Description Usage Arguments Value

Wrapper-function to compile a list of input needed to run TMB

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`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 |

List of input data ready for use in TMB-call

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