kfsst {kfsst}R Documentation

Kalman Filter based optimization of the tracking model including Sea Surface Temperature

Description

After the track has been read in and the SST-field has been constructed (see the road.map function for advice) this function does the actual optimization of the model and reconstruction of the track.

Basically this function only needs the raw track and the SST file, but it has a lot of options to modify the model, which are presented here. Quite often it is necessary to simplify the model to get a converging fit - especially for short tracks.

Usage

kfsst(data, sst.file = "sst.dat", fix.first = TRUE, fix.last = TRUE, 
      theta.active = c(u.active, v.active, D.active, bx.active, by.active, bsst.active, sx.active, sy.active, ssst.active, a0.active, b0.active), 
      theta.init = c(u.init, v.init, D.init, bx.init, by.init, bsst.init, sx.init, sy.init, ssst.init, a0.init, b0.init), 
      u.active = TRUE, v.active = TRUE, D.active = TRUE, bx.active = TRUE, by.active = TRUE, bsst.active = TRUE, 
      sx.active = TRUE, sy.active = TRUE, ssst.active = TRUE, a0.active = TRUE, b0.active = TRUE, 
      u.init = 0, v.init = 0, D.init = 100, bx.init = 0, by.init = 0, bsst.init = 0, 
      sx.init = 0.1, sy.init = 1, ssst.init = 0.1, a0.init = 0.001, b0.init = 0, 
      var.struct = "solstice", dev.pen = 0, save.dir = NULL, admb.string = "")

Arguments

data A data.frame consisting of six columns. The first three columns should contain day, month and year corresponding to valid dates. The dates must be sorted in ascending order. Column four and five should contain the longitude and latitude in degrees. The final column should contain the SST measurement derived from the tag on the fish.
sst.file A string containing the filename (including path) to a file returned from the function write.sst.field.
fix.first TRUE (default) if the first position in the data set is the true release position (known without error), FALSE otherwise.
fix.last TRUE (default) if the last position in the data set is the true recapture/popoff position (known without error), FALSE otherwise.
theta.active A logical vector of eleven elements, each corresponding to a model parameter. If an element is set to TRUE the value of corresponding parameter is optimized, otherwise it is kept at its initial value. The default value is TRUE for all parameters. The values 1/0 can be used instead of TRUE/FALSE. The order of the elements in this vector is c(u.active, v.active, D.active, bx.active, by.active, bsst.active, sx.active, sy.active, ssst.active, a0.active, b0.active), hence a value of c(0,0,1,1,1,1,1,1,1,1,1) would result in a model where u and v were fixed at there initial values.
theta.init A numeric vector of eleven elements, each corresponding to a model parameter. The order of the elements in this vector is c(u.init, v.init, D.init, bx.init, by.init, bsst.init, sx.init, sy.init, ssst.init, a0.init, b0.init) and the default value is c(0, 0, 100, 0, 0, 0, 0.1, 1.0, 0.1, 0.001, 0). It is unwise to initialize elements D.init, sx.init, sy.init, and ssst.init below zero, as they correspond to standard deviations.
u.active TRUE (default) if u should be optimized, FALSE if it should be fixed at its initial value.
v.active TRUE (default) if v should be optimized, FALSE if it should be fixed at its initial value.
D.active TRUE (default) if D should be optimized, FALSE if it should be fixed at its initial value.
bx.active TRUE (default) if b[x] should be optimized, FALSE if it should be fixed at its initial value.
by.active TRUE (default) if b[y] should be optimized, FALSE if it should be fixed at its initial value.
bsst.active TRUE (default) if b[sst] should be optimized, FALSE if it should be fixed at its initial value.
sx.active TRUE (default) if sigma[x] should be optimized, FALSE if it should be fixed at its initial value.
sy.active TRUE (default) if sigma[y] should be optimized, FALSE if it should be fixed at its initial value.
ssst.active TRUE (default) if sigma[sst] should be optimized, FALSE if it should be fixed at its initial value.
a0.active If the variance structure var.struct="solstice" is chosen this flag should be set to TRUE (default) if a[0] should be optimized, FALSE if it should be fixed at its initial value. If a different variance structure is selected this flag is ignored.
b0.active If the variance structure var.struct="solstice" is chosen this flag should be set to TRUE (default) if b[0] should be optimized, FALSE if it should be fixed at its initial value. If a different variance structure is selected this flag is ignored.
u.init The initial value of u. Default is 0.
v.init The initial value of v. Default is 0.
D.init The initial value of D. Default is 100.
bx.init The initial value of b[x]. Default is 0.
by.init The initial value of b[y]. Default is 0.
bsst.init The initial value of b[sst]. Default is 0.
sx.init The initial value of sigma[x]. Default is 0.1.
sy.init The initial value of sigma[y]. Default is 1.0.
ssst.init The initial value of sigma[sst]. Default is 0.1.
a0.init If the variance structure var.struct="solstice" is chosen this sets the initial value of a[0]. Default is 0.001. If a different variance structure is selected this is ignored.
b0.init If the variance structure var.struct="solstice" is chosen this sets the initial value of b[0]. Default is 0. If a different variance structure is selected this is ignored.
var.struct Three options are available: "uniform", "solstice"(default), and "daily".
dev.pen If var.struct="daily" is set, this parameter sets the derivative penalty.
save.dir NULL (default) if the estimation should be done in a temporary directory, otherwise the quoted name of the directory where the estimation should be saved.
admb.string Additional command line arguments to the underlying AD Model Builder program can be passed as a string. For instance "-est". The available command line arguments can be found in the AD Model Builder documentation (see http://otter-rsch.com)

Details

Here should the model briefly be described, but for now read all about it in the reference given below.

Value

An object of class kftrack is returned. This object contains information about the fit and estimated tracks.

Author(s)

Anders Nielsen anielsen@dina.kvl.dk, John Sibert sibert@hawaii.edu

References

http://www.tracking.nielsensweb.org

See Also

road.map, link{blue.shark}

Examples

  # No example supplied here, but check out the example 
  # in the blue.shark dataset documentation

[Package kfsst version 0.2 Index]