echoIBM.setup: Returns a list of the following strings: (1) the path to the...

Description Usage Arguments

View source: R/echoIBM.setup.R

Description

Returns a list of the following strings: (1) the path to the event, (2) the event name, (3) the event number, (4) the path to the cruise, and (5) the cruise name.

Returns a list of the following strings: (1) the path to the event, (2) the event name, (3) the event number, (4) the path to the cruise, and (5) the cruise name.

Writes beams files to simulation events based on resource files.

Writes CTD files to simulation events based on resource files.

Writes calibration files to simulation events based on resource files.

Writes noise files to simulation events based on resource files.

Returns a list of the following strings: (1) the path to the event, (2) the event name, (3) the event number, (4) the path to the cruise, and (5) the cruise name.

The vessel information can be given in 4 ways:

Returns a list of the following strings: (1) the path to the event, (2) the event name, (3) the event number, (4) the path to the cruise, and (5) the cruise name.

Gets pulse duration from the max range of the sonar.

Replaces values in a list but keeping dimension

Usage

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echoIBM.getPath(starttime = "2015-01-01 00:00:00", origin = NULL,
  heading = NULL, distance = NULL, speed = NULL, duration = NULL,
  nodesLocal = NULL, nodesEarth = NULL, utim = NULL, pingduration = 1,
  heave = 0, rtx = 0, rty = 0, rtz = NULL, type = "v")

echoIBM.readFile(path, ext = "vessel", t = 1)

echoIBM.setBeams(event, files = NULL, maxrange = list(),
  mode = "CWNormal", ...)

echoIBM.setCTD(event, files = NULL, ...)

echoIBM.setCalibration(event, files = NULL, ...)

echoIBM.setNoise(event, files = NULL, nr0a = list(), ...)

echoIBM.setSchool(event, surveyRegion = NULL, target = c("herring",
  "mackerel", "point"), schools = c("layer", "uniform", "flat"),
  schoolSize = list(x = 100, y = 100, z = 20, type = "Weibull", shape = 5, cor
  = 0.4), schoolDens = 1852^-2, schoolDist = NULL, schoolCount = NULL,
  fillSurveyRegion = TRUE, seed = 0, depthRange = c(-100, 0),
  onlyFirstEvent = FALSE, ...)

echoIBM.setVessel(event, starttime = "2015-01-01 00:00:00", utim = NULL,
  origin = c(0, 0), heading = 0, distance = NULL, duration = 1,
  speed = NULL, nodesLocal = NULL, nodesEarth = NULL, pingduration = 1,
  numt = NULL, heave = 0, rtxv = 0, rtyv = 0, rtzv = 0, ...)

echoIBM.getVesselPath(starttime = "2015-01-01 00:00:00", origin = NULL,
  heading = NULL, distance = NULL, speed = NULL, duration = NULL,
  nodesLocal = NULL, nodesEarth = NULL, utim = NULL, pingduration = 1,
  numt = NULL, heave = 0, rtxv = 0, rtyv = 0, rtzv = 0)

echoIBM.setVessel_old(events, eventName, starttime = "2015-01-01 00:00:00",
  origin = NULL, heading = NULL, distance = NULL, speed = NULL,
  duration = NULL, nodesLocal = NULL, nodesEarth = NULL, utim = NULL,
  numt = 1, pingduration = 1, heave = 0, rtxv = 0, rtyv = 0,
  rtzv = NULL, ...)

plslTable(range = NULL, mode = "CWNormal")

replaceKeepDim(x, replacement, esnm, ...)

Arguments

starttime

The start time of the event, i.e., the time of the first ping/vessel position, either given as a time object or a string such as "2015-01-01 00:00:00".

origin

The origin of the event, i.e., a vector of two elements giving the longitude and latitude of the first ping.

heading

The heading of the vessel in radians counter clockwise from East, either given as a single numeric, or as a vector of headings associated with vessel track segments.

distance

The distance associated with each vessel track segment.

speed

The speed of the vessel in knots associated with each vessel track segment.

duration

The duration of each vessel track segment in seconds.

nodesLocal

The nodes defining the vessel track segments, given as local nodes relative to the origin (can include the origin c(0, 0))

nodesEarth

The nodes defining the vessel track segments, given as global nodes in the coordinate system of the earth relative to the origin (can include the origin c(0, 0)).

utim

The UNIX time points of the event. If not given, the starttime and pingduration will define the UNIX time points.

pingduration

The duration of the pings in seconds. Currently only one single fixed value is allowed.

heave

The heave of the vessel in meters, either given as a single value, a vector of length equal to the number of vessel track segments, or alternatively a funciton of the number of time steps such as rnorm() or the more appropriate function(x) set.seed(x); runif(x), which sets the seed as the number of time steps.

path

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

ext

A string naming the file extension of the file to read.

t

The time steps to read.

