray.colors.1, reverse.gray.colors.2, reverse.heat.colors, reverse.terrain.colors, reverse.topo.colors, reverse.cm.colors, heat.colors, terrain.colors, topo.colors, cm.colors. The function could be slow when working on files of length > 5min.

Examples

data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4"))
writeWave(Phae.long1,"Phae.long1.wav")
writeWave(Phae.long2,"Phae.long2.wav")
writeWave(Phae.long3,"Phae.long3.wav")
writeWave(Phae.long4,"Phae.long4.wav")
manualoc()