Create catalogs of vocal signals

catalog produces spectrograms of selections (signals) split into multiple rows and columns.

Usage

catalog(
  X,
  flim = NULL,
  nrow = 4,
  ncol = 3,
  same.time.scale = TRUE,
  collevels = seq(-40, 0, 1),
  ovlp = 50,
  parallel = 1,
  mar = 0.05,
  prop.mar = NULL,
  lab.mar = 1,
  wl = 512,
  wn = "hanning",
  gr = FALSE,
  pal = reverse.gray.colors.2,
  it = "jpeg",
  path = NULL,
  pb = TRUE,
  fast.spec = FALSE,
  res = 100,
  orientation = "v",
  labels = c("sound.files", "selec"),
  height = NULL,
  width = NULL,
  tags = NULL,
  tag.pal = list(temp.colors, heat.colors, topo.colors),
  legend = 3,
  cex = 1,
  leg.wd = 1,
  img.suffix = NULL,
  img.prefix = NULL,
  tag.widths = c(1, 1),
  hatching = 0,
  breaks = c(5, 5),
  group.tag = NULL,
  spec.mar = 0,
  spec.bg = "white",
  max.group.cols = NULL,
  sub.legend = FALSE,
  rm.axes = FALSE,
  title = NULL,
  by.row = TRUE,
  box = TRUE,
  highlight = FALSE,
  alpha = 0.5
)

Arguments

X

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

flim

A numeric vector of length 2 indicating the highest and lowest frequency limits (kHz) of the spectrogram, as in spectro. Default is NULL.

nrow

A numeric vector of length 1. Specifies number of rows. Default is 4.

ncol

A numeric vector of length 1. Specifies number of columns. Default is 3.

same.time.scale

Logical. Controls if all spectrograms are in the same time scale (i.e. have the same duration).

collevels

A numeric vector of length 3. Specifies levels to partition the amplitude range of the spectrogram (in dB). The more levels the higher the resolution of the spectrogram. Default is seq(-40, 0, 1). seq(-115, 0, 1) will produces spectrograms similar to other acoustic analysis software packages.

ovlp

Numeric vector of length 1 specifying % of overlap between two consecutive windows, as in spectro. Default is 50. High values of ovlp slow down the function but produce more accurate selection limits (when X is provided).

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).

mar

Numeric vector of length 1. Specifies the margins (in seconds) adjacent to the start and end points of selections, delineating spectrogram limits. Default is 0.05.

prop.mar

Numeric vector of length 1. Specifies the margins adjacent to the start and end points of selections as a proportion of the duration of the signal. If provided 'mar' argument is ignored. Default is NULL. Useful when having high variation in signal duration. Ignored if same.time.scale = FALSE. Must be > 0 and <= 1.

lab.mar

Numeric vector of length 1. Specifies the space allocated to labels and tags (the upper margin). Default is 1.

wl

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

wn

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

gr

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

pal

Color palette function for spectrogram. Default is reverse.gray.colors.2. See spectro for more palettes. Palettes as gray.2 may work better when fast.spec = TRUE.

it

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

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.spec' spectrograms. Palette colors gray.1, gray.2, gray.3 offer decreasing darkness levels.

res

Numeric argument of length 1. Controls image resolution. Default is 100 (faster) although 300 is recommended for publication/presentation quality. Note that high resolution produce significantly bigger image files. This could be problematic when creating pdf files using catalog.

orientation

String. Indicates whether a letter page size image is produced in vertical ('v' option) or horizontal orientation ('h' option). Note that width and height can also be specified.

labels

String vector. Provides the column names that will be used as labels above the corresponding spectrograms.

height

Numeric. Single value (in inches) indicating the height of the output image files. Default is 11 for vertical orientation.

width

Numeric. Single value (in inches) indicating the width of the output image files. Default is 8.5 for vertical orientation.

tags

String vector. Provides the column names that will be used for the color tagging legend above. Tags can also be numeric. Continuous variables would be break down in 10 color classes.