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.

files

An optional vector of file names to be read and written to the simulation events. If empty (default) the resource files of the echoIBM package are used.

maxrange

The maximum range of the sonar in meters.

mode

The mode of the sonar. See available modes with plslTable().

...

Data overriding the variables generated by the funciton.

surveyRegion

A data frame of two rows and the three columns x, y and z, defining the survey region.

target

A code word defining the target. One of "herring", "mackerel" and "point".

schools

A code word defining the distribution of schools. One of "layer", "uniform" (equal probability of encountering a school in all directions but the z direction, corresponding to a homogenious Poisson point process in the x-y-plane), "flat" (random ordering of schools sequenced between the survey bounds).

schoolSize

Definition of the school sizes, either given as a list of dimensions in the x, y and z direction (repeated to the number of schools), or a list of dimensions added a type of random generator for the sizes, such as type = "weibull", indicating correlated Weibull distributed sizes, where the shape and correlation are specified by 'shape' and 'cor'. Alternatively schoolSize can be a list to be used as input the a function schoolSize$type, which must be a function including the ... argument to avoid errors. For correlated Weibull distributed sizes use e.g. list(x = 100, y = 100, z = 20, type = "Weibull", shape = 5, cor = 0.4), where 0.4 is the maximum available correlation. For correlated uniform variables use e.g. list(x = c(30, 300), y = c(30, 300), z = c(30, 300) / 5, type = "Uniform", cor = 0.5), where 0.5 is the maximum available correlation. For schoolSize$type=="Uniform", if schoolSize$x is given as a single numeric, this is interpreted as uniform between 0 and 2 * x.

schoolDens

The area reserved for each school.

schoolDist

The mean distance betseen schools. Use rather schoolDens.

schoolCount

The number of schools.

fillSurveyRegion

Logical: If TRUE fill the survey region so that schools are generated also outside of the original survey region, elliminating edge effects in the spatial distribution of fish.

seed

The seed of the school generation

depthRange

The depth range of the schools. Should be given in the surveyRegion.

onlyFirstEvent

Logical: If TRUE generate school files only for the first event (saving storage).

rtxv

The pitch of the vessel in radians positive for uppwards pitch (bow lifting). See info.TSD("rtxv")

rtyv

The roll of the vessel in radians positive for starboard side tilted down. See info.TSD("rtyv")

rtzv

The orientation of the vessel in radians counter clockwise, IN ADDITION to the heading of the vessel specified in heading. See info.TSD("rtzv")

range

The max range of the sonar.

x

The list to replace values in.

replacement

A list of the values to replace.

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.

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 to be read.

dir.type

is the name of the directory holding the data files (usually one of "tsd" and "raw")

event

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

event

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

files

An optional vector of file names to be read and written to the simulation events. If empty (default) the resource files of the echoIBM package are used.

...

Data overriding the variables generated by the funciton.

event

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

files

An optional vector of file names to be read and written to the simulation events. If empty (default) the resource files of the echoIBM package are used.

...

Data overriding the variables generated by the funciton.

event

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

files

An optional vector of file names to be read and written to the simulation events. If empty (default) the resource files of the echoIBM package are used.

...

Data overriding the variables generated by the funciton.

event

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

...

Data overriding the variables generated by the funciton.

event

A list of the following elements: (1) 'path', giving the paths to the sub-events, (2) 'esnm', giving the names of the acoustic instruments in the events (same length as 'path'), and (3) 'name', giving the name of the event.

...

Data overriding the variables generated by the funciton.

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.

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 to be read.

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.

dir.type

is the name of the directory holding the data files (usually one of "tsd" and "raw")

...

is used in agrep() for locating events based on approximate string matching.

mode

The mode of the sonar. Use plslTable() to get avaialbe modes.

esnm

The name of the sonar, used when the replacement is a list with esnm as names.

...

Arguments passed on to replacement functions.


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