warbleR (version 1.1.17)

spec_param: Plot a mosaic of spectrograms with varying display parameters

Description

spec_param plots a mosaic of spectrograms with varying display parameters to facilitate selection of display parameters

Usage

spec_param(X, length.out = 5, ovlp = 90, wl = c(100, 1000), wn = "hanning",
 collev.min = -40, pal = "reverse.gray.colors.2", path = NULL, rm.axes = TRUE, ...)

Arguments

X

object of class 'selection_table', 'extended_selection_table' or data frame with a single row and columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end). Default is NULL.

length.out

Numeric vector of length 1 controling the number of sublevels of the numeric arguments for which a range has been provided. Ranges are allowed for 'ovlp', 'wl', and 'collev.min' arguments.

ovlp

Numeric vector of length 1 or 2 specifying % of overlap (or lower/upper values the desired range) between two consecutive windows, as in spectro. Default is 90.

wl

A numeric vector of length 1 or 2 specifying the window length (length 1) or the lower and upper range limits of the desired window length range (length 2) for creating spectrograms. Default is c(100, 1000).

wn

Character vector specifying the window function names to be used. Several names can be provided. See ftwindow for name options. Default is "hanning". If "all", then all window functions available are used.

collev.min

A (negative) numeric vector of length 1 or 2. Determines the first argument to use in 'collevels' for the internal spectrogram creating function. This replaces the first element in the 'collevels' as in spectro. Note that 'collevels' is not available in this function spec_param.

pal

Color palette function for spectrogram. Default is "reverse.gray.colors.2". Several palettes can be provided in a character vector. Note that, contrary to other warbleR and seewave functions, the palette most be provided as character string rather than as a function. See spectro for more palettes.

path

Character string containing the directory path where the sound file are located.

rm.axes

Logical. If TRUE frequency and time axes are excluded. Default is TRUE.

...

Additional arguments to be passed to catalog function for customizing graphical output. Check out catalog for more details.

Value

Image files with spectrograms of whole sound files in the working directory. Multiple pages can be returned, depending on the length of each sound file.

Details

This functions aims to simplify the selection of spectrogram parameters. The function plots, for a single selection, a mosaic of spectrograms with varying display parameters. For numeric arguments the upper and lower limits of a range can be provided. The following arguments accept can have varying values:

• wl: Windows length (numeric range)

• ovlp: Overlap (numeric range)

• collev.min: Minimum value of the color levels (numeric range)

• wn: window function names (character)

• pal: palette (character)

Outputs are similar to those of catalog. The output image files can be put together in a single pdf file with catalog2pdf. We recommend using low resolution (~60-100) and smaller dimensions (width & height < 10) if aiming to generate pdfs (otherwise pdfs could be pretty big).

See Also

blog post on creating catalogs, blog post on customizing catalogs , catalog2pdf

Examples

# NOT RUN {
# Save to temporary working directory

# save sound file examples
data(list = c("Phae.long1", "lbh_selec_table"))
writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav")) 

# variable collevels
spec_param(X = lbh_selec_table, wl = 164, ovlp = c(90), wn = c("flattop"), 
length.out = 16, nrow = 4, ncol = 4, width = 20, height = 11.3, rm.axes = TRUE, 
cex = 1, box = F, collev.min = c(-20, -150), path = tempdir())

# variable overlap and wn
spec_param(X = lbh_selec_table, wl = 164, ovlp = c(50, 90), 
wn = c("hanning", "hamming", "rectangle", "bartlett", "blackman", "flattop"),
length.out = 7, nrow = 6, ncol = 7, width = 20, height = 11.3, rm.axes = TRUE, 
cex = 1, box = F), path = tempdir()

# variable wl and wn
spec_param(X = lbh_selec_table, wl = c(100, 1000), ovlp = c(50, 90), wn = "all", 
length.out = 5, nrow = 10, ncol = 14, width = 20, height = 11.3, rm.axes = TRUE, 
cex = 0.7, path = tempdir())

# variable wl, collev.min and wn 
spec_param(X = lbh_selec_table, wl = c(100, 1000), ovlp = 90, 
wn = c("hanning", "hamming", "rectangle"), collev.min = c(-110, -25), 
length.out = 3, nrow = 10, ncol = 14, width = 20, height = 11.3, rm.axes = TRUE,
 cex = 0.7, path = tempdir())
 
 # variable wl, wn and pal
 spec_param(X = lbh_selec_table, wl = c(100, 1000), ovlp = 90, 
 wn = c("hanning", "hamming", "rectangle"), 
 pal = c("reverse.gray.colors.2", "reverse.topo.colors", 
 "reverse.terrain.colors", "reverse.cm.colors"), 
 length.out = 4, nrow = 5, ncol = 10, width = 20, height = 11.3,
  rm.axes = TRUE, cex = 0.7, lab.mar = 2, path = tempdir())
  
  # wl, wn and pal
  spec_param(X = lbh_selec_table, wl = c(100, 1000), ovlp = 90,
   wn = c("hanning", "hamming", "rectangle"), 
  pal = c("reverse.gray.colors.2", "reverse.topo.colors", 
  "reverse.terrain.colors", "reverse.cm.colors"), 
  length.out = 4, nrow = 5, ncol = 10, width = 20, height = 11.3, rm.axes = TRUE,
   cex = 0.7, group.tag = "wn",  spec.mar = 0.4, lab.mar = 0.8, box = FALSE, 
   tag.pal = list(reverse.cm.colors), path = tempdir())

check this floder
tempdir()
# }