tag.pal

List of color palette function for tags. Should be of length 1, 2 or 3. Default is list(temp.colors, heat.colors, topo.colors).

legend

A numeric vector of length 1 controlling a legend for color tags is added. Ignored if no tags are provided. Four values are allowed:

0: No label
1: Label for the first color tag
2: Label for the second color tag
3: Labels both color tags

Default is 3. Currently no legend can be set for group tags. Use labels instead.

cex

A numeric vector of length 1 giving the amount by which text (including labels and axis) should be magnified. Default is 1.

leg.wd

Numeric. Controls the width of the legend column. Default is 1.

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 (no suffix). Useful to label catalogs from different individuals, species or sites.

img.prefix

A character vector of length 1 with a prefix (label) to add at the beginning of the names of image files. Default is NULL (no prefix). Useful to label catalogs from different individuals, species or sites and ensure they will be grouped together when sorted by file name.

tag.widths

A numeric vector of length 2 to control the relative width of the color tags (when 2 tags are provided).

hatching

A numeric vector of length 1 controlling cross-hatching is used for color tags. Several cross-hatching patterns are used to make tags with similar colors more distinguishable. Four values are allowed:

0: No cross-hatching
1: Cross-hatching the first color tag
2: Cross-hatching the second color tag
3: Cross-hatching both color tags

breaks

Numeric vector of length 1 or 2 controlling the number of intervals in which a numeric tag will be divided. The numbers control the first and second tags respectively. Ignored if tags are not numeric. Default is c(5, 5).

group.tag

Character vector of length 1 indicating the column name to be used to color the empty plot areas around the spectrograms. If provided selections that belong to the same tag level are clumped together in the catalog (the 'X' data frame is sorted by that column). This tags cannot be included in the legend so it would be better to use the label field to identify the different levels.

spec.mar

Numeric vector of length 1 to add space at the top, left and right sides of the spectrogram. Useful to better display the grouping of selections when 'group.tag' is provided. Internally applied for setting 'mar' using par.

spec.bg

Character vector of length 1 to control the background color of the spectrogram. Default is 'white'. Ignored if group.tag = NULL.

max.group.cols

Numeric vector of length 1 indicating the number of different colors that will be used for group tags (see 'group.tag' argument). If provided (and the number is smaller than the number of levels in the 'group.tag' column) the colors will be recycled, although ensuring that adjacent groups do not share the same color. Useful when the 'group.tag' has many levels and the colors assigned become very similar. Default is NULL.

sub.legend

Logical. If TRUE then only the levels present on each page are shown in the legend. Default is FALSE.

rm.axes

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

title

Character vector of length 1 to set the title of catalogs.

by.row

Logical. If TRUE (default) catalogs are filled by rows.

box

Logical. If TRUE (default) a box is drawn around spectrograms and corresponding labels and tags.

highlight

Logical. If TRUE a transparent white layer is plotted on the spectrogram areas outside the selection. The level of transparency is controlled with the argument 'alpha'. Default is FAlSE.

alpha

Numeric vector of length 1 controlling the level of transparency when highlighting selections (i.e. when highlight = TRUE, see highlight argument. Default is 0.5.

Value

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

Details

This functions aims to simplify the visual exploration of multiple vocalizations. The function plots a matrix of spectrograms from a selection table. Spectrograms can be labeled or color tagged to facilitate exploring variation related to a parameter of interest (e.g. location, song type). A legend will be added to help match colors with tag levels (if legend is > 0). Different color palettes can be used for each tag. Numeric tags are split in intervals (the number of intervals can be controlled with break argument). The width and height can also be adjusted to fit more column and/or rows. This 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).

References

Araya-Salas, M., & Smith-Vidaurre, G. (2017). warbleR: An R package to streamline analysis of animal acoustic signals. Methods in Ecology and Evolution, 8(2), 184-191.

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)