echogram: Echogram visualisation

Description

This function allows to produce echogram visualisations from imported hac data. The user can define the visualisation Sv threshold and select between two built-in color schemes or define a custom scheme.

Usage

echogram(echogram, Svthr = -70, Svmax = 0, col.sep = NULL, col.nb = NULL,
         scheme = NULL, depth.grid = NULL, x.grid = NULL, 
         x.ref = c("pings", "nmi", "seconds"), seabed = FALSE, 
         depth.max = NULL, ping.ini = NULL, ping.max = NULL, colbar=TRUE, 
         main = NULL, tformat = "%H:%M", ...)

Arguments

echogram: an object of class ``echogram'' as returned by read.echogram.
Svthr: Sv visualisation threshold, in decibels (dB).
Svmax: maximum Sv visualisation value, in dB.
col.sep: separation between colors. Defaults to 1 dB.
col.nb: number of colors.
scheme: color scheme for echogram, ``parula'' (the default), ``EK500'', or ``echov''. It can also be a vector of valid color names, or a function generating color names.
depth.grid: spacing between depth labels (in m).
x.grid: spacing between labels in the horizontal dimension according to x.ref.
x.ref: horizontal reference in echogram: ``pings'' (the default), ``nmi'' or ``seconds''.
seabed: logical. When TRUE and data on detected bottom is present, a line is added to the echogram.
depth.max: maximum depth to visualise.
ping.ini: initial ping to visualise.
ping.max: last ping to visualise.
colbar: logical. If TRUE a color bar is added to the echogram.
main: the acoustic frequency, by default.
tformat: time format for annotating when horizontal dimension when x.ref = 'seconds'.
...: other options to image.

Author

Héctor Villalobos

Details

Besides the two built-in color schemes, the user can define its own by specifying a vector of valid color names (see examples). This function uses imageScale function from sinkr package by Marc Taylor.

Examples

Run this code

# import hac file
hacfile <- system.file("hac", "D20150510-T202500.hac", package = "echogram")
echo2.038 <- read.echogram(hacfile)

# echogram by default 
echogram(echo2.038)

# using alternative color schemes
echogram(echo2.038, Svthr = -70, col.sep = 1.5, scheme = "EK500")
echogram(echo2.038, Svthr = -70, col.sep = 3, scheme = c("white", "blue", "grey", "black"))