echoIBM.vbsc2p.event: Estimates the probability of not school in voxels of the MS70...

Description Usage Arguments

View source: R/echoIBM.vbsc2p.event.R

Description

Estimates the probability of not school in voxels of the MS70 sonar.

Usage

1
2
3
4
5
6
echoIBM.vbsc2p.event(event = 1, t = 1, cruise = 2009116, bgns = NULL,
  beta0 = NULL, beta1 = NULL, factor = NULL, ind = list(-(1:30), NULL),
  nsind = 0.75, smind = list(-(1:300)), range = list(), subset = NULL,
  h = NULL, alpha = NULL, dir.data = NULL, hins_add = 10,
  phase = TRUE, TVG.exp = 2, esnm = "MS70", subtractNoise = TRUE,
  adds = list(), sim = TRUE, na.rm = 1, allow.old = FALSE, TOV = 0)

Arguments

event

is the identifier of the event, either given as the number of the event, a string contained in the name of the event, or the path of the event directory.

t

is either the indexes of the pings to be treated, as listed from 1 to the number of pings in the event, or the time point given as a string "yyyymmddHHMMSS.FFF" or "HHMMSS.FFF".

cruise

is either the idenfication number of the cruise, given as specified by the IMR (yyyynnn), or the path to the directory containing the event.

bgns

is an optional list of noise estimates (must contain the background noise 'bgns', and may contain the periodic noise estimates 'pns1', 'pns2' and 'harm'). The phase parameter 'pns2' is extracted from the data. Use 'bgns' to suppress adding periodic noise or near range noise in the noise which is compared to the data, by setting bgns=list(acfq=NULL) or bgns=list(nr0a=NULL).

beta0

is the minimum schooling threshold for the volume backscattering coefficient. For voxels where beta0<noise: beta0=noise.

beta1

is the maximum schooling threshold for the volume backscattering coefficient, defining the probability distribution of the signal. Should be chosen on the basis of the maximum packing density of the observed species.

factor

is one or several factors to multiply the schooling thresholds 'beta0' and 'beta1' by, increasing the memory occupied by the function by 50 % of the original memory (factor==NULL) for each element of 'factor'. This option was included to reduce CPU time in the case that both an unbiased and an enlarged segmentation mask is requested.

ind

is a vector or list of indexes along the beams, as input to ind.expand(), used to select the subset over which the estimation of background noise is done. Also voxels not included in this subset are assigned p=1.

nsind

is a vector of indexes along the beams, as input to ind.expand(), used to select the subset over which the estimation of the phase of the periodic noise is done. If given as a single numeric, the outermost 'nsind' voxels are used in each beam.

smind

is a list of indexes used to define the subset which is smoothed spatially to accumulate the probabilities. The default avoids smoothing densely packed voxels, which reduces computational time.

h

is the bandwidth of the spatial Gaussian kernel smoother, given as the standard deviation of the Gaussian distribution. For no smoothing use h=NULL.

alpha

is the significance level of the hypothesis testing of H0: school not present in the voxel, against H1: school present in the voxel. To return non-thresholded data, use alpha=NULL.

dir.data

is the path to the directory in which the projects are stored, defaulted by the variable Acoustics_datasets_directory().

hins_add

is the number of voxels that should be discarded on both sides of high intensity noise voxels voxels along beams, used for accounting for possible high values that are related to the high intensity noise but not classified as such voxels.

phase

is FALSE if any of 'pn3M' (phase for each time step) or 'pns3' (phase equal for all time steps) given in 'bgns' or read from the noise file located by the funciton noise.path.event() should be used, as oposed to estimating the phase from the data for each time step. This is only recommended for simulated data where the phase is constant over all time steps, and saves some CPU time.

TVG.exp

is the exponent of the eamotric spreading of the sound wave, theoretically 2 for Sv and 4 for TS.

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.

subtractNoise

is TRUE if the original acoustic data should be subtracted noise, which is used when returning the total and mean volume backscatter from the segment.

adds

is an optional list of variables overriding the variables in read from the event.

sim

is a TRUE if smoothing should be done only along the first dimensions, simultaneously over the stages of the last dimension. If 'sim' is an integer larger than 1, the positions 'coords' are used 'sim' times, and the data 'x' should have length 'sim' times the length of one coordinate of 'coords'.

na.rm

is single integer representing the dimension along which NAs are discarded from the smoothing in the case that sim==1. For example, if na.rm=2 and the dimension of 'x' is [5,12,7], and x[3,2:4,5]=NA, then all data x[,2:4,] will be excluded from the smoothing and set to NA. If na.rm=FALSE, no NAs should be contained in the data.


arnejohannesholmin/cpplot3d documentation built on March 19, 2018, 9:15 a.m.