echoIBM.oneschool: Simulates echo sounder observations based on positions,...

In arnejohannesholmin/echoIBM: Simulation of multibeam sonar data

Simulates echo sounder observations based on positions, orientations, sizes and other specifics of each fish in a known (simulated) school.

Description

Simulates echo sounder observations based on positions, orientations, sizes and other specifics of each fish in a known (simulated) school.

Usage

echoIBM.oneschool(
  files,
  event,
  t = 1,
  tvessel,
  vesselutim,
  pingsSchool,
  areCompact,
  adds = NULL,
  pingsdir,
  pingsname,
  esnm = NULL,
  TVG.exp = 2,
  compensated = c("pitch", "roll"),
  filesize = 3e+08,
  calibrate = TRUE,
  noise = c("nr", "bg", "ex"),
  mode = c("active", "passive"),
  max.memory = 1e+09,
  ow = TRUE,
  origin = 1,
  dumpfile = "dump.txt",
  dumpsize = 1e+07,
  timedumpfile = "timedump.txt",
  rand.sel = 1,
  scls = 1,
  volsc = c(1, 1, 1),
  method = c("closest", "linear"),
  ask = FALSE,
  parlist = list(),
  bptfile = NULL,
  max.radius = 0.2,
  cores = 1,
  saveBrkt = FALSE,
  msg = FALSE,
  discardOutside = c(r = Inf, az = Inf, el = Inf),
  fishReaction = list()
)

Arguments

files	is a vector of the paths to the files on which the simulation is based.
t	is a vector of the numbers of the pings to be simulated, as listed from 1 to the number of time steps of the simulated school. If t=="all", all time steps are simulated.
pingsSchool	is a list of four-column matrices:
adds	is an optional list of variables overriding the variables located in the files given by 'files'.
pingsdir	is a character string holding the path to the directory in which the .pings files should be put.
pingsname	is a character string holding the name of the .pings files, after which the time point of the first ping of each file will be added.
esnm	is the name of the acoustical instrument, given as a four character string. See sonR_implemented() for the implemented systems. May be given in 'data', and in lower case.
TVG.exp	is the exponent of the eamotric spreading of the sound wave, theoretically 2 for Sv and 4 for TS.
compensated	specifies which rotations are compensated for by the echo sounder:
filesize	is the maximum size of the files, used both for temporal and final files.
calibrate	is FALSE if calibration data are to be discarded if present.
noise	See echoIBM.add.noise().
max.memory	is the maximum amount of memory to allow for the function to occupy. The level of for loops is chosen according to this value, i.e. if the method using only two loops, one for the radial distances and one for the unique frequencies, demands more memory than 'max.memory', the method usint three for loops is chosen.
ow	is TRUE if the user wish to overwrite existing file.
origin	is a vector of two elements representing the origin of the global coordinate system (G), or the numbering index of the ping regarded as the origin of (G) (ignoring heave so that the x-y-plane of (G) is on the surface of the sea).
dumpfile	is the name of the file to which information and warnings about the simulation is written.
rand.sel	is a numeric specifying a random selection of the school to use in the simulations. If 'rand.sel' is not >0 and <1 no random selection is done. If given as a vector of length 2, the second element is regarded as the seed for the random selection.
method	is "closest" if the beam pattern value of the closest grid point is to be selected, and "linear" if linear interpolation should be used to extract the beam pattern value (time demanding and only available for 2D grids).
ask	is TRUE if the used should be asked to for approval if the memory of the least memory demanding calculation method of the individual radial sampling intervals exceed the memory limit 'max.memory'.
parlist	is a list of input parameters to the function echoIBM.add.noise(), which generates noise and randomness. See echoIBM.add.noise() for explaination of the possible variables.
bptfile	is the name of the file to which 'sllf', 'rad1', 'rad2', 'pbp1' and 'pbp2' is written (use NULL for no writing).
cores	is an integer specifying the number of cores to run the simulations over in parallel (should be lower than the number of cores in the computer).
saveBrkt	is TRUE to save the variables 'Brkt' and 'nsig', which contain data only when the number of significant targets is low enough (<=2) for the exact Barakat distribution to kick in instead of the approximation of the exponential distribution.
msg	Logical: If TRUE, show messages to the console and to dump files.
discardOutside	A vector of three elements specifying the size of the margin around the -3 dB main beam, specifide in units of the range/angular resolution, inside which targets are considered. Using e.g. c(2, 3, 3) will discard targest outside of a volume extending three beam widths around the beam width of the system (and to 2 times the radial range beyond the maximum range). This may save process time, but is not recommended without testing, as higher order side lobes encounter a larger volume than lower order side lobes.
fishReaction	A list of variables specifying the fish reaction to the vessel. Must contain the following variables: "magR", "mxrR", "mxdR", "facR". See info.TSD(c("magR", "mxrR", "mxdR", "facR")) for definition of these variables.

arnejohannesholmin/echoIBM documentation built on April 14, 2024, 11:37 p.m.