getInp: Get prepared inp-object for use in TMB-call

Description Usage Arguments Value

View source: R/prepTmb.R

Description

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

Usage

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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)

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

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

Value

List of input data ready for use in TMB-call


baktoft/yaps documentation built on Dec. 24, 2019, 8:04 p.m.