warbleR (version 1.1.12)

specreator: Spectrograms of selected signals

Description

specreator creates spectrograms of signals selected by manualoc or autodetec.

Usage

specreator(X, wl = 512, flim = c(0, 22), wn = "hanning", pal
  = reverse.gray.colors.2, ovlp = 70, inner.mar = c(5, 4, 4, 2), outer.mar =
  c(0, 0, 0, 0), picsize = 1, res = 100, cexlab = 1, title = TRUE,
  propwidth = FALSE, xl = 1, osci = FALSE, gr = FALSE,  sc = FALSE, line = TRUE,
  col = adjustcolor("red2", 0.6), lty = 3, mar = 0.05, it = "jpeg", 
  parallel = 1, path = NULL, pb = TRUE, fast.spec = FALSE, ...)

Arguments

X

'selection.table' or data frame containing columns for sound file name (sound.files), selection number (selec), and start and end time of signals (start and end). Low and high frequency columns are optional. The ouptut of manualoc or autodetec can be used as the input data frame.

wl

A numeric vector of length 1 specifying the window length of the spectrogram, default is 512.

flim

A numeric vector of length 2 for the frequency limit (in kHz) of the spectrogram, as in spectro. Default is c(0, 22).

wn

Character vector of length 1 specifying window name. Default is "hanning". See function ftwindow for more options.

pal

A color palette function to be used to assign colors in the plot, as in spectro. Default is reverse.gray.colors.2.

ovlp

Numeric vector of length 1 specifying the percent overlap between two consecutive windows, as in spectro. Default is 70.

inner.mar

Numeric vector with 4 elements, default is c(5,4,4,2). 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 1. Controls relative size of spectrogram. Default is 1. Ignored when propwidth is TRUE.

res

Numeric argument of length 1. Controls image resolution. Default is 100 (faster) although 300 - 400 is recommended for publication/ presentation quality.

cexlab

Numeric vector of length 1 specifying the relative size of axis labels. See spectro.

title

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

propwidth

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

xl

Numeric vector of length 1. 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.

line

Logical argument to add red lines at start and end times of selection (or box if bottom.freq and top.freq columns are provided). Default is TRUE.

col

Color of 'line'. Default is `adjustcolor("red2", alpha.f = 0.7)`.`

lty

Type of 'line' as in par. Default is 1.

mar

Numeric vector of length 1. Specifies the margins adjacent to the start and end points of selections, dealineating spectrogram limits. Default is 0.05.

it

A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".

parallel

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

path

Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used.

pb

Logical argument to control progress bar. Default is TRUE.

fast.spec

Logical. If TRUE then image function is used internally to create spectrograms, which substantially increases performance (much faster), although some options become unavailable, as collevels, and sc (amplitude scale). This option is indicated for signals with high background noise levels. Palette colors gray.1, gray.2, gray.3, topo.1 and rainbow.1 (which should be imported from the package monitoR) seem to work better with 'fast' spectograms. Palette colors gray.1, gray.2, gray.3 offer decreasing darkness levels.

...

Additional arguments to be passed to the internal spectrogram creating function for customizing graphical output. The function is a modified version of spectro, so it takes the same arguments.

Value

Image files containing spectrograms of the signals listed in the input data frame.

Details

This function provides access to batch process of (a modified version of) the spectro function from the 'seewave' package. The function creates spectrograms for visualization of vocalizations. 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. Setting 'fast' argument to TRUE significantly increases speed, although some options become unavailable, as collevels, and sc (amplitude scale). This option is indicated for signals with high background noise levels.

See Also

trackfreqs for creating spectrograms to visualize frequency measurements by specan, snrspecs for creating spectrograms to optimize noise margins used in sig2noise

Other spectrogram creators: color.spectro, dfDTW, dfts, ffDTW, ffts, snrspecs, sp.en.ts, trackfreqs

Examples

# NOT RUN {
{ 
# First set empty folder
# setwd(tempdir())
data(list = c("Phae.long1", "Phae.long2","selec.table"))
writeWave(Phae.long1, "Phae.long1.wav") #save sound files 
writeWave(Phae.long2, "Phae.long2.wav")

# make spectrograms

specreator(selec.table, flim = c(0, 11), res = 300, mar = 0.05, wl = 300)
 
 #check this folder
getwd()
}

# }