Kichhoff-Ray Mode Model for fish in R
Sven Gastauer, February 2023, Thünen Institute for Sea Fisheries
Based on the model description found in Clay, C. S., & Horne, J. K. (1994).
Notes on model validity: The KRM model is only valid for incident angles between 65° and 115° (i.e. +/- 25° from incidence).
Current features of the package:
- Model fish with swimbladders / internal features
- Select soft or fluid model for internal features
- shiny app for easy feature extraction from X Rays or Pictures and translation into KRM shape files (experimental)
- Translate xyz (for example as extracted from ImageJ) into KRM shape files
To be done:
- Document shiny app
| Model | Accuracy / Type | Range of Validity | Limitations | Examples |
|---|---|---|---|---|
| KRM | Approximate | All frequencies, homogenous material; at high frequencies: high aspect ratios; at low frequencies: near-normal incidence | Off-normal incidence, no circumferential waves, no longitudinal modes of vibration near resonance | Clay and Horne (1994), Horne et al. (2000); Macaulay et al. (2013); Gastauer et al. (2016) |
References
- Clay, C. S., & Horne, J. K. (1994). Acoustic models of fish: the Atlantic cod (Gadus morhua). The Journal of the Acoustical Society of America, 96(3), 1661-1668
- Gastauer, S., Scoulding, B., Fässler, S. M., Benden, D. P., & Parsons, M. (2016). Target strength estimates of red emperor (Lutjanus sebae) with Bayesian parameter calibration. Aquatic Living Resources, 29(3), 301.
- Horne, J. K., Walline, P. D., & Jech, J. M. (2000). Comparing acoustic model predictions to in situ backscatter measurements of fish with dual‐chambered swimbladders. Journal of fish Biology, 57(5), 1105-1121.
- Macaulay, G. J., Peña, H., Fässler, S. M., Pedersen, G., & Ona, E. (2013). Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models. PloS one, 8(5), e64055.
MIT License
Copyright (c) 2023 Sven Gastauer
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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The above copyright notice and this permission notice shall be included in all
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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SOFTWARE.
Install package with vignettes:
devtools::install_github("SvenGastauer/KRMr", build_vignettes = TRUE)
Install package without vignettes:
devtools::install_github("SvenGastauer/KRMr")
To get a list of all available vignettes:
vignette(package="KRMr")
It is recommended to view vignettes in your preferred browser:
browseVignettes("KRMr")
Please notify the author if you are using this package in any presentation or publication, so we can keep an up to date list of references for the package. Please cite this package as:
Gastauer S (2023). KRMr: Kirchhoff Ray Mode Model for fisheries acoustics. R package version 0.4.7.
Bibtex:
@Manual{,
title = {KRMr: Kirchhoff Ray Mode Model for fisheries acoustics},
author = {Sven Gastauer},
year = {2023},
note = {R package version 0.4.6},
DOI = {10.5281/zenodo.7795866}
}
View citation in R:
citation("KRMr")
For KRMr specific questions make a feature request or post an issue on GitHub.
For general R questions visit Stack Overflow.
If none of those options seem appropriate and you are getting really desperate, contact one the authors.
Defining the the sphere parameters:
freqs = 10:400 * 1000 #Hz frequencies to be considered in Hz
a = 0.01 #m radius of the sphere
cw = 1477.4 #m/s sound speed surrounding water
cfb = 1480.3 #m/s soundspeed inside the sphere
rhow = 1026.8 #kg/m3 density surrounding water
rhofb = 1028.9 #kg/m3 density fluid inside sphere
Construct the shape information of the sphere:
ang = seq(-90,90,length.out=30) #angles to consider
shape=data.frame(
xfb = sin(ang * pi / 180), #x coordinates of a sphere
wfb = (2*cos(ang * pi / 180)), #diameter of the sphere
zfbU = cos(ang * pi / 180), #upper z coordinates
zfbL = -cos(ang * pi / 180)) #lower z coordiates
KRMr::shplot(x_fb = shape$xfb,w_fb = shape$wfb,z_fbU = shape$zfbU, z_fbL=shape$zfbL)
Plot in 3D:
KRMr::get_shp3d(shape)
Now we can run the KRM simulation:
kfs = KRMr::krm(frequency =freqs,
c.w = cw,
rho.w = rhow,
theta=90,
cs = cfb,
rhos = rhofb,
modes="fluid",
L=0.02,
shape=shape)
First we define the shape of a sardine like fish. Here we take the sardine shape profile from the NOAA SWFSC website.
#Sardine
fb = KRMr::pil_fb #fish body sardine
sb = KRMr::pil_sb #swimbladder sardine
Now we can have a look at the shape:
KRMr::shplot(x_fb = fb$x_fb, w_fb = fb$w_fb, x_sb = sb$x_sb, w_sb = sb$w_sb,z_fbU = fb$z_fbU,z_fbL = fb$z_fbL,z_sbU = sb$z_sbU,z_sbL = sb$z_sbL)
KRMr::get_shp3d(list(fb, sb))
Because we have defined the fishbody coordinates and the swimbladder coordinates in a dataframe, the most simple way to run one KRM simulation in KRMr is:
KRMr::krm(shape = list(fb, sb))
Now we are ready to run a KRM simulation. Let's have a look at the TS for a 21 cm sardine from 120 to 200 kHz. Here we will define the different coordinates separately and add the parameters we want to simulate:
TS = KRMr::krm(frequency =seq(20,200.1) * 1000,
c.w = 1490,
rho.w = 1030,
theta=90,
cs = c(1570, 345),
rhos = c(1070,1.24),
L=0.21,
shape=list(fb,sb))
Plot the results:
plot(TS$frequency/1000,
TS$TS,
type='l',
xlab='Frequency (kHz)',
ylab=expression(TS~'('~dB~re~ m^-2~')'))
We can also run a simulation over multiple parameters, for example frequencies from 120-200 kHz and incident angles from 65-115 degrees:
TS = KRMr::krm(frequency =seq(120,200.1) * 1000,
c.w = 1490,
rho.w = 1030,
theta=65:115,
cs = c(1570, 345),
rhos = c(1070,1.24),
L=0.21,
shape=list(fb,sb))
We can for example use ggplot2 to plot a 2D map of the results:
ggplot2::ggplot(data=TS, ggplot2::aes(x= frequency/1000, y= theta, fill=TS))+
ggplot2::geom_tile()+
ggplot2::scale_fill_viridis_c(expression(TS~'('~dB~re~ m^-1~')'))+
ggplot2::xlab('Frequency (kHz)')+
ggplot2::ylab(expression(theta~'(°)'))+
ggplot2::scale_x_continuous(expand=c(0,0))+
ggplot2::scale_y_continuous(expand=c(0,0))+
ggplot2::theme_classic()+
ggplot2::theme(legend.position='top',
legend.text=element_text(angle=45),
text=element_text(size=16))
90° corresponds to braodside incidence. Remember that the model is only valid for angles between 65 and 115° (+/- 25° from broadside incidence).
- Yang Yang, Sven Gastauer, Roland Proud, Richard Mangeni-Sande, Inigo Everson, Robert J Kayanda, Andrew S Brierley, Modelling and in situ observation of broadband acoustic scattering from the Silver cyprinid (Rastrineobola argentea) in Lake Victoria, East Africa, ICES Journal of Marine Science, 2023;, fsad137, https://doi.org/10.1093/icesjms/fsad137
- Palermino, A., De Felice, A., Canduci, G. et al. Application of an analytical approach to characterize the target strength of ancillary pelagic fish species. Sci Rep 13, 15182 (2023). https://doi.org/10.1038/s41598-023-42326-4