Wrapper-function to compile a list of input needed to run TMB
getInp( hydros, toa, E_dist, n_ss, pingType, sdInits = 1, rbi_min = 0, rbi_max = 0, ss_data_what = "est", ss_data = 0, biTable = NULL, z_vec = NULL, bbox = NULL )
| 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 |
| sdInits | If >0 initial values will be randomized around the normally fixed value using rnorm(length(inits), mean=inits, sd=sdInits) |
| rbi_min, 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 |
| 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. |
List of input data ready for use in TMB-call