Calculates the average spectra of all the clicks present in an event
calculateAverageSpectra(
x,
evNum = 1,
calibration = NULL,
wl = 512,
channel = 1:2,
filterfrom_khz = 0,
filterto_khz = NULL,
sr = NULL,
snr = 0,
norm = TRUE,
plot = TRUE,
noise = FALSE,
decimate = 1,
sort = FALSE,
mode = "spec",
title = NULL,
ylim = NULL,
flim = NULL,
cmap = hcl.colors(30, "YlOrRd", rev = TRUE),
brightness = 0,
contrast = 0,
q = 0.01,
showBreaks = TRUE,
...
)invisibly returns a list with six items: freq - the frequency,
UID - the UID of each click, avgSpec - the average spectra of the event,
allSpec - the individual spectrum of each click in the event as a matrix with
each spectrum in a separate column, avgNoise - the average noise spectra,
allNoise - the individual noise spectrum for each click
an AcousticEvent or AcousticStudy object
if x is a study, the event index number to calculate the average
spectra for. Note that this is the index in the order that they appear in the
AcousticStudy object, not the actual event number. Alternatively
full event names can be used
a calibration function to apply, if desired
the size of the click clips to use for calculating the spectrum. If greater than the clip present in the binary, clip will be zero padded
channel(s) to include in calculations. Currently does not correspond to actual channel in instrument, just the order present in the binary file
frequency in khz of highpass filter to apply, or the lower
bound of a bandpass filter if filterto_khz is not NULL
if a bandpass filter is desired, set this as the upper bound.
If only a highpass filter is desired, leave as the default NULL value.
Currently only highpass and bandpass filters are supported, so if
filterfrom_khz is left as zero then this parameter will have no effect
a sample rate to use if the sample rate present in the database needs to be overridden (typically not needed)
minimum signal-to-noise ratio to be included in the average, in dB. SNR is
calculated as difference between the signal and noise spectra at the peak frequency
of the signal. This can be inaccurate if noise is inaccurate (see noise for
issues with noise calculations)
logical flag to normalize dB magnitude to maximum of 0
logical flag whether or not to plot the result. This will create two plots, the first is a concatenated spectrogram where the y-axis is frequency and the x-axis is click number. The second plot is the average spectrogram of all clicks, the y-axis is dB, x-axis is frequency. Can be a vector of length two to create only one of the two plots
logical flag to plot an average noise spectrum. This is estimated
by taking a window of length wl immediately before click. Since there
are only a limited number of samples saved in the Pamguard binary files, this
can be very inaccurate when wl is a large proportion of the total samples
saved. In these cases the noise floor will appear nearly identical to the signal,
reducing wl can help get a more accurate noise floor.
integer factor to reduce sample rate by
logical flag to sort concatenated spectrogram by peak frequency
one of 'spec' or 'ceps' to plot the spectrum or cepstrum
replacement titles for plots, can be length vector of length two to provide separate titles
optional y limits for mean spectra plot
optional frequency limits for both plots
colors to use for concatenated click spectrogram, either a palette function or vector of colors
value from -255 to 255, positive values increase brightness, negative values decrease brightness of concatenated spectrogram image
value from -255 to 255, positive values increase contrast, negative values decrease contrast of concatenated spectrogram image
lower and upper quantiles to remove for scaling concatenated spectrogram.
Or if a single value, then quantiles q and 1-q will be used. Ex.
if q=.01, then the bottom 1
plotting the image. This is done purely for cosmetic reasons, no output data is
affected
logical flag to show lines separating events when plotting multiple events
optional args
Taiki Sakai taiki.sakai@noaa.gov
data(exStudy)
# need to update binary file locations to users PAMpal installation
binUpd <- system.file('extdata', 'Binaries', package='PAMpal')
dbUpd <- system.file('extdata', package='PAMpal')
exStudy <- updateFiles(exStudy, bin = binUpd, db=dbUpd)
avSpec <- calculateAverageSpectra(exStudy)
str(avSpec$avgSpec)
range(avSpec$freq)
str(avSpec$allSpec)
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