warbleR (version 1.0.1)

snrspecs: Spectrograms with noise margins

Description

snrspecs create spectrograms to visualize margins over which noise will be measured by sig2noise().

Usage

snrspecs(X, wl = 512, flim = c(0, 22), wn = "hanning", pal =
  reverse.gray.colors.2, ovlp = 70, inner.mar = c(5, 4, 4, 2) + 0.1, outer.mar =
  c(0, 0, 0, 0), picsize = 1, res = 100, cexlab = 1, title = TRUE, trel =
  FALSE, propwidth = FALSE, xl=1, osci = FALSE, gr = FALSE, sc = FALSE, mar =
  0.2, snrmar = 0.1, it = "jpeg")

Arguments

X

Data frame output from manualoc().

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 spectro. Default is c(0, 22).

wn

Character vector of length one specifying window name. Default is "hanning", as in spectro.

pal

Color palette function for spectrogram. Default is reverse.gray.colors.2.

ovlp

Numeric vector of length one specifyingconsecutive windows, as in spectro. Default is 70.

inner.mar

Numeric vector with 4 elements, default is c(5,4,4,2)+0.1. Specifies number of lines in inner plot margins where axis labels fall, with form c(bottom, left, top, right). See par.

outer.mar

Numeric vector with 4 elements, default is c(0,0,0,0). Specifies number of lines in outer plot margins beyond axis labels, with form c(bottom, left, top, right). See par.

picsize

Numeric argument of length one, controls relative size of spectrogram. Default is 1.

res

Numeric argument of length one, controls resolution of image image. Default is 100 (faster) although 300 - 400 is recommended for publication/ presentation quality.

cexlab

Numeric vector of length one, specifies relative size of axis labels. See spectro.

title

Logical argument to add a title to individual spectrograms. Default is TRUE.

trel

Logical argument to add a time axis scale relative to the wave. Default is FALSE.

propwidth

Logical argument to scale the width of spectrogram proportionally to duration of the selected call. Default is FALSE.

xl

Numeric vector of length one, a constant by which to scale spectrogram width if propwidth = TRUE. Default is 1.

osci

Logical argument to add an oscillogram underneath spectrogram, as in spectro. Default is FALSE.

gr

Logical argument to add grid to spectrogram. Default is FALSE.

sc

Logical argument to add amplitude scale to spectrogram, default is FALSE.

mar

Numeric vector of length one. Specifies the margins to subtract from/add to start and end points of manualoc() selection, respectively, delineating spectrogram limits. Default is 0.2.

snrmar

Numeric vector of length one. Specifies the margins to subtract from/add to start and end points of manualoc() selection, respectively, where noise will be measured. Default is 0.1.

it

A character vector of length one giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".

Value

• Spectrograms per individual call marked with margins and arrows where noise will be measured.

Details

This function can be used to test different margins to facilitate accurate SNR measurements when using sig2noise down the line. Setting margins for individual calls that have been previously clipped from larger files may take some optimization, as will margins for calls within a larger file that are irregularly separated. Setting inner.mar to c(4,4.5,2,1) and outer.mar to c(4,2,2,1) works well when picsize = 2 or 3. Title font size, inner.mar and outer.mar (from mar and oma) don't work well when osci or sc = TRUE, this may take some optimization by the user.

See Also

trackfreqs for creating spectrograms to visualize frequency measurements by specan, specreator for creating spectrograms after using manualoc

Other spectrogram.creators: specreator; trackfreqs

Examples

data(list = c("Arre.aura", "Phae.cuvi"))
data(manualoc.df)
writeWave(Arre.aura, "Arre.aura.wav") #save sound.files
writeWave(Phae.cuvi, "Phae.cuvi.wav")

# make Arre.aura and Phae.cuvi spectrograms
# snrmar needs to be smaller before moving on to sig2noise()

snrspecs(manualoc.df, flim = c(0, 14), inner.mar = c(4,4.5,2,1), outer.mar = c(4,2,2,1),
picsize = 2, res = 300, cexlab = 2, mar = 0.2, snrmar = 0.1, it = "jpeg")

# make only Arre.aura spectrograms
# snrmar now doesn't overlap neighboring calls

snrspecs(manualoc.df[grepl(c("Arre"), manualoc.df$sound.files), ], flim = c(3, 14),
inner.mar = c(4,4.5,2,1), outer.mar = c(4,2,2,1), picsize = 2, res = 300, cexlab = 2,
mar = 0.2, snrmar = 0.01)