echoIBM.interpolate.event: Runs through segmentation data and interpolates between...

Description Usage Arguments

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

Description

Runs through segmentation data and interpolates between pings, calculating the probability that voxels in neighboring pings, corresponding to each voxel included in the segmentation mask at a time step, are occupied by the school as well.

Usage

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echoIBM.interpolate.event(event = 1, t = 1, cruise = 2009116,
  adds = NULL, esnm = "MS70", type = c("le", "lg", "e", "g", "emax"),
  bw = 0.9, thr = NULL, kernelthr = 0.1, ind = list(-(1:30), NULL),
  range = list(), subset = NULL, segpar = list(), spar = NULL,
  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 number of the ping 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". Only one time step alowed!

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.

adds

is an optional list of variables overriding the variables in 'data'.

esnm

is the name of the acoustical instrument, given as a four character string. Currently implemented are "EK60", "ME70", "MS70" and "SH80"/"SX80"/"SH90"/"SX90" (may be given in lover case)

type

is the type of interpolation:

bw

is the smooting parameter of the interpolation, given as the standard deviation for Gaussian kernel and the base of the exponential decays (bw^x).

thr

is the threshold for the interpolated probabilities og school, defining the interpolated segmentation masks.

kernelthr

is the threshold below which the kernel is set to 0.

ind

is a list of indexes, as typed into the [] of an array, where 0 and NULL denotes all indexes.

range

is a list of elements with names matching names of 'data', specifying the range of the corresponding elements. If range is given as a list of 3 elements, xyz

subset

is a numeric or logical vector/expression indicating elements or rows to keep. Missing values are taken as false, and subset=0 or subset=NULL indicates no subsetting.

segpar

is a list of elements named "bwGp", "lsth"/"rlst", "usth"/"rust", or "sgth"/"sgt0" specifying the parameters of the segmentation data to read.

spar

is used in smooth.spline() when the interpolated probabilities of school are smoothed.

TOV

is the time offset of the vessel information, discovered by Holmin and Korneliussen in 2013. The default is found in "/Applications/echoIBM/Documentation/Error in yaw MS70/Error in yaw MS70.R".


arnejohannesholmin/echoIBM documentation built on March 19, 2018, 9:16 a.m.