Assembles control parameters into a list suitable for passing to strike()
and the functions that it calls. If file is provided, then all the other
arguments are read from that source. Note that updateParameters() may
be used to modify the results of parameters, e.g. for use in sensitivity
tests.
parameters(
ms = 45000,
Ss = NULL,
Ly = 1.15,
Lz = 1.15,
species = "N. Atl. Right Whale",
lw = 13.7,
mw = NULL,
Sw = NULL,
l = NULL,
a = NULL,
b = NULL,
s = NULL,
theta = 55,
Cs = 0.01,
Cw = 0.0025,
logistic = list(logStressCenter = 5.38, logStressWidth = 0.349, tau25 = 1e+05, tau50 =
241000, tau75 = 581000),
file = NULL
)Arguments
- ms
Ship mass (kg).
- Ss
Ship wetted area (m^2). This, together with
Cs, is used byshipWaterForce()to estimate ship drag force. IfSsis not given, then an estimate is made by callingshipAreaFromMass()with the provided value ofms.- Ly
Ship impact horizontal extent (m); defaults to 1.15m if not specified, based on an analysis of the shape of the bow of typical coastal fishing boats of the Cape Islander variety.
- Lz
Ship impact vertical extent (m); defaults to 1.15m if not specified, based on the same analysis as for Ly.
- species
A string indicating the whale species. For the permitted values, see
whaleMassFromLength().- lw
Whale length (m). This is used by
whaleAreaFromLength()to calculate area, which is needed for the water drag calculation done bywhaleWaterForce().- mw
Whale mass (kg). If this value is not provided, then it is calculated from whale length, using
whaleMassFromLength()withtype="wetted".- Sw
Whale surface area (m^2). If not provided, this is calculated from whale length using
whaleAreaFromLength().- l
Numerical vector of length 4, giving thickness (m) of skin, blubber, sublayer, and bone. If not provided, this is set to
c(0.025, 0.16, 1.12, 0.1). The skin thickness default of 0.025 m represents the 0.9-1.0 inch value stated in Section 2.2.3 of Raymond (2007). The blubber default of 0.16 m is a rounded average of the values inferred by whale necropsy, reported in Appendix 2 of Daoust et al., 2018. The sublayer default of 1.12 m may be reasonable at some spots on the whale body. The bone default of 0.1 m may be reasonable at some spots on the whale body. The sum of these default values, 1.40 m, is a whale radius that is consistent with a half-circumference of 4.4 m, reported in Table 2.2 of Raymond (2007).- a, b
Numerical vectors of length 4, giving values to use in the stress-strain law
stress=a*(exp(b*strain)-1), whereais in Pa andbis unitless. By construction,a*bis the local modulus at low strain (i.e. at lowb*strainvalues), and thatbis the efolding scale for nonlinear increase in stress with strain. This exponential relationship has been mapped out for whale blubber, using a curve fit to Figure 2.13 of Raymond (2007), and these values are used for the second layer (blubber); see the documentation for the raymond2007 dataset, to see for how that fit was done. If not provided,adefaults toc(17.8e6/0.1, 1.58e5, 1.58e5, 8.54e8/0.1)andbdefaults toc(0.1, 2.54, 2.54, 0.1). The skin defaults are set up to give a linear shape (sincebis small) with thea*bproduct being 17.8e6 Pa, which is the adult-seal value given in Table 3 of Grear et al. (2017). The blubber defaults are from a regression of the stress-strain relationship shown in Figure 2.13 of Raymond (2007). The sublayer defaults are set to match those of blubber, lacking any other information. The bone default forbis small, to set up a linear function, anda*bis set to equal 8.54e8 Pa, given in Table 2.3 of Raymond (2007) and Table 4.5 of Campbell-Malone (2007).- s
Numerical vector of length 4, giving the ultimate strengths (Pa) of skin, blubber, sublayer, and bone, respectively. If not provided, the value is set to
1e6 * c(19.600,0.255,0.255,22.900)with reasoning as follows. The skin default of 19.6 MPa is a rounded value from Table 3 of Grear et al. (2018) for adult seal skin strength at an orientation of 0 degrees. The blubber and sublayer values were chosen as the central point of a logistic fit of whale collision damage to maximal stress during a default impact simulation. (For comparison, a strength of 0.437 MPa may be inferred by multiplying Raymond's (2007) Figure 2.13 elastic modulus of 0.636 MPa by the ratio 0.97/1.41 determined for adult seal strength/modulus, as reported in Table 3 of Grear et al. (2018).) The bone default o 22.9 MPa is from Table 2.3 of Raymond (2007) and Table 4.5 of Campbell-Malone (2007).- theta
Whale skin deformation angle (deg); defaults to 55 degrees, if not supplied, because that angle produces a good match to Raymond's (2007) Figure 6.1 for the total force as a function of vessel speed, for large vessels. Note that the match works almost as well in the range 50 deg to 70 deg.
