Get data for input to TMB

Compile data for input to TMB.

getDatTmb(
  hydros,
  toa,
  E_dist,
  n_ss,
  pingType,
  rbi_min,
  rbi_max,
  ss_data_what,
  ss_data,
  biTable,
  inp_params,
  z_vec,
  bbox
)

Arguments

hydros	Dataframe from simHydros() or Dataframe with columns hx and hy containing positions of the receivers. Translate the coordinates to get the grid centre close to (0;0).
toa	TOA-matrix: matrix with receivers in rows and detections in columns. Make sure that the receivers are in the same order as in hydros, and that the matrix is very regular: one ping per column (inlude empty columns if a ping is not detected).
E_dist	Which distribution to use in the model - "Gaus" = Gaussian, "Mixture" = mixture of Gaussian and t or "t" = pure t-distribution
n_ss	Number of soundspeed estimates: one estimate per hour is usually enough
pingType	Type of transmitter to simulate - either stable burst interval ('sbi'), random burst interval ('rbi') or random burst interval but where the random sequence is known a priori
rbi_min	Minimum and maximum BI for random burst interval transmitters
rbi_max	Minimum and maximum BI for random burst interval transmitters
ss_data_what	What speed of sound (ss) data to be used. Default ss_data_what='est': ss is estimated by the model. Alternatively, if ss_data_what='data': ss_data must be provided and length(ss_data) == ncol(toa)
ss_data	Vector of ss-data to be used if ss_data_what = 'est'. Otherwise ss_data <- 0 (default)
biTable	Table of known burst intervals. Only used when pingType == "pbi". Default=NULL
inp_params	Selection of parameters used to setup and run YAPS.
z_vec	Vector of known depth values (positive real). Default=NULL is which case no 3D is assumed. If z_vec = "est" depth will be estimated.
bbox	Spatial constraints in the form of a bounding box. See ?getBbox for details.

Value

List for use in TMB.