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(0.6, 1),  threshold = 15, contour = "both", col = c("skyblue", "red2"), pch = c(21, 24),  mar = 0.05, lpos = "topright", it = "jpeg", parallel = 1,  path = NULL, img.suffix = NULL, custom.contour = NULL, pb = TRUE, type = "p",  leglab = c("Ffreq", "Dfreq"), col.alpha = 0.6, line = TRUE)

Arguments

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 autodetec can be used as the input data frame.

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).

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.

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.

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

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

A numeric vector of length 2 for the lower and upper limits of a frequency bandpass filter (in kHz) or "frange" to indicate that values in low.f and high.f columns will be used as bandpass limits. Default is c(0, 22).

cex

Numeric vector of length 2, 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 1 or 2 specifying colors of points plotted to mark fundamental and dominant frequency measurements respetively (if both are plotted). Default is c("skyblue", "red2").

pch

Numeric vector of length 1 or 2 specifying plotting characters for the frequency measurements. Default is c(21, 24).

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 coordinate for the legend's position. Default is "topright".

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.

img.suffix

A character vector of length 1 with a suffix (label) to add at the end of the names of image files. Default is NULL.

custom.contour

A data frame with frequency contours for exactly the same sound files and selection as in X. The frequency values are assumed to be equally spaced in between the start and end of the signal. The first 2 colums of the data frame should contain the 'sound.files' and 'selec' columns and should be identical to the corresponding columns in X (same order).

Logical argument to control progress bar. Default is TRUE. Note that progress bar is only used when parallel = 1.

type

A character vector of length 1 indicating the type of frequency contour plot to be drawn. Possible types are "p" for points, "l" for lines and "b" for both.

leglab

A character vector of length 1 or 2 containing the label(s) of the frequency contour legend in the output image.

col.alpha

A numeric vector of length 1 within [0,1] indicating how transparent the lines/points should be.

line

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

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 as the ones made by specan. Frequency measures can be made by the function or input by the user (see 'custom.contour' argument) 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. Note that if no amplitude was detected for a particular time bin, then the image will show a dark dot at the bottom of the time bin.

Examples

Run this code

## Not run: 
# #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, wl = 300, flist = "Cryp.soui.wav")
# 
# #track dominant frequency graphs
# trackfreqs(X = ad[!is.na(ad$start),], flim = c(0, 5), ovlp = 90, it = "tiff",
# bp = c(1, 3), contour = "df", wl = 300)
# 
# #using users frequency data (custom.contour argument) 
# #first get contours using dfts
# df <- dfts(X = ad[!is.na(ad$start),], flim = c(0, 5), ovlp = 90, img = FALSE,
# bp = c(1, 3),  wl = 300)
# 
# # now input the dfts output into trackfreqs         
# trackfreqs(X = ad[!is.na(ad$start),], custom.contour = df ,flim = c(0, 5), ovlp = 90, it = "tiff")
# 
# # Check this folder
# getwd()
# 
# #track both frequencies 
# trackfreqs(X = ad[!is.na(ad$start),], flim = c(0, 5), ovlp = 90, it = "tiff",
# bp = c(1, 3), contour = "both", wl = 300)
# 
# ## End(Not run)

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