- Cs
Drag coefficient for ship (dimensionless), used by
shipWaterForce()to estimate ship drag force. Defaults to 1e-2, which is 4 times the frictional coefficient of 2.5e-3 inferred from Figure 4 of Manen and van Oossanen (1988), assuming a Reynolds number of 5e7, computed from speed 5m/s, lengthscale 10m and viscosity 1e-6 m^2/s. The factor of 4 is under the assumption that frictional drag is about a quarter of total drag. The drag force is computed withshipWaterForce().- Cw
Drag coefficient for whale (dimensionless), used by
whaleWaterForce()to estimate whale drag force. Defaults to 2.5e-3, for Reynolds number 2e7, computed from speed 2 m/s, lengthscale 5m which is chosen to be between radius and length, and viscosity 1e-6 m^2/s. The drag force is computed withwhaleWaterForce().- logistic
a list containing
logStressCenterandlogStressWidth, which define an empirical logistic fit of an index of whale injury in observed strikes (ranging from 0 for no injury to 1 for fatal injury), as a function of the base-10 logarithm of compressive stress, as well astau25,tau50andtau75, which are the stresses in that fit that yield index values of 0.25, 0.50 and 0.75, respectively; these values set colour boundaries inplot.strike()plots that havewhich="threat".- file
Optional name a comma-separated file that holds all of the previous values, except
CsandCw. If provided, then other parameters exceptCsandCware ignored, because values are sought from the file. The purpose of this is in shiny apps that want to save a simulation framework. The file should be savedwrite.csv()withrow.names=FALSE.
Value
A named list holding the parameters, with defaults and alternatives reconciled
according to the system described above, along with some items used internally,
including lsum, which is the sum of the values in l, and stressFromStrain(),
a function created by stressFromStrainFunction() that computes compression
force from engineering strain.
References
Campbell-Malone, Regina. "Biomechanics of North Atlantic Right Whale Bone: Mandibular Fracture as a Fatal Endpoint for Blunt Vessel-Whale Collision Modeling." PhD Thesis, Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2007. doi:10.1575/1912/1817 .
Daoust, Pierre-Yves, Emilie L. Couture, Tonya Wimmer, and Laura Bourque. "Incident Report. North Atlantic Right Whale Mortality Event in the Gulf of St. Lawrence, 2017." Canadian Wildlife Health Cooperative, Marine Animal Response Society, and Fisheries and Oceans Canada, 2018. https://publications.gc.ca/site/eng/9.850838/publication.html.
Grear, Molly E., Michael R. Motley, Stephanie B. Crofts, Amanda E. Witt, Adam P. Summers, and Petra Ditsche. "Mechanical Properties of Harbor Seal Skin and Blubber - a Test of Anisotropy." Zoology 126 (2018): 137-44. doi:10.1016/j.zool.2017.11.002 .
Raymond, J. J. "Development of a Numerical Model to Predict Impact Forces on a North Atlantic Right Whale during Collision with a Vessel." University of New Hampshire, 2007. https://scholars.unh.edu/thesis/309/.
