warbleR (version 1.1.1)

trackfreqs: Spectrograms with frequency measurements

Description

trackfreqs creates spectrograms to visualize dominant and fundametal frequency measurements (contours) of signals selected by manualoc or autodetec.

Usage

trackfreqs(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, bp = c(0, 22), cex = c(0.8, 1), 
  threshold = 15, contour = "both", col = c("chartreuse3", "dodgerblue"),
   pch = c(17, 16),  mar = 0.05, lpos = "topright", it = "jpeg", parallel = 1)

Arguments

X

Data frame with results containing columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end). The ouptut of manualoc or

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 of the spectrogram (in kHz), 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 % of 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.

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 selected call. Default is FALSE.

xl

Numeric vector of length 1. A constant by which to scale spectrogram width. 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.

bp

A numeric vector of length 2 for the lower and upper limits of a frequency bandpass filter (in kHz). Default is c(0, 22).

cex

Numeric vector of length 1, specifies relative size of points plotted for frequency measurements and legend font/points, respectively. See spectro.

threshold

amplitude threshold (%) for fundamental frequency and dominant frequency detection. Default is 15.

contour

Character vector, one of "df", "ff" or "both", specifying whether the dominant or fundamental frequencies or both should be plotted. Default is "both".

col

Vector of length 2 specifying colors of points plotted to mark fundamental and dominant frequency measurements. Default is c("chartreuse3", "dodgerblue").

pch

Numeric vector of length 2 specifying plotting characters for the frequency measurements. Default is c(17, 16).

mar

Numeric vector of length 1. Specifies the margins adjacent to the selections to set spectrogram limits. Default is 0.05.

lpos

Character vector of length 1 or numeric vector of length 2, specifiying position of legend. If the former, any keyword accepted by xy.coords can be used (see below). If the latter, the first value will be the x coordinate and the second value the y coo

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 (e.i. no parallel computing). For windows OS the warbleR from github to run parallel. Note that creating images is not compat

Value

• Spectrograms of the signals listed in the input data frame showing the location of the dominant and fundamental frequencies.

Details

This function provides visualization of frequency measurements made by specan. Arguments that are accepted by xy.coords and can be used for lpos are: "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". 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

specreator for creating spectrograms from selections, snrspecs for creating spectrograms to optimize noise margins used in sig2noise

Other spectrogram.creators: dfDTW, dfts, ffDTW, ffts, snrspecs, specreator

Examples

#Set temporal folder as working directory
setwd(tempdir())

#load data
data("Cryp.soui")
writeWave(Cryp.soui, "Cryp.soui.wav") #save sound files 

#autodetec location of signals
ad <- autodetec(threshold = 6, bp = c(1, 3), mindur = 1.2,
maxdur = 3, img = FALSE, ssmooth = 600)

#track dominant frequency graphs
trackfreqs(X = ad[!is.na(ad$start),], flim = c(0, 5), ovlp = 90, it = "tiff",
 bp = c(1, 3), contour = "df")
 
# Check this folder
getwd()

#track both frequencies 
trackfreqs(X = ad[!is.na(ad$start),], flim = c(0, 5), ovlp = 90, it = "tiff",
bp = c(1, 3), contour = "both")