echogram (version 0.1.3)

add.echogram: Add two echograms

Description

This function allows addition or subtraction of Sv data matrices of corresponding echograms from two frequencies in the linear or logarithmic domain.

Usage

add.echogram(echogram1, echogram2, operator = c("plus", "minus"), 
    domain = c("linear", "dB"))

Value

An object of class ``echogram'' where the Sv component is the result of the performed operation.

Arguments

echogram1

an object of class ``echogram'' as returned by read.echogram.

echogram2

an object of class ``echogram'' from a different acoustic frequency than echogram1 above.

operator

a string indicating addition (``plus'') or subtraction (``minus''). May be abbreviatted.

domain

a string indicating the domain where the operation will be performed (see details).

Author

Héctor Villalobos

Details

Corresponding echograms refers to data acquired at the same time with different acoustic frequencies. In order to add echograms, the Sv data matrices must have the same dimensions. If they don't, match.echogram can be used for this purpose. It is also important to mask undesired echoes beforehand, as those belonging to the bottom and below. When domain = "dB" (the default), the Sv matrices are added as they are. When domain = "linear", the Sv values are transformed with 10^(Sv/10) before addition, and the result (X) is then back transformed to dB (10*log10(X)).

See Also

match.echogram, mask.echogram

Examples

# import 38 and 120 kHz data from an HAC file 
hacfile <- system.file("hac", "D20150510-T202500.hac", package = "echogram")
echo2.038 <- read.echogram(hacfile, channel = 1)
echo2.120 <- read.echogram(hacfile, channel = 2)

if (FALSE) {
# attempting to add the two frequencies with unequal number of pings gives an error
add.echogram(echo2.038, echo2.120, "plus", "dB")
}

# running match.echogram() solves this
tmp <- match.echogram(echo2.038, echo2.120)
str(tmp) # both frequencies are in a list, need to split
echo2.038 <- tmp$echogram1
echo2.120 <- tmp$echogram2

# we don't want to add bottom echoes, mask bottom and surface from both frequencies
echo2.038m <- mask.echogram(echo2.038, surf.off = 2, bott.off = 0.2)
echo2.120m <- mask.echogram(echo2.120, surf.off = 2, bott.off = 0.2)

# adding Sv values and plot result
echo.sum <- add.echogram(echo2.038m, echo2.120m, "plus", "dB")
Min <- min(as.vector(echo.sum$Sv), na.rm=TRUE) # useful to set Sv threshold
echogram(echo.sum, Svthr=floor(Min), scheme = "EK500")

# subtract 38 from 120 kHz
echo.minus <- add.echogram(echo2.120m, echo2.038m, "minus", "dB")
Min <- min(as.vector(echo.minus$Sv), na.rm=TRUE)
echogram(echo.minus, Svthr=floor(Min), scheme = "EK